1 @Article{Abreu2003:fl_albumin,
2 author = {Magda S C Abreu and Lu\'is M B B Estronca and Maria Jo{\~{a}}o Moreno
4 title = {Binding of a fluorescent lipid amphiphile to albumin and its
5 transfer to lipid bilayer membranes},
12 abstract = {Kinetics and thermodynamics of the binding of a fluorescent
13 lipid amphiphile, Rhodamine Green(TM)-tetradecylamide
14 (RG-C(14:0)), to bovine serum albumin were characterized in
15 an equilibrium titration and by stopped-flow fluorimetry.
16 The binding equilibrium of RG-C(14:0) to albumin was then
17 used to reduce its concentration in the aqueous phase to a
18 value below its critical micelle concentration. Under these
19 conditions, the only two species of RG-C(14:0) in the
20 system were the monomer in aqueous solution in equilibrium
21 with the protein-bound species. After previous
22 determination of the kinetic and thermodynamic parameters
23 for association of RG-C(14:0) with albumin, the kinetics of
24 insertion of the amphiphile into and desorption off lipid
25 bilayer membranes in different phases (solid,
26 liquid-ordered, and liquid-disordered phases, presented as
27 large unilamellar vesicles) were studied by stopped-flow
28 fluorimetry at 30 degrees C. Insertion and desorption rate
29 constants for association of the RG-C(14:0) monomer with
30 the lipid bilayers were used to obtain lipid/water
31 equilibrium partition coefficients for this fluorescent
32 amphiphile. The direct measurement of these partition
33 coefficients is shown to provide a new method for the
34 indirect determination of the equilibrium partition
35 coefficient of similar molecules between two defined lipid
36 phases if they coexist in the same membrane.},
38 doi = {10.1016/S0006-3495(03)74859-0},
40 @Article{Abreu2004:kinetics_ld_lo,
41 author = {Magda S C Abreu and Maria Jo{\~{a}}o Moreno and Winchil L C Vaz},
42 title = {Kinetics and thermodynamics of association of a phospholipid
43 derivative with lipid bilayers in liquid-disordered and
44 liquid-ordered phases},
45 journal = {Biophys J},
51 abstract = {We have measured the rates of insertion into, desorption
52 from, and spontaneous interlayer translocation (flip-flop)
53 in liquid-disordered and liquid-ordered phase lipid bilayer
54 membranes, of the fluorescent phospholipid derivative
55 NBD-dimyristoylphosphatidyl ethanolamine. This study made
56 use of a recently described method that exploits a detailed
57 knowledge of the binding kinetics of an amphiphile to
58 bovine serum albumin, to recover the insertion and
59 desorption rate constants when the albumin-bound amphiphile
60 is transferred through the aqueous phase to the membrane
61 and vice versa. The lipid bilayers, studied as large
62 unilamellar vesicles, were prepared from pure
63 1-palmitoyl-2-oleoylphosphatidylcholine in the
64 liquid-disordered phase; and from two
65 cholesterol-containing binary lipid mixtures,
66 1-palmitoyl-2-oleoylphosphatidylcholine and cholesterol
67 (molar ratio of 1:1), and egg sphingomyelin and cholesterol
68 (molar ratio of 6:4), both in the liquid-ordered phase.
69 Insertion, desorption, and translocation rate constants and
70 equilibrium constants for association of the amphiphile
71 monomer with the lipid bilayers were directly measured
72 between 15 degrees and 35 degrees C, and the standard free
73 energies, enthalpies, and entropies, as well as the
74 activation energies for these processes, were derived from
75 this data. The equilibrium partition coefficients for
76 partitioning of the amphiphile between the aqueous phase
77 and the different membrane phases were also derived, and
78 permitted the estimation of hypothetical partition
79 coefficients and the respective energetic parameters for
80 partitioning between the different lipid phases if these
81 were to coexist in the same membrane.},
83 doi = {10.1529/biophysj.104.040576},
85 @Book{Arrhenius1908:world_in_making,
86 author = {Svante Arrhenius},
87 title = {Worlds in the making; the evolution of the universe},
88 publisher = {New York, London, Harper},
90 address = {http://www.archive.org/details/worldsinmakingev00arrhrich}
93 @Article{Bachmann1992:autocatalysis_micelles,
94 author = {Pascale Angelica Bachmann and Pier Luigi Luisi and Jacques Lang},
95 title = {Autocatalytic self-replicating micelles as models for prebiotic structures},
101 abstract = {MICELLES that can catalyse their replication have been
102 described recently1–3. In the previous experiments,
103 micelles (or bilayer vesicles4) were always present
104 in the initial reaction mixture—that is, the system
105 was presented with the bounded structures required
106 for autocatalysis. Here we describe a system in
107 which autocatalytic micelles are formed from
108 amphiphiles that are themselves generated from a
109 hydrolysis reaction in the absence of compartmental
110 structures. Alkaline hydrolysis of ethyl caprylate
111 (itself insoluble in water) yields sodium caprylate,
112 initially at a very slow rate; but as soon as
113 sufficient caprylate is formed for aggregation into
114 micelles to take place, there is an exponential
115 increase in reaction rate owing to micellar
116 catalysis. These self-assembling surfactant
117 structures may consequently provide a model system
118 for studies of prebiotic chemistry. The possible
119 relevance of this process to prebiotic chemistry is
120 emphasized by our observation that the micelles can
121 be converted into more-robust vesicles by a pH
122 change induced by dissolved CO2.},
123 doi = {10.1038/357057a0}
125 @Article{Bai1997:lipid_movementbodipy,
126 author = {J Bai and R E Pagano},
127 title = {Measurement of spontaneous transfer and transbilayer movement
128 of BODIPY-labeled lipids in lipid vesicles},
129 journal = {Biochemistry},
135 abstract = {An assay was developed to study the spontaneous transfer
136 and transbilayer movement (flip-flop) of lipid analogs
137 labeled with the fluorescent fatty acid, 5-(5,7-dimethyl
138 BODIPY)-1-pentanoic acid (C5-DMB-) in large unilamellar
139 lipid vesicles comprised of 1-palmitoyl-2-oleoyl
140 phosphatidylcholine (POPC). The assay is based on the
141 concentration-dependent changes in fluorescence intensity
142 that occur when donor vesicles containing a C5-DMB-lipid
143 are mixed with nonfluorescent acceptor vesicles. A kinetic
144 model was developed to describe the time-dependent changes
145 in concentration of a lipid undergoing both spontaneous
146 transfer between unilamellar vesicles and transbilayer
147 movement within the vesicle membranes, and a mathematical
148 solution was obtained. Data were obtained using
149 C5-DMB-labeled analogs of sphingomyelin (C5-DMB-SM),
150 ceramide (C5-DMB-Cer), phosphatidylcholine (C5-DMB-PC), and
151 diacylglycerol (C5-DMB-DAG), and kinetic parameters for
152 each lipid were determined using a nonlinear least-squares
153 fitting program. The half-times for interbilayer transfer
154 of the lipids were C5-DMB-SM (21 s) < C5-DMB-PC (350 s)
155 approximately C5-DMB-Cer (400 s) << C5-DMB-DAG (100 h).
156 C5-DMB-Cer (t1/2 approximately 22 min) and C5-DMB-DAG (t1/2
157 approximately 70 ms) exhibited rapid spontaneous
158 transbilayer movement, while C5-DMB-SM (t1/2 approximately
159 3.3 h) and C5-DMB-PC (t1/2 approximately 7.5 h) moved
160 across the bilayer very slowly. These results provide a
161 basis for interpreting the behavior of these lipid analogs
164 doi = {10.1021/bi970145r},
166 @Article{Baron2004:sm_raft_composition,
167 author = {Carl B Baron and Ronald F Coburn},
168 title = {Smooth muscle raft-like membranes},
169 journal = {J Lipid Res},
175 abstract = {We developed a method for extracting raft-like,
176 liquid-ordered membranes from the particulate fraction
177 prepared from porcine trachealis smooth muscle. This
178 fraction, which contains most of the plasma membrane in
179 this tissue, was homogenized in the presence of cold 0.5\%
180 Triton X-100. After centrifugation, membranes containing
181 high contents of sphingomyelin (SM) and cholesterol and low
182 phosphatidylcholine (PC) contents remained in the pellet.
183 Thirty-five millimolar octyl glucoside (OG) extracted 75\%
184 of these membranes from the Triton X-100-resistant pellet.
185 These membranes had low buoyant densities and accounted for
186 28\% of the particulate fraction lipid. Their lipid
187 composition, 22\% SM, 60\% cholesterol, 11\%
188 phosphatidylethanolamine, 8\% PC, <1\%
189 phosphatidylinositol, and coisolation with 5'-nucleotidase
190 and caveolin-1 suggest that they are liquid-ordered
191 membranes. We compared characteristics of OG and Triton
192 X-100 extractions of the particulate fraction. In contrast
193 to Triton X-100 extractions, membranes released from the
194 particulate fraction by OG were mainly collected in low
195 buoyant fractions at densities ranging from 1.05 to 1.11
196 g/ml and had phospholipid and cholesterol contents
197 consistent with a mixture of liquid-ordered and
198 liquid-disordered membranes. Thus, OG extraction of
199 apparent liquid-ordered membranes from Triton
200 X-100-resistant pellets was not due to selective extraction
201 of these membranes. Low buoyant density appears not to be
202 unique for liquid-ordered membranes.},
204 doi = {10.1194/jlr.M300402-JLR200},
206 @Article{Baumgart2003:curvature_and_line_tension,
207 author = {Tobias Baumgart and Samuel T Hess and Watt W Webb},
208 title = {Imaging coexisting fluid domains in biomembrane models
209 coupling curvature and line tension},
216 abstract = {Lipid bilayer membranes--ubiquitous in biological systems
217 and closely associated with cell function--exhibit rich
218 shape-transition behaviour, including bud formation and
219 vesicle fission. Membranes formed from multiple lipid
220 components can laterally separate into coexisting liquid
221 phases, or domains, with distinct compositions. This
222 process, which may resemble raft formation in cell
223 membranes, has been directly observed in giant unilamellar
224 vesicles. Detailed theoretical frameworks link the
225 elasticity of domains and their boundary properties to the
226 shape adopted by membranes and the formation of particular
227 domain patterns, but it has been difficult to
228 experimentally probe and validate these theories. Here we
229 show that high-resolution fluorescence imaging using two
230 dyes preferentially labelling different fluid phases
231 directly provides a correlation between domain composition
232 and local membrane curvature. Using freely suspended
233 membranes of giant unilamellar vesicles, we are able to
234 optically resolve curvature and line tension interactions
235 of circular, stripe and ring domains. We observe long-range
236 domain ordering in the form of locally parallel stripes and
237 hexagonal arrays of circular domains, curvature-dependent
238 domain sorting, and membrane fission into separate vesicles
239 at domain boundaries. By analysing our observations using
240 available membrane theory, we are able to provide
241 experimental estimates of boundary tension between fluid
244 doi = {10.1038/nature02013},
246 @Article{Budin2010:ool_review,
247 author = {Itay Budin and Jack W Szostak},
248 title = {Expanding roles for diverse physical phenomena during the
250 journal = {Annu Rev Biophys},
256 abstract = {Recent synthetic approaches to understanding the origin of
257 life have yielded insights into plausible pathways for the
258 emergence of the first cells. Here we review current
259 experiments with implications for the origin of life,
260 emphasizing the ability of unexpected physical processes to
261 facilitate the self-assembly and self-replication of the
262 first biological systems. These laboratory efforts have
263 uncovered novel physical mechanisms for the emergence of
264 homochirality; the concentration and purification of
265 prebiotic building blocks; and the ability of the first
266 cells to assemble, grow, divide, and acquire greater
267 complexity. In the absence of evolved biochemical
268 capabilities, such physical processes likely played an
269 essential role in early biology.},
271 doi = {10.1146/annurev.biophys.050708.133753},
273 @Article{Cascales1996:mds_dpps_area,
274 author = {J. J. L\'opez Cascales and H. J. C. Berendsen and J. Garc\'ia de la Torre},
275 title = {Molecular Dynamics Simulation of Water between Two Charged Layers of Dipalmitoylphosphatidylserine},
276 journal = {J. Phys. Chem.},
282 abstract = {A molecular dynamics simulation of water between two
283 charged layers of dipalmitoylphosphatidylserine in
284 its liquid-crystalline state with atomic detail was
285 carried out. From an analysis of a trajectory of 184
286 ps of length, we obtained information about the
287 dynamics and structure of water between such charged
288 layers. The most remarkable conclusions of this work
289 indicate that the presence of counterions and charge
290 interactions between adjacent phospholipids produce
291 a screening of the electric field which reduces the
292 strength of the lipid-water interactions. In this
293 way, only minor differences of the behavior of the
294 water compared to uncharged phospholipids were
295 found. This conclusion was based on the calculation
296 of the following properties: electric potential and
297 water dipole orientation across the water layer,
298 radial distribution function of water about lipid
299 atoms, and diffusion and orientational relaxation
301 doi = {10.1021/jp9516405}
303 @Article{Chen2004:competition_model_protocells,
304 author = {Irene A Chen and Richard W Roberts and Jack W Szostak},
305 title = {The emergence of competition between model protocells},
312 abstract = {The transition from independent molecular entities to
313 cellular structures with integrated behaviors was a crucial
314 aspect of the origin of life. We show that simple physical
315 principles can mediate a coordinated interaction between
316 genome and compartment boundary, independent of any genomic
317 functions beyond self-replication. RNA, encapsulated in
318 fatty acid vesicles, exerts an osmotic pressure on the
319 vesicle membrane that drives the uptake of additional
320 membrane components, leading to membrane growth at the
321 expense of relaxed vesicles, which shrink. Thus, more
322 efficient RNA replication could cause faster cell growth,
323 leading to the emergence of Darwinian evolution at the
326 doi = {10.1126/science.1100757},
328 @Article{Copley2007:rna_world,
329 author = {Shelley D Copley and Eric Smith and Harold J Morowitz},
330 title = {The origin of the RNA world: co-evolution of genes and
332 journal = {Bioorg Chem},
338 abstract = {Discoveries demonstrating that RNA can serve genetic,
339 catalytic, structural, and regulatory roles have provided
340 strong support for the existence of an RNA World that
341 preceded the origin of life as we know it. Despite the
342 appeal of this idea, it has been difficult to explain how
343 macromolecular RNAs emerged from small molecules available
344 on the early Earth. We propose here a mechanism by which
345 mutual catalysis in a pre-biotic network initiated a
346 progression of stages characterized by ever larger and more
347 effective catalysts supporting a proto-metabolic network,
348 and the emergence of RNA as the dominant macromolecule due
349 to its ability to both catalyze chemical reactions and to
350 be copied in a template-directed manner. This model
351 suggests that many features of modern life, including the
352 biosynthetic pathways leading to simple metabolites, the
353 structures of organic and metal ion cofactors,
354 homochirality, and template-directed replication of nucleic
355 acids, arose long before the RNA World and were retained as
356 pre-biotic systems became more sophisticated.},
358 doi = {10.1016/j.bioorg.2007.08.001},
360 @Article{Deamer1986:aphiphile_origin,
361 author = {D W Deamer},
362 title = {Role of amphiphilic compounds in the evolution of membrane
363 structure on the early earth},
364 journal = {Orig Life Evol Biosph},
369 abstract = {A variety of amphiphilic compounds have the capacity to
370 self-assemble into membranous structures in the form of
371 bilayers. The earliest cellular organisms must have
372 incorporated such compounds into boundary membranes, and
373 this review discusses amphiphilic components of the
374 prebiotic environment which would be candidates. One
375 possible source is organic material carried to the earth's
376 surface by meteoritic infall. To test this, we have
377 extracted and analysed non-polar substances from the
378 Murchison carbonaceous chondrite, and found that at least
379 some of the components can produce boundary structures
380 which resemble membranes. This observation suggests that
381 membranous boundary structures were present on the early
382 earth, and available to participate in the origin and
383 evolution of the first cellular forms of life.},
386 @Article{Deamer1989:murchison_chondrite,
387 author = {D W Deamer and R M Pashley},
388 title = {Amphiphilic components of the Murchison carbonaceous
389 chondrite: surface properties and membrane formation},
390 journal = {Orig Life Evol Biosph},
395 abstract = {We have investigated physicochemical properties of
396 amphiphilic compounds in carbonaceous meteorites. The
397 primary aim was to determine whether such materials
398 represent plausible sources of lipid-like compounds that
399 could have been involved as membrane components in
400 primitive cells. Samples of the Murchison CM2 chondrite
401 were extracted with chloroform-methanol, and the
402 chloroform-soluble material was separated by
403 two-dimensional thin layer chromatography. Fluorescence,
404 iodine stains and charring were used to identify major
405 components on the plates. These were then scraped and
406 eluted as specific fractions which were investigated by
407 fluorescence and absorption spectra, surface chemical
408 methods, gas chromatography-mass spectrometry, and electron
409 microscopy. Fraction 5 was strongly fluorescent, and
410 contained pyrene and fluoranthene, the major polycyclic
411 aromatic hydrocarbons of the Murchison chondrite. This
412 fraction was also present in extracts from the Murray and
413 Mighei CM2 chondrites. Fraction 3 was surface active,
414 forming apparent monomolecular films at air-water
415 interfaces. Surface force measurements suggested that
416 fraction 3 contained acidic groups. Fraction 1 was also
417 surface active, and certain components could self-assemble
418 into membranous vesicles which encapsulated polar solutes.
419 The observations reported here demonstrate that organic
420 compounds plausibly available on the primitive Earth
421 through meteoritic infall are surface active, and have the
422 ability to self-assemble into membranes.},
425 @Article{Deamer1991:amphiphile_origin,
426 author = {D Deamer and S I Kuzina and A I Mikhailov and E I Maslikova
428 title = {Origin of amphiphilic molecules and their role in primary
429 structure formation},
430 journal = {J Evol Biochem Physiol},
436 abstract = {Attempts to solve two fundamental questions are described:
437 the first concerns which mechanisms were responsible for
438 the self-assembly of membrane structures on the prebiotic
439 Earth, and the second concerns the routes by which
440 considerable amounts of membrane amphiphiles formed from
441 simpler hydrocarbons. The physicochemical properties of
442 several amphiphilic compounds extracted from the Murchison
443 carbonaceous chondrite were studied, using infra-red and
444 fluorescent spectroscopy, measurements of surface activity,
445 chromato-mass spectrometry, and polarization and electron
446 microscopy. The results supported previous observations
447 that amphiphilic and aromatic hydrocarbons were present in
448 significant quantities, and the first demonstration of
449 surface activity among a number of acidic derivatives of
450 hydrocarbons is reported. In addition, one fraction of the
451 surface-active compounds can form bilayer structures,
452 showing that membranes could have self-assembled on the
453 prebiotic Earth. Photochemical oxidation of hydrocarbons
454 is shown to be a likely source of the amphiphilic molecules
455 required for the self-assembly of primary membrane
459 @Article{Demel1987:ps_area,
460 author = {R A Demel and F Paltauf and H Hauser},
461 title = {Monolayer characteristics and thermal behavior of natural and
462 synthetic phosphatidylserines},
463 journal = {Biochemistry},
469 abstract = {The monolayer properties and thermal behavior of different
470 phosphatidylserines are presented. At neutral pH and 22
471 degrees C, saturated phosphatidylserines form condensed
472 monolayers while unsaturated phosphatidylserines form
473 liquid-expanded films. Under similar conditions,
474 dimyristoylphosphatidylserine undergoes a transition from
475 the liquid-expanded to the condensed state. At pH 4 and 22
476 degrees C, the surface pressure-area isotherms are shifted
477 to smaller areas relative to the monolayers recorded at
478 neutral pH. The condensation observed at pH 4 is close to
479 that produced at pH 7.4 by the addition of 10 mM CaCl2. As
480 regards the molecular packing in monolayers and the thermal
481 behavior, 1,2-dipalmitoyl-sn-glycero-3-phospho-L-serine
482 (DPPS) and its ether analogue are similar, albeit not
483 identical. Below 30 mN/m, monolayers of the ether analogue
484 are even more condensed than those of DPPS. The
485 order-disorder transition of the ether analogue occurs
486 usually at higher temperatures than that of the diacyl
487 compound. Sonicated phosphatidylserine dispersions
488 consisting of small unilamellar vesicles show anomalous
489 thermal properties compared to sonicated
490 phosphatidylcholine dispersions. They exhibit sharp
491 order-disorder transitions at similar or even slightly
492 elevated temperatures compared to unsonicated
493 phosphatidylserine dispersions. This anomaly is explained
494 in terms of a pH gradient across the bilayer membrane of
495 the small unilamellar phosphatidylserine vesicle. The
496 internal surface pH is more acidic than the external pH,
497 leading to some protonation of phosphatidylserine
498 molecules. This in turn leads to a condensation of
499 phosphatidylserine molecules on the inner bilayer surface.
500 Such a gradient is proposed to be responsible for the
501 thermodynamic stability of highly curved negatively charged
505 @Article{Dworkin2001:amphiphile_assembly,
506 author = {J Dworkin and D Deamer and S Sandford and L Allamandola},
507 title = {Self-assembling amphiphilic molecules: Synthesis in simulated
508 interstellar/precometary ices},
509 journal = {Proc Natl Acad Sci U S A},
515 abstract = {Interstellar gas and dust constitute the primary material
516 from which the solar system formed. Near the end of the hot
517 early phase of star and planet formation, volatile, less
518 refractory materials were transported into the inner solar
519 system as comets and interplanetary dust particles. Once
520 the inner planets had sufficiently cooled, late
521 accretionary infall seeded them with complex organic
522 compounds [Oró, J. (1961) Nature (London) 190, 389-390;
523 Delsemme, A. H. (1984) Origins Life 14, 51-60; Anders, E.
524 (1989) Nature (London) 342, 255-257; Chyba, C. F. & Sagan,
525 C. (1992) Nature (London) 355, 125-131]. Delivery of such
526 extraterrestrial compounds may have contributed to the
527 organic inventory necessary for the origin of life.
528 Interstellar ices, the building blocks of comets, tie up a
529 large fraction of the biogenic elements available in
530 molecular clouds. In our efforts to understand their
531 synthesis, chemical composition, and physical properties,
532 we report here that a complex mixture of molecules is
533 produced by UV photolysis of realistic, interstellar ice
534 analogs, and that some of the components have properties
535 relevant to the origin of life, including the ability to
536 self-assemble into vesicular structures.},
538 doi = {10.1073/pnas.98.3.815},
540 @Article{Estronca2007:dhe_kinetics,
541 author = {Lu\'is M B B Estronca and Maria Jo{\~{a}}o Moreno and Winchil L C
543 title = {Kinetics and thermodynamics of the association of
544 dehydroergosterol with lipid bilayer membranes},
545 journal = {Biophys J},
551 abstract = {We have examined the detailed kinetics and thermodynamics
552 of the association of Ergosta-5,7,9(11),22-tetraen-3beta-ol
553 (dehydroergosterol, DHE) with lipid bilayers prepared from
554 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), a 1:1
555 binary mixture of POPC and cholesterol (Chol), and a 6:4
556 binary mixture of egg sphingomyelin (SpM) and Chol.
557 Association of DHE with all three membranes was shown to be
558 entropically driven, most so in the case of SpM-Chol
559 bilayers. Equilibrium partition coefficients for
560 partitioning of DHE between the lipid phase and the aqueous
561 phase were shown to be similar for POPC and POPC-Chol
562 bilayers between 15 and 35 degrees C. Partitioning into the
563 SpM-Chol bilayer is favored at higher temperatures and
564 there is a crossover in solubility preference at
565 approximately 25 degrees C. Insertion (k(+)) and desorption
566 (k(-)) rate constants were shown to be very similar for
567 POPC and POPC-Chol bilayer membranes, but were lower for
568 SpM-Chol bilayers. Similar results were previously reported
569 by us for the association of other amphiphiles with these
570 membranes. We propose a model for the microscopic structure
571 of a POPC-Chol (1:1) bilayer membrane that is consistent
572 with these observations.},
574 doi = {10.1529/biophysj.107.112847},
576 @Article{Ferris1987:prebiotic_synthesis,
577 author = {J P Ferris},
578 title = {Prebiotic synthesis: problems and challenges},
579 journal = {Cold Spring Harb Symp Quant Biol},
585 @Article{Gaus2005:macrophage_lipid_distribution,
586 author = {Katharina Gaus and Macarena Rodriguez and Kalani R Ruberu and
587 Ingrid Gelissen and Timothy M Sloane and Leonard Kritharides
589 title = {Domain-specific lipid distribution in macrophage plasma
591 journal = {J. Lipid Res.},
597 abstract = {Lipid rafts, defined as cholesterol- and sphingolipid-rich
598 domains, provide specialized lipid environments understood
599 to regulate the organization and function of many plasma
600 membrane proteins. Growing evidence of their existence,
601 protein cargo, and regulation is based largely on the study
602 of isolated lipid rafts; however, the consistency and
603 validity of common isolation methods is controversial.
604 Here, we provide a detailed and direct comparison of the
605 lipid and protein composition of plasma membrane "rafts"
606 prepared from human macrophages by different methods,
607 including several detergent-based isolations and a
608 detergent-free method. We find that detergent-based and
609 detergent-free methods can generate raft fractions with
610 similar lipid contents and a biophysical structure close to
611 that previously found on living cells, even in cells not
612 expressing caveolin-1, such as primary human macrophages.
613 However, important differences between isolation methods
614 are demonstrated. Triton X-100-resistant rafts are less
615 sensitive to cholesterol or sphingomyelin depletion than
616 those prepared by detergent-free methods. Moreover, we show
617 that detergent-based methods can scramble membrane lipids
618 during the isolation process, reorganizing lipids
619 previously in sonication-derived nonraft domains to
620 generate new detergent-resistant rafts. The role of rafts
621 in regulating the biological activities of macrophage
622 plasma membrane proteins may require careful reevaluation
623 using multiple isolation procedures, analyses of lipids,
624 and microscopic techniques.},
626 doi = {10.1194/jlr.M500103-JLR200},
628 @Article{Hanczyc2003:protocell_model,
629 author = {Martin M Hanczyc and Shelly M Fujikawa and Jack W Szostak},
630 title = {Experimental models of primitive cellular compartments:
631 encapsulation, growth, and division},
638 abstract = {The clay montmorillonite is known to catalyze the
639 polymerization of RNA from activated ribonucleotides. Here
640 we report that montmorillonite accelerates the spontaneous
641 conversion of fatty acid micelles into vesicles. Clay
642 particles often become encapsulated in these vesicles, thus
643 providing a pathway for the prebiotic encapsulation of
644 catalytically active surfaces within membrane vesicles. In
645 addition, RNA adsorbed to clay can be encapsulated within
646 vesicles. Once formed, such vesicles can grow by
647 incorporating fatty acid supplied as micelles and can
648 divide without dilution of their contents by extrusion
649 through small pores. These processes mediate vesicle
650 replication through cycles of growth and division. The
651 formation, growth, and division of the earliest cells may
652 have occurred in response to similar interactions with
653 mineral particles and inputs of material and energy.},
655 doi = {10.1126/science.1089904},
657 @Article{Hargreaves1977:pl_synthesis,
658 author = {W R Hargreaves and S J Mulvihill and D W Deamer},
659 title = {Synthesis of phospholipids and membranes in prebiotic
669 @Article{Hargreaves1978:liposome_from_aphiphiles,
670 author = {W R Hargreaves and D W Deamer},
671 title = {Liposomes from ionic, single-chain amphiphiles},
672 journal = {Biochemistry},
678 abstract = {In studies of the minimum physiochemical requirements for
679 lipid membrane formation, we have made liposomes from
680 dilute, aqueous dispersions of C(8)-C(18) single-chain
681 amphiphiles. In general, membrane formation from ionic
682 soaps and detergents requires the presence of uncharged
683 amphiphiles. Vesicles were characterized by phase-contrast
684 microscopy, by trapping of ionic dyes, as well as by
685 negativestain and freez-frature electron microscopy. They
686 were typically heterogeneous in size, but the average
687 diameter could be experimentally varied in some cases over
688 the range of 1 to 100 micrometer. Uni-, oligo-, and
689 multilamellar vesicles were observed. Membrane permeability
690 to various solutes was determined in part by a new
691 technique which utilized phase-contract microscopy; when
692 impermeable vesciles exclude added solutes such as sucrose,
693 refractive index differences are created between vesicle
694 contents and surrounding medium, so that the vesicles
695 appear bright in the phase microscope. Permeant solutes do
696 not produce this effect. Spectrophotometric permeability
697 determinations confirmed the results of this technique and
698 provided quantitative measures of permeability. Monoalkyl
699 liposomes have potential uses as models of biomembranes and
700 in drug delivery. They are also relevant to the prebiotic
701 origin of biomembranes.},
704 @Article{Huang1999:chol_solubility_model,
705 author = {J Huang and G W Feigenson},
706 title = {A microscopic interaction model of maximum solubility of
707 cholesterol in lipid bilayers},
708 journal = {Biophys. J},
714 abstract = {We recently reported the equilibrium maximum solubility of
715 cholesterol in a lipid bilayer, chi*chol, to be 0.66 in
716 four different phosphatidylcholines, and 0.51 in a
717 phosphatidylethanolamine (Huang, J.,J.T. Buboltz, and G. W.
718 Feigenson. 1999. Biochim. Biophys. Acta. in press). Here we
719 present a model of cholesterol-phospholipid mixing that
720 explains these observed values of chi*chol. Monte Carlo
721 simulations show that pairwise-additivity of
722 nearest-neighbor interactions is inadequate to describe all
723 the chi*chol values. Instead, if cholesterol multibody
724 interactions are assigned highly unfavorable energy, then
725 jumps occur in cholesterol chemical potential that lead to
726 its precipitation from the bilayer. Cholesterol
727 precipitation is most likely to occur near three discrete
728 values of cholesterol mole fraction, 0.50, 0.57, and 0.67,
729 which correspond to cholesterol/phospholipid mole ratios of
730 1/1, 4/3, and 2/1, respectively. At these solubility
731 limits, where cholesterol chemical potential jumps, the
732 cholesterol-phospholipid bilayer mixture forms highly
733 regular lipid distributions in order to minimize
734 cholesterol-cholesterol contacts. This treatment shows that
735 dramatic structural and thermodynamic changes can occur at
736 particular cholesterol mole fractions without any
737 stoichiometric complex formation. The physical origin of
738 the unfavorable cholesterol multibody interaction is
739 explained by an "umbrella model": in a bilayer, nonpolar
740 cholesterol relies on polar phospholipid headgroup coverage
741 to avoid the unfavorable free energy of cholesterol contact
742 with water. Thus, at high cholesterol mole fraction, this
743 unfavorable free energy, not any favorable
744 cholesterol-phospholipid interaction, dominates the mixing
745 behavior. This physical origin also explains the
746 "cholesterol condensing effect" and the increase in acyl
747 chain order parameter in cholesterol-phospholipid
751 @Article{Huang1999:cholesterol_solubility,
752 author = {J Huang and J T Buboltz and G W Feigenson},
753 title = {Maximum solubility of cholesterol in phosphatidylcholine and
754 phosphatidylethanolamine bilayers},
758 journal = {Biochim. Biophys. Acta},
761 abstract = {In any lipid bilayer membrane, there is an upper limit on
762 the cholesterol concentration that can be accommodated
763 within the bilayer structure; excess cholesterol will
764 precipitate as crystals of pure cholesterol monohydrate.
765 This cholesterol solubility limit is a well-defined
766 quantity. It is a first-order phase boundary in the
767 phospholipid/cholesterol phase diagram. There are many
768 different solubility limits in the literature, but no clear
769 picture has emerged that can unify the disparate results.
770 We have studied the effects that different sample
771 preparation methods can have on the apparent experimental
772 solubility limit. We find that artifactual demixing of
773 cholesterol can occur during conventional sample
774 preparation and that this demixed cholesterol may produce
775 artifactual cholesterol crystals. Therefore,
776 phospholipid/cholesterol suspensions which are prepared by
777 conventional methods may manifest variable, falsely low
778 cholesterol solubility limits. We have developed two novel
779 preparative methods which are specifically designed to
780 prevent demixing during sample preparation. For detection
781 of the cholesterol crystals, X-ray diffraction has proven
782 to be quantitative and highly sensitive. Experiments based
783 on these methods yield reproducible and precise cholesterol
784 solubility limits: 66 mol\% for phosphatidylcholine (PC)
785 bilayers and 51 mol\% for phosphatidylethanolamine (PE)
786 bilayers. We present evidence that these are true,
787 equilibrium values. In contrast to the dramatic headgroup
788 effect (PC vs. PE), acyl chain variations had no effect on
789 the cholesterol solubility limit in four different
790 PC/cholesterol mixtures.},
793 @Article{Inger2009:gard_mutations,
794 author = {Aron Inger and Ariel Solomon and Barak Shenhav and Tsviya
795 Olender and Doron Lancet},
796 title = {Mutations and lethality in simulated prebiotic networks},
797 journal = {J Mol Evol},
803 abstract = {The Graded Autocatalysis Replication Domain (GARD) model
804 describes an origin of life scenario which involves
805 non-covalent compositional assemblies, made of monomeric
806 mutually catalytic molecules. GARD constitutes an
807 alternative to informational biopolymers as a mechanism of
808 primordial inheritance. In the present work, we examined
809 the effect of mutations, one of the most fundamental
810 mechanisms for evolution, in the context of the networks of
811 mutual interaction within GARD prebiotic assemblies. We
812 performed a systematic analysis analogous to single and
813 double gene deletions within GARD. While most deletions
814 have only a small effect on both growth rate and molecular
815 composition of the assemblies, $\approx$10\% of the deletions
816 caused lethality, or sometimes showed enhanced fitness.
817 Analysis of 14 different network properties on 2,000
818 different GARD networks indicated that lethality usually
819 takes place when the deleted node has a high molecular
820 count, or when it is a catalyst for such node. A
821 correlation was also found between lethality and node
822 degree centrality, similar to what is seen in real
823 biological networks. Addressing double knockout mutations,
824 our results demonstrate the occurrence of both synthetic
825 lethality and extragenic suppression within GARD networks,
826 and convey an attempt to correlate synthetic lethality to
827 network node-pair properties. The analyses presented help
828 establish GARD as a workable alternative prebiotic
829 scenario, suggesting that life may have begun with large
830 molecular networks of low fidelity, that later underwent
831 evolutionary compaction and fidelity augmentation.},
833 doi = {10.1007/s00239-009-9281-y},
835 @Article{Israelachvili1975:amphiphile_self_assembly,
836 author = {Jacob N Israelachvili and D John Mitchell and Barry W Ninham},
837 title = {Theory of Self-Assembly of Hydrocarbon Amphiphiles
838 into Micelles and Bilayers},
839 journal = {J. Chem. Soc., Faraday Trans. 2,},
843 abstract = {A simple theory is developed that accounts for many of
844 the observed physical properties of micelles, both
845 globular and rod-like, and of bilayer vesicles
846 composed of ionic or zwitterionic amphiphiles. The
847 main point of departure from previous theories lies
848 in the recognition and elucidation of the role of
849 geometric constraints in self-assembly. The linking
850 together of thermodynamics, interaction free
851 energies and geometry results in a general framework
852 which permits extension to more complicated
853 self-assembly problems.},
854 doi = {10.1039/F29767201525}
857 @Article{Janas2004:rna_membrane_transporter,
858 author = {Teresa Janas and Tadeusz Janas and Michael Yarus},
859 title = {A membrane transporter for tryptophan composed of RNA},
866 abstract = {We have incorporated an RNA binding site for the biological
867 amino acid tryptophan within an RNA complex with affinity
868 for phospholipid bilayer membranes. The resulting RNA
869 (9:10Trp) creates a selective route through the bilayer for
870 the amino acid. Binding and enhanced tryptophan
871 permeability are nonlinear in RNA concentration, suggesting
872 that RNA aggregation is required for both. Tryptophan
873 permeability saturates with increased concentration, though
874 at approximately 1000-fold greater level than when binding
875 a free aptamer. The RNA (9:10Trp) complex, bound at a mean
876 of two per liposome, halves the activation energy for
877 tryptophan transport (to 46 kJ/mole), specifically
878 increasing tryptophan entry to a maximal velocity of 0.5
879 sec(-1) per liposome with little or no accompanying
880 increase in general permeability. Individual RNAs turn over
881 tens of thousands of times at high tryptophan
882 concentration. Thus, a specific passive membrane
883 transporter whose properties overlap those of
884 single-molecule transporter proteins, can be made of RNA
885 alone. Permeability changes probably rely on disturbances
886 in lipid conformation as well as on an advantageous low
887 free energy position for tryptophan at the membrane. Other
888 RNA activities may yield other RNA-membrane nanosystems via
891 doi = {10.1261/rna.7112704},
893 @Article{Jones1990:lipid_transfer,
894 author = {J D Jones and T E Thompson},
895 title = {Mechanism of spontaneous, concentration-dependent phospholipid
896 transfer between bilayers},
897 journal = {Biochemistry},
903 abstract = {We have previously demonstrated that spontaneous
904 phospholipid transfer between bilayer vesicles at higher
905 vesicle concentrations is characterized not only by a
906 first-order desorption rate but also by a second-order
907 process dependent on vesicle concentration (Jones &
908 Thompson, 1989b). We have extended our studies to examine
909 the mechanism of this second-order process by investigating
910 transfer as a function of lipid type, temperature, aqueous
911 medium composition, and vesicle size. The results suggest a
912 mechanism of concentration-dependent transfer in which the
913 rate of lipid monomer desorption from vesicle bilayers is
914 enhanced in transient vesicle-vesicle complexes.},
917 @Article{Joyce2002:rna_world,
918 author = {Gerald F Joyce},
919 title = {The antiquity of RNA-based evolution},
926 abstract = {All life that is known to exist on Earth today and all life
927 for which there is evidence in the geological record seems
928 to be of the same form--one based on DNA genomes and
929 protein enzymes. Yet there are strong reasons to conclude
930 that DNA- and protein-based life was preceded by a simpler
931 life form based primarily on RNA. This earlier era is
932 referred to as the 'RNA world', during which the genetic
933 information resided in the sequence of RNA molecules and
934 the phenotype derived from the catalytic properties of
937 doi = {10.1038/418214a},
939 @Article{Kafri2010:enantiomer_gard,
940 author = {Ran Kafri and Omer Markovitch and Doron Lancet},
941 title = {Spontaneous chiral symmetry breaking in early molecular
943 journal = {Biol Direct},
948 doi = {10.1186/1745-6150-5-38},
950 @Article{Katz1988:pl_packing_chol,
951 author = {S Lund-Katz and H M Laboda and L R McLean and M C Phillips},
952 title = {Influence of molecular packing and phospholipid type on rates
953 of cholesterol exchange},
954 journal = {Biochemistry},
960 abstract = {The rates of [14C]cholesterol transfer from small
961 unilamellar vesicles containing cholesterol dissolved in
962 bilayers of different phospholipids have been determined to
963 examine the influence of phospholipid-cholesterol
964 interactions on the rate of cholesterol desorption from the
965 lipid-water interface. The phospholipids included
966 unsaturated phosphatidylcholines (PC's) (egg PC,
967 dioleoyl-PC, and soybean PC), saturated PC (dimyristoyl-PC
968 and dipalmitoyl-PC), and sphingomyelins (SM's) (egg SM,
969 bovine brain SM, and N-palmitoyl-SM). At 37 degrees C, for
970 vesicles containing 10 mol\% cholesterol, the half-times
971 for exchange are about 1, 13, and 80 h, respectively, for
972 unsaturated PC, saturated PC, and SM. In order to probe how
973 differences in molecular packing in the bilayers cause the
974 rate constants for cholesterol desorption to be in the
975 order unsaturated PC greater than saturated PC greater than
976 SM, nuclear magnetic resonance (NMR) and monolayer methods
977 were used to evaluate the cholesterol physical state and
978 interactions with phospholipid. The NMR relaxation
979 parameters for [4-13C]cholesterol reveal no differences in
980 molecular dynamics in the above bilayers. Surface pressure
981 (pi)-molecular area isotherms for mixed monolayers of
982 cholesterol and the above phospholipids reveal that SM
983 lateral packing density is greater than that of the PC with
984 the same acyl chain saturation and length (e.g., at pi = 5
985 mN/m, where both monolayers are in the same physical state,
986 dipalmitoyl-PC and palmitoyl-SM occupy 87 and 81
987 A2/molecule, respectively).(ABSTRACT TRUNCATED AT 250
991 @Article{Kumar1991:lipid_packing,
992 author = {V V Kumar},
993 title = {Complementary molecular shapes and additivity of the packing
994 parameter of lipids},
995 journal = {Proc Natl Acad Sci U S A},
1001 abstract = {Physical dimensions of a membrane component influence its
1002 phase preference upon hydration. A dimensionless packing
1003 parameter, S, given by S = V/al, where V is the hydrocarbon
1004 volume, a is the area of the head group, and l is the
1005 critical length of the hydrocarbon chain, is useful in
1006 determining the phase preference of a lipid, and the value
1007 of S usually lies between 0.5 and 1 for bilayers. Here, the
1008 value of S is calculated for phosphatidylcholine (PC) and
1009 lysophosphatidylcholine (lysoPC) as a function of chain
1010 length, and it is shown that diacylPC having an S value of
1011 less than 0.74 does not form bilayers. For example,
1012 diacylPC, up to a chain length of eight carbon atoms, forms
1013 only micelles, whereas higher homologs with S greater than
1014 0.74 form bilayers. It is also shown that when lipid
1015 molecules having complementary shapes associate, the value
1016 of S becomes additive. Using the additivity of S, a number
1017 of experimental results for lipid mixtures can be
1018 explained. For example, lysoPC and cholesterol form
1019 lamellar structures between 45 and approximately 80 mol\%
1020 cholesterol, and the additive value of S for this region is
1021 between 0.74 and 1. Similarly, the additivity of S shows
1022 that the maximum amount of cholesterol that can be
1023 incorporated into PC bilayers is 50 mol\%, in agreement
1024 with experimental studies.},
1027 @Article{Lange1983:chol_distribution,
1028 author = {Y Lange and B V Ramos},
1029 title = {Analysis of the distribution of cholesterol in the intact
1031 journal = {J. Biol. Chem.},
1037 abstract = {We have used the enzyme cholesterol oxidase, which
1038 catalyzes the oxidation of cholesterol to
1039 cholest-4-en-3-one, to examine the distribution of
1040 cholesterol in cultured fibroblasts, Chinese hamster ovary
1041 cells, and isolated rat liver hepatocytes. While the plasma
1042 membrane normally was not attacked by cholesterol oxidase,
1043 we found that treating cells with low ionic strength buffer
1044 and glutaraldehyde rendered their cholesterol highly
1045 susceptible to oxidation. Most of the cholesterol was
1046 oxidized in all three cell types: 94\% in fibroblasts, 92\%
1047 in Chinese hamster ovary cells, and 80\% in hepatocytes.
1048 Given that the enzyme had access only to the outer surface
1049 of the cells and cholesterol can move rapidly across the
1050 fixed plasma membrane, these values are taken to reflect
1051 the fraction of cellular cholesterol present in the plasma
1052 membrane. Additional experiments confirmed this
1053 interpretation. Fibroblasts were labeled with
1054 [3H]cholesterol by brief exposure to exogenous radiolabel
1055 and incubated with [14C]mevalonic acid to label cholesterol
1056 biosynthetically. Cholesterol oxidase attacked at least
1057 97\% of the exogenous label but as little as 10\% of the
1058 biosynthetically labeled cholesterol. These data suggest
1059 that the cholesterol oxidase did not reach the
1060 intracellular pool and that cholesterol in the plasma
1061 membrane is not in rapid equilibrium with internal
1062 membranes. A study of the transfer of cholesterol to plasma
1063 from cells labeled biosynthetically with [3H]cholesterol
1064 and exogenously with [14C]cholesterol confirmed the
1065 different subcellular distribution of the two labels. These
1066 studies demonstrate that an unexpectedly high proportion of
1067 cell cholesterol is associated with plasma membranes and
1068 that this cholesterol pool can be rapidly and selectively
1069 labeled and oxidized. These features make cholesterol a
1070 useful specific marker for the plasma membrane.},
1073 @Article{Leirer2009:vesicle_fission,
1074 author = {C Leirer and B Wunderlich and V M Myles and M F Schneider},
1075 title = {Phase transition induced fission in lipid vesicles},
1076 journal = {Biophys Chem},
1082 abstract = {In this work we demonstrate how the first order phase
1083 transition in giant unilamellar vesicles (GUVs) can
1084 function as a trigger for membrane fission. When driven
1085 through their gel-fluid phase transition GUVs exhibit
1086 budding or pearl formation. These buds remain connected to
1087 the mother vesicle presumably by a small neck. Cooling
1088 these vesicles from the fluid phase (T>T(m)) through the
1089 phase transition into the gel state (T<T(m)), leads to
1090 complete rupture and fission of the neck, while the mother
1091 vesicle remains intact. Pearling tubes which formed upon
1092 heating break-up and decay into multiple individual
1093 vesicles which then diffuse freely. Finally we demonstrate
1094 that mimicking the intracellular bulk viscosity by
1095 increasing the bulk viscosity to 40 cP does not affect the
1096 overall fission process, but leads to a significant
1097 decrease in the size of the released vesicles.},
1099 doi = {10.1016/j.bpc.2009.04.002},
1101 @article{McConnell2003,
1102 author = {Harden M McConnell and Arun Radhakrishnan},
1103 title = {Condensed complexes of cholesterol and phospholipids},
1104 journal = {Biochem. Biophys. Acta},
1110 abstract = {There is overwhelming evidence that lipid bilayer regions
1111 of animal cell membranes are in a liquid state.
1112 Quantitative models of these bilayer regions must then be
1113 models of liquids. These liquids are highly non-ideal. For
1114 example, it has been known for more than 75 years that
1115 mixtures of cholesterol and certain phospholipids undergo
1116 an area contraction or condensation in lipid monolayers at
1117 the air-water interface. In the past 3 years, a
1118 thermodynamic model of "condensed complexes" has been
1119 proposed to account for this non-ideal behavior. Here we
1120 give an overview of the model, its relation to other
1121 models, and to modern views of the properties of animal
1125 @Article{McConnell2006,
1126 author = {Harden McConnell and Arun Radhakrishnan},
1127 title = {Theory of the deuterium NMR of sterol-phospholipid membranes},
1128 journal = {Proc Natl Acad Sci U S A},
1132 pages = {1184--1189},
1134 abstract = {A general theoretical model is described for the NMR
1135 spectra of mixtures of sterols and deuterium-labeled
1136 phospholipids. In the case of homogeneous membranes, the
1137 average quadrupole splittings are determined by equilibria
1138 between lipids in cholesterol-phospholipid complexes and
1139 lipids not in complexes. Chemical exchange of lipids
1140 between those in the free state and those in the complex
1141 state affects the deuterium resonance line shapes. The
1142 lifetime of a phospholipid molecule in an
1143 ergosterol-dipalmitoylphosphatidylcholine complex is
1144 estimated to be of the order of 10(-5) s on the basis of
1145 the observed line broadenings. In the vicinity of a
1146 critical point of a cholesterol-phospholipid mixture,
1147 fluctuations in the concentration of complexes also can
1148 contribute to the deuterium nuclear resonance line
1149 broadening. At the critical point, the temperature
1150 derivative of the concentration of complexes is
1151 discontinuous. There is a corresponding jump in the
1152 calculated heat capacity as well as in the temperature
1153 derivative of the deuterium NMR first moment.},
1155 doi = {10.1073/pnas.0510514103},
1157 @Article{Nichols1982:ret_amphiphile_transfer,
1158 author = {J W Nichols and R E Pagano},
1159 title = {Use of resonance energy transfer to study the kinetics of
1160 amphiphile transfer between vesicles},
1161 journal = {Biochemistry},
1169 @Article{Nichols1985:phospholipid_monomer_vesicle_thermodynamics,
1170 author = {J W Nichols},
1171 title = {Thermodynamics and kinetics of phospholipid monomer-vesicle
1173 journal = {Biochemistry},
1179 abstract = {Resonance energy transfer between acyl chain labeled
1180 (7-nitro-2,1,3-benzoxadiazol-4-yl)phosphatidylcholine
1181 (NBD-PC) and head group labeled (lissamine rhodamine B
1182 sulfonyl)phosphatidylethanolamine (N-Rh-PE) was used to
1183 monitor the rate of NBD-PC transfer between two populations
1184 of dioleoylphosphatidylcholine (DOPC) vesicles.
1185 Equilibration of NBD-PC between DOPC vesicles occurs by the
1186 diffusion of soluble monomers through the water phase,
1187 which is a first-order process. Conditions were used such
1188 that the apparent transfer rate constant is equal to the
1189 rate constant for monomer-vesicle dissociation into
1190 solution. The partition distribution of NBD-PC between DOPC
1191 vesicles and water was determined by measuring the loss of
1192 NBD-PC from vesicles into solution following the dilution
1193 of small amounts of vesicles in buffer. The acyl chain
1194 length and temperature dependence of both the rate and
1195 partition measurements were determined, and a free energy
1196 diagram for NBD-PC-soluble monomer-vesicle interactions was
1197 constructed. The conclusions of this analysis are the
1198 following: NBD-PC dissociation from and association with
1199 the bilayer require passage through a high-energy
1200 transition state resulting predominantly from enthalpic
1201 energy. The activation energy for NBD-PC-vesicle
1202 dissociation becomes more positive and the standard free
1203 energy of NBD-PC transfer from water to vesicles becomes
1204 more negative with increasing acyl chain length. The
1205 standard free energy of transfer for NBD-PC from water to
1206 vesicles results predominantly from differences in enthalpy
1207 between the membrane and water phases. The enthalpy of
1208 activation for association increases with acyl chain length
1209 and is larger than expected for an aqueous
1210 diffusion-limited process in bulk water.},
1213 @Book{Oparin1938:origin_of_life,
1214 author = {Aleksandr Ivanovich Oparin},
1215 translator = {Sergius Morgulis},
1216 title = {The origin of life},
1217 publisher = {Macmillan, New York},
1219 href = {http://ucr.worldcat.org/title/origin-of-life/oclc/958765}}
1220 @Article{Pandit2002:mds_dpps,
1221 author = {Sagar A Pandit and Max L Berkowitz},
1222 title = {Molecular dynamics simulation of dipalmitoylphosphatidylserine
1223 bilayer with Na+ counterions},
1224 journal = {Biophys J},
1230 abstract = {We performed a molecular dynamics simulation of
1231 dipalmitoylphosphatidylserine (DPPS) bilayer with Na+
1232 counterions. We found that hydrogen bonding between the NH
1233 group and the phosphate group leads to a reduction in the
1234 area per headgroup when compared to the area in
1235 dipalmitoylphosphatidylcholine bilayer. The Na+ ions bind
1236 to the oxygen in the carboxyl group of serine, thus giving
1237 rise to a dipolar bilayer similar to
1238 dipalmitoylphosphatidylethanolamine bilayer. The results of
1239 the simulation show that counterions play a crucial role in
1240 determining the structural and electrostatic properties of
1243 doi = {10.1016/S0006-3495(02)75532-X},
1245 @Article{Pankov2005:chol_distribution,
1246 author = {Roumen Pankov and Tania Markovska and Rusina Hazarosova and
1247 Peter Antonov and Lidia Ivanova and Albena Momchilova},
1248 title = {Cholesterol distribution in plasma membranes of $\betaup$1
1249 integrin-expressing and $\betaup$1 integrin-deficient fibroblasts},
1250 journal = {Archives of biochemistry and biophysics},
1256 abstract = {The effect of integrin receptors on the level and
1257 transmembrane localization of cholesterol molecules was
1258 investigated in beta1 integrin-expressing (beta1) and beta1
1259 integrin-deficient (beta1 null) cells. We found that the
1260 content of specific raft components-cholesterol,
1261 sphingomyelin, and caveolin-was increased in
1262 integrin-expressing cells. Integrin presence affected as
1263 well the transmembrane distribution of cholesterol-a higher
1264 percent was found in the plasma membrane outer monolayer of
1265 beta1 compared to beta1 null cells. Sphingomyelin depletion
1266 reduced the presence of cholesterol in the outer membrane
1267 monolayer of both cell lines, but the differences in
1268 cholesterol asymmetry, observed between beta1 and beta1
1269 null cells before sphingomyelinase treatment were
1270 preserved. These findings implied that integrin receptors
1271 affected the non-random transmembrane distribution of
1272 cholesterol. Finally, a higher percent of
1273 detergent-resistant membranes was obtained from beta1
1274 integrin-expressing cells, suggesting that the presence of
1275 these receptors in the membranes influenced the formation
1276 and/or stabilization of lipid raft domains.},
1279 @Article{Pike2002:lipid_raft_composition,
1280 author = {Linda J Pike and Xianlin Han and Koong-Nah Chung and Richard
1282 title = {Lipid rafts are enriched in arachidonic acid and
1283 plasmenylethanolamine and their composition is independent of
1284 caveolin-1 expression: a quantitative electrospray
1285 ionization/mass spectrometric analysis.},
1286 journal = {Biochemistry},
1292 abstract = {Lipid rafts are specialized cholesterol-enriched membrane
1293 domains that participate in cellular signaling processes.
1294 Caveolae are related domains that become invaginated due to
1295 the presence of the structural protein, caveolin-1. In this
1296 paper, we use electrospray ionization mass spectrometry
1297 (ESI/MS) to quantitatively compare the phospholipids
1298 present in plasma membranes and nondetergent lipid rafts
1299 from caveolin-1-expressing and nonexpressing cells. Lipid
1300 rafts are enriched in cholesterol and sphingomyelin as
1301 compared to the plasma membrane fraction. Expression of
1302 caveolin-1 increases the amount of cholesterol recovered in
1303 the lipid raft fraction but does not affect the relative
1304 proportions of the various phospholipid classes.
1305 Surprisingly, ESI/MS demonstrated that lipid rafts are
1306 enriched in plasmenylethanolamines, particularly those
1307 containing arachidonic acid. While the total content of
1308 anionic phospholipids was similar in plasma membranes and
1309 nondetergent lipid rafts, the latter were highly enriched
1310 in phosphatidylserine but relatively depleted in
1311 phosphatidylinositol. Detergent-resistant membranes made
1312 from the same cells showed a higher cholesterol content
1313 than nondetergent lipid rafts but were depleted in anionic
1314 phospholipids. In addition, these detergent-resistant
1315 membranes were not enriched in arachidonic acid-containing
1316 ethanolamine plasmalogens. These data provide insight into
1317 the structure of lipid rafts and identify potential new
1318 roles for these domains in signal transduction.},
1323 title = {R: A Language and Environment for Statistical
1325 author = {R Development Core Team},
1326 organization = {R Foundation for Statistical Computing},
1327 address = {Vienna, Austria},
1329 note = {{ISBN} 3-900051-07-0},
1330 url = {http://www.R-project.org}
1332 @Article{Rao1982:pc_synthesis,
1333 author = {M Rao and M R Eichberg and J Or\'o},
1334 title = {Synthesis of phosphatidylcholine under possible primitive
1336 journal = {J Mol Evol},
1341 abstract = {Using a primitive Earth evaporating pond model, the
1342 synthesis of phosphatidylcholine was accomplished when a
1343 reaction mixture of choline chloride and disodium
1344 phosphatidate, in the presence of cyanamide and traces of
1345 acid, was evaporated and heated at temperatures ranging
1346 from 25 degrees to 100 degrees C for 7 hours. Optimum
1347 yields of about 15\% were obtained at 80 degrees C.
1348 Phosphatidylcholine was identified by chromatographic,
1349 chemical and enzymatic degradation methods. On enzymatic
1350 hydrolysis with phospholipase A2 and phospholipase C,
1351 lysophosphatidylcholine and phosphorylcholine were formed,
1352 respectively. Alkaline hydrolysis gave
1353 glycerophosphorylcholine. The synthesis of
1354 phosphatidylcholine as the major compound was accompanied
1355 by the formation of lysophosphatidylcholine in smaller
1356 amounts. Cyanamide was found to be essential for the
1357 formation of phosphatidylcholine, and only traces of HCl,
1358 of the order of that required to convert the disodium
1359 phosphatidate to free phosphatidic acid were found
1360 necessary for the synthesis. This work suggests that
1361 phosphatidylcholine, which is an essential component of
1362 most biological membranes, could have been synthesized on
1363 the primitive Earth.},
1367 @Book{Rasmussen2008:protocells,
1368 editor = {Steen Rasmussen and Mark A. Bedau and Liaohai Chen and David Deamer and David C. Krakauer and Norman H. Packard and Peter F. Stadler},
1369 title = {Protocells: Bridging Nonliving and Living Matter},
1370 publisher = {The MIT Press},
1373 @Article{Robinson1995:mds_chol_area,
1374 author = {A J Robinson and W G Richards and P J Thomas and M M Hann},
1375 title = {Behavior of cholesterol and its effect on head group and chain
1376 conformations in lipid bilayers: a molecular dynamics study},
1377 journal = {Biophys J},
1383 abstract = {Cholesterol molecules were put into a computer-modeled
1384 hydrated bilayer of dimyristoyl phosphatidyl choline
1385 molecules, and molecular dynamics simulations were run to
1386 characterize the effect of this important molecule on
1387 membrane structure and dynamics. The effect was judged by
1388 observing differences in order parameters, tilt angles, and
1389 the fraction of gauche bonds along the hydrocarbon chains
1390 between lipids adjacent to cholesterol molecules and
1391 comparing them with those further away. It was observed
1392 that cholesterol causes an increase in the fraction of
1393 trans dihedrals and motional ordering of chains close to
1394 the rigid steroid ring system with a decrease in the kink
1395 population. The hydrogen-bonding interactions between
1396 cholesterol and lipid molecules were determined from radial
1397 distribution calculations and showed the cholesterol
1398 hydroxyl groups either solvated by water, or forming
1399 hydrogen bond contacts with the oxygens of lipid carbonyl
1400 and phosphate groups. The dynamics and conformation of the
1401 cholesterol molecules were investigated and it was seen
1402 that they had a smaller tilt with respect to the bilayer
1403 normal than the lipid chains and furthermore that the
1404 hydrocarbon tail of the cholesterol was conformationally
1407 doi = {10.1016/S0006-3495(95)80171-2},
1409 @article{Rousseeuw1987:silhouettes,
1410 title = "Silhouettes: A graphical aid to the interpretation
1411 and validation of cluster analysis",
1412 journal = "Journal of Computational and Applied Mathematics",
1417 doi = "10.1016/0377-0427(87)90125-7",
1419 "http://www.sciencedirect.com/science/article/B6TYH-45GN65V-6/2/18986ecfab1157f7f05da39a3b08ea73",
1420 author = "Peter J. Rousseeuw",
1421 keywords = "Graphical display",
1422 keywords = "cluster analysis",
1423 keywords = "clustering validity",
1424 keywords = "classification",
1425 abstract = "A new graphical display is proposed for partitioning
1426 techniques. Each cluster is represented by a
1427 so-called silhouette, which is based on the
1428 comparison of its tightness and separation. This
1429 silhouette shows which objects lie well within their
1430 cluster, and which ones are merely somewhere in
1431 between clusters. The entire clustering is displayed
1432 by combining the silhouettes into a single plot,
1433 allowing an appreciation of the relative quality of
1434 the clusters and an overview of the data
1435 configuration. The average silhouette width provides
1436 an evaluation of clustering validity, and might be
1437 used to select an [`]appropriate' number of
1440 @Article{Segre2000:agard,
1441 author = {D Segr\'e and D Ben-Eli and D Lancet},
1442 title = {Compositional genomes: prebiotic information transfer in
1443 mutually catalytic noncovalent assemblies},
1444 journal = {Proc Natl Acad Sci U S A},
1450 abstract = {Mutually catalytic sets of simple organic molecules have
1451 been suggested to be capable of self-replication and
1452 rudimentary chemical evolution. Previous models for the
1453 behavior of such sets have analyzed the global properties
1454 of short biopolymer ensembles by using graph theory and a
1455 mean field approach. In parallel, experimental studies with
1456 the autocatalytic formation of amphiphilic assemblies
1457 (e.g., lipid vesicles or micelles) demonstrated
1458 self-replication properties resembling those of living
1459 cells. Combining these approaches, we analyze here the
1460 kinetic behavior of small heterogeneous assemblies of
1461 spontaneously aggregating molecules, of the type that could
1462 form readily under prebiotic conditions. A statistical
1463 formalism for mutual rate enhancement is used to
1464 numerically simulate the detailed chemical kinetics within
1465 such assemblies. We demonstrate that a straightforward set
1466 of assumptions about kinetically enhanced recruitment of
1467 simple amphiphilic molecules, as well as about the
1468 spontaneous growth and splitting of assemblies, results in
1469 a complex population behavior. The assemblies manifest a
1470 significant degree of homeostasis, resembling the
1471 previously predicted quasi-stationary states of biopolymer
1472 ensembles (Dyson, F. J. (1982) J. Mol. Evol. 18, 344-350).
1473 Such emergent catalysis-driven, compositionally biased
1474 entities may be viewed as having rudimentary "compositional
1475 genomes." Our analysis addresses the question of how
1476 mutually catalytic metabolic networks, devoid of
1477 sequence-based biopolymers, could exhibit transfer of
1478 chemical information and might undergo selection and
1479 evolution. This computed behavior may constitute a
1480 demonstration of natural selection in populations of
1481 molecules without genetic apparatus, suggesting a pathway
1482 from random molecular assemblies to a minimal protocell.},
1485 @Article{Segre2001:compositional_inheritance,
1486 author = {D Segr\'e and B Shenhav and R Kafri and D Lancet},
1487 title = {The molecular roots of compositional inheritance},
1488 journal = {J Theor Biol},
1494 abstract = {Non-covalent compositional assemblies, made of monomeric
1495 mutually catalytic molecules, constitute an alternative to
1496 alphabet-based informational biopolymers as a mechanism of
1497 primordial inheritance. Such assemblies appear implicitly
1498 in many "Metabolism First" origin of life scenarios, and
1499 more explicitly in the Graded Autocatalysis Replication
1500 Domain (GARD) model [Segré et al. (2000). Proc. Natl Acad.
1501 Sci. U.S.A.97, 4112-4117]. In the present work, we provide
1502 a detailed analysis of the quantitative molecular roots of
1503 such behavior. It is demonstrated that the fidelity of
1504 reproduction provided by a newly defined heritability
1505 measure eta(*)(s), strongly depends on the values of
1506 molecular recognition parameters and on assembly size. We
1507 find that if the catalytic rate acceleration coefficients
1508 are distributed normally, transfer of compositional
1509 information becomes impossible, due to frequent
1510 "compositional error catastrophes". In contrast, if the
1511 catalytic acceleration rates obey a lognormal distribution,
1512 as actually predicted by a statistical formalism for
1513 molecular repertoires, high reproduction fidelity is
1514 obtained. There is also a clear dependence on assembly size
1515 N, whereby maximal eta is seen in a narrow range around N
1516 approximately 3.5 N(G)/lambda, where N(G)is the size of the
1517 primordial molecular repertoire and lambda is a molecular
1518 interaction statistical parameter. Such relationships help
1519 define the physicochemical conditions that could underlie
1520 the early steps in pre-biotic evolution.},
1522 doi = {10.1006/jtbi.2001.2440},
1524 @Article{Segre2001:lipid_world,
1525 author = {D Segre and D Ben-Eli and D W Deamer and D Lancet},
1526 title = {The lipid world},
1527 journal = {Orig Life Evol Biosph},
1533 abstract = {The continuity of abiotically formed bilayer membranes with
1534 similar structures in contemporary cellular life, and the
1535 requirement for microenvironments in which large and small
1536 molecules could be compartmentalized, support the idea that
1537 amphiphilic boundary structures contributed to the
1538 emergence of life. As an extension of this notion, we
1539 propose here a 'Lipid World' scenario as an early
1540 evolutionary step in the emergence of cellular life on
1541 Earth. This concept combines the potential chemical
1542 activities of lipids and other amphiphiles, with their
1543 capacity to undergo spontaneous self-organization into
1544 supramolecular structures such as micelles and bilayers. In
1545 particular, the documented chemical rate enhancements
1546 within lipid assemblies suggest that energy-dependent
1547 synthetic reactions could lead to the growth and increased
1548 abundance of certain amphiphilic assemblies. We further
1549 propose that selective processes might act on such
1550 assemblies, as suggested by our computer simulations of
1551 mutual catalysis among amphiphiles. As demonstrated also by
1552 other researchers, such mutual catalysis within random
1553 molecular assemblies could have led to a primordial
1554 homeostatic system displaying rudimentary life-like
1555 properties. Taken together, these concepts provide a
1556 theoretical framework, and suggest experimental tests for a
1557 Lipid World model for the origin of life.},
1560 @Article{Shaikh2002:pe_phase_sm_area,
1561 author = {Saame Raza Shaikh and Michael R Brzustowicz and Noah
1562 Gustafson and William Stillwell and Stephen R Wassall},
1563 title = {Monounsaturated PE does not phase-separate from the lipid raft
1564 molecules sphingomyelin and cholesterol: role for
1566 journal = {Biochemistry},
1570 pages = {10593--602},
1572 abstract = {We investigated interactions of the lipid raft molecules
1573 sphingomyelin (SM) and cholesterol (CHOL) in monolayers and
1574 bilayers composed of
1575 1-palmitoyl-2-oleoyl-sn-glycerophosphatidylethanolamine
1577 1-palmitoyl-2-docosahexaenoyl-sn-glycerophosphatidylethanol
1578 amine (PDPE) at 35 degrees C. Techniques employed were
1579 pressure-area (pi-A) isotherms generated from
1580 Langmuir-Blodgett films, solid-state (2)H and (31)P NMR
1581 spectroscopies, and differential scanning calorimetry
1582 (DSC). Condensation calculated from pi-A isotherms and
1583 reduction in the enthalpy of the gel-liquid-crystalline
1584 transition in DSC scans showed CHOL has a strong affinity
1585 for POPE, comparable to that observed between SM-CHOL.
1586 Order parameters derived from (2)H NMR spectra of the
1587 perdeuterated sn-1 chain of POPE-d(31) increased by >50\%
1588 upon addition of equimolar CHOL to POPE-d(31)/SM (1:1 mol)
1589 bilayers. Close proximity of CHOL to POPE even in the
1590 presence of SM is indicated. Chemical shift anisotropy
1591 (Deltasigma(csa)) measured from (1)H-decoupled (31)P NMR
1592 spectra also implied intimate lipid mixing in POPE/SM/CHOL
1593 (1:1:1 mol). In contrast, pi-A isotherms and corroborating
1594 DSC studies of PDPE/SM (1:1 mol) indicate phase separation
1595 between SM and PDPE, which was maintained in the presence
1596 of CHOL. The cholesterol-associated increase in order of
1597 the perdeuterated sn-1 chain of PDPE determined by (2)H NMR
1598 was 2-fold less for PDPE-d(31)/SM/CHOL (1:1:1 mol) than
1599 POPE-d(31)/SM/CHOL (1:1:1 mol). Our findings support the
1600 notion that acyl chain dependent lateral phase separation
1601 occurs in the presence of a docosahexaenoic acid
1602 (DHA)-containing phospholipid (PDPE), but not an oleic
1603 acid-containing phospholipid (POPE). We propose that
1604 monounsaturated lipids do not promote formation of stable
1605 lipid rafts and that polyunsaturation may be important for
1609 @Article{Shenhav2005:pgard,
1610 author = {Barak Shenhav and Arren Bar-Even and Ran Kafri and Doron
1612 title = {Polymer GARD: computer simulation of covalent bond formation
1613 in reproducing molecular assemblies},
1614 journal = {Orig Life Evol Biosph},
1620 abstract = {The basic Graded Autocatalysis Replication Domain (GARD)
1621 model consists of a repertoire of small molecules,
1622 typically amphiphiles, which join and leave a non-covalent
1623 micelle-like assembly. Its replication behavior is due to
1624 occasional fission, followed by a homeostatic growth
1625 process governed by the assembly's composition. Limitations
1626 of the basic GARD model are its small finite molecular
1627 repertoire and the lack of a clear path from a 'monomer
1628 world' towards polymer-based living entities. We have now
1629 devised an extension of the model (polymer GARD or P-GARD),
1630 where a monomer-based GARD serves as a 'scaffold' for
1631 oligomer formation, as a result of internal chemical rules.
1632 We tested this concept with computer simulations of a
1633 simple case of monovalent monomers, whereby more complex
1634 molecules (dimers) are formed internally, in a manner
1635 resembling biosynthetic metabolism. We have observed events
1636 of dimer 'take-over' - the formation of compositionally
1637 stable, replication-prone quasi stationary states
1638 (composomes) that have appreciable dimer content. The
1639 appearance of novel metabolism-like networks obeys a
1640 time-dependent power law, reminiscent of evolution under
1641 punctuated equilibrium. A simulation under constant
1642 population conditions shows the dynamics of takeover and
1643 extinction of different composomes, leading to the
1644 generation of different population distributions. The
1645 P-GARD model offers a scenario whereby biopolymer formation
1646 may be a result of rather than a prerequisite for early
1647 life-like processes.},
1650 @Article{Shenhav2007:comp_protocells,
1651 author = {Barak Shenhav and Aia Oz and Doron Lancet},
1652 title = {Coevolution of compositional protocells and their
1654 journal = {Philos Trans R Soc Lond B Biol Sci},
1660 abstract = {The coevolution of environment and living organisms is well
1661 known in nature. Here, it is suggested that similar
1662 processes can take place before the onset of life, where
1663 protocellular entities, rather than full-fledged living
1664 systems, coevolve along with their surroundings.
1665 Specifically, it is suggested that the chemical composition
1666 of the environment may have governed the chemical
1667 repertoire generated within molecular assemblies,
1668 compositional protocells, while compounds generated within
1669 these protocells altered the chemical composition of the
1670 environment. We present an extension of the graded
1671 autocatalysis replication domain (GARD) model--the
1672 environment exchange polymer GARD (EE-GARD) model. In the
1673 new model, molecules, which are formed in a protocellular
1674 assembly, may be exported to the environment that surrounds
1675 the protocell. Computer simulations of the model using an
1676 infinite-sized environment showed that EE-GARD assemblies
1677 may assume several distinct quasi-stationary compositions
1678 (composomes), similar to the observations in previous
1679 variants of the GARD model. A statistical analysis
1680 suggested that the repertoire of composomes manifested by
1681 the assemblies is independent of time. In simulations with
1682 a finite environment, this was not the case. Composomes,
1683 which were frequent in the early stages of the simulation
1684 disappeared, while others emerged. The change in the
1685 frequencies of composomes was found to be correlated with
1686 changes induced on the environment by the assembly. The
1687 EE-GARD model is the first GARD model to portray a possible
1688 time evolution of the composomes repertoire.},
1690 doi = {10.1098/rstb.2007.2073},
1692 @Article{Smaby1997:pc_area_with_chol,
1693 author = {J M Smaby and M M Momsen and H L Brockman and R E Brown},
1694 title = {Phosphatidylcholine acyl unsaturation modulates the decrease
1695 in interfacial elasticity induced by cholesterol},
1696 journal = {Biophys J},
1700 pages = {1492--505},
1702 abstract = {The effect of cholesterol on the interfacial elastic
1703 packing interactions of various molecular species of
1704 phosphatidylcholines (PCs) has been investigated by using a
1705 Langmuir-type film balance and analyzing the elastic area
1706 compressibility moduli (Cs(-1)) as a function of average
1707 cross-sectional molecular area. Emphasis was on the high
1708 surface pressure regions (pi > or = 30 mN/m) which are
1709 thought to mimic biomembrane conditions. Increasing levels
1710 of cholesterol generally caused the in-plane elasticity of
1711 the mixed monolayers to decrease. Yet, the magnitude of the
1712 cholesterol-induced changes was markedly dependent upon PC
1713 hydrocarbon structure. Among PC species with a saturated
1714 sn-1 chain but different sn-2 chain cis unsaturation levels
1715 [e.g., myristate (14:0), oleate (18:1delta9(c), linoleate
1716 (18:2delta9,12(c), arachidonate (20:4delta5,8,11,14(c), or
1717 docosahexenoate (22:6delta4,7,10,13,16,19(c)], the in-plane
1718 elasticity moduli of PC species with higher sn-2
1719 unsaturation levels were less affected by high cholesterol
1720 mol fractions (e.g., >30 mol \%) than were the more
1721 saturated PC species. The largest cholesterol-induced
1722 decreases in the in-plane elasticity were observed when
1723 both chains of PC were saturated (e.g., di-14:0 PC). When
1724 both acyl chains were identically unsaturated, the
1725 resulting PCs were 20-25\% more elastic in the presence of
1726 cholesterol than when their sn-1 chains were long and
1727 saturated (e.g., palmitate). The mixing of cholesterol with
1728 PC was found to diminish the in-plane elasticity of the
1729 films beyond what was predicted from the additive behavior
1730 of the individual lipid components apportioned by mole and
1731 area fraction. Deviations from additivity were greatest for
1732 di-14:0 PC and were least for diarachidonoyl PC and
1733 didocosahexenoyl PC. In contrast to Cs(-1) analyses,
1734 sterol-induced area condensations were relatively
1735 unresponsive to subtle structural differences in the PCs at
1736 high surface pressures. Cs(-1) versus average area plots
1737 also indicated the presence of cholesterol
1738 concentration-dependent, low-pressure (<14 mN/m) phase
1739 boundaries that became more prominent as PC acyl chain
1740 unsaturation increased. Hence, area condensations measured
1741 at low surface pressures often do not accurately portray
1742 which lipid structural features are important in the
1743 lipid-sterol interactions that occur at high membrane-like
1744 surface pressures.},
1747 @Article{Stano2010:vesicle_self_reproduction,
1748 author = {Pasquale Stano and Pier Luigi Luisi},
1749 title = {Achievements and open questions in the self-reproduction of
1750 vesicles and synthetic minimal cells},
1751 journal = {Chem Commun (Camb)},
1757 abstract = {Supramolecular chemistry was enriched, about twenty years
1758 ago, by the discovery of the self-reproduction of micelles
1759 and vesicles. The dynamic aspects and complexity of these
1760 systems makes them good models for biological compartments.
1761 For example, the self-reproduction of vesicles suggests
1762 that the growth in size and number of a vesicle population
1763 resembles the pattern of living cells in several aspects,
1764 but it take place solely due to physical forces. Several
1765 reports demonstrate that reverse micelles, micelles,
1766 sub-micrometric and giant vesicles can self-reproduce,
1767 generating new particles at the expenses of a suitable
1768 precursor. Recently, similar studies are in progress on
1769 more complex vesicle-based systems, namely semi-synthetic
1770 minimal cells. These are artificial cell-like compartments
1771 that are built by filling liposomes with the minimal number
1772 of biomolecules, such as DNA, ribosomes, enzymes, etc., in
1773 order to construct a living cell in the laboratory. This
1774 approach aims to investigate the minimal requirements for
1775 molecular systems in order to display some living
1776 properties, while it finds relevance in origins of life
1777 studies and in synthetic (constructive) biology.},
1779 doi = {10.1039/b913997d},
1781 @Article{Svetina2009:vesicle_budding,
1782 author = {Sasa Svetina},
1783 title = {Vesicle budding and the origin of cellular life},
1784 journal = {Chemphyschem},
1790 abstract = {This Minireview provides an appropriate opportunity to
1791 demonstrate the connection between the results of some
1792 early experimental and theoretical investigations of
1793 vesicle budding and the more recent application of the
1794 concepts developed there to the process of vesicle
1795 self-reproduction. Herein, we also explain why vesicle
1796 budding could have preceded the establishment of cellular
1799 doi = {10.1002/cphc.200900577},
1801 @Article{Szostak2001:synthesizing_life,
1802 author = {J W Szostak and D P Bartel and P L Luisi},
1803 title = {Synthesizing life},
1811 doi = {10.1038/35053176},
1813 @Article{Tamulis2011:lipid_world_evolution,
1814 author = {Arvydas Tamulis and Mantas Grigalavicius},
1815 title = {The emergence and evolution of life in a "fatty acid world"
1816 based on quantum mechanics},
1817 journal = {Orig Life Evol Biosph},
1823 abstract = {Quantum mechanical based electron correlation interactions
1824 among molecules are the source of the weak hydrogen and Van
1825 der Waals bonds that are critical to the self-assembly of
1826 artificial fatty acid micelles. Life on Earth or elsewhere
1827 could have emerged in the form of self-reproducing
1828 photoactive fatty acid micelles, which gradually evolved
1829 into nucleotide-containing micelles due to the enhanced
1830 ability of nucleotide-coupled sensitizer molecules to
1831 absorb visible light. Comparison of the calculated
1832 absorption spectra of micelles with and without nucleotides
1833 confirmed this idea and supports the idea of the emergence
1834 and evolution of nucleotides in minimal cells of a
1835 so-called Fatty Acid World. Furthermore, the
1836 nucleotide-caused wavelength shift and broadening of the
1837 absorption pattern potentially gives these molecules an
1838 additional valuable role, other than a purely genetic one
1839 in the early stages of the development of life. From the
1840 information theory point of view, the nucleotide sequences
1841 in such micelles carry positional information providing
1842 better electron transport along the nucleotide-sensitizer
1843 chain and, in addition, providing complimentary copies of
1844 that information for the next generation. Nucleotide
1845 sequences, which in the first period of evolution of fatty
1846 acid molecules were useful just for better absorbance of
1847 the light in the longer wavelength region, later in the PNA
1848 or RNA World, took on the role of genetic information
1851 doi = {10.1007/s11084-010-9211-4},
1853 @Article{Tanford1974:micelle_formation_thermodynamics,
1854 author = {C Tanford},
1855 title = {Thermodynamics of micelle formation: prediction of micelle
1856 size and size distribution},
1857 journal = {Proc Natl Acad Sci U S A},
1863 abstract = {This paper presents a simple theory for the calculation of
1864 micelle size and other properties of micelleforming
1865 systems. The theory is based on the separate estimation of
1866 the components of the free energy arising from hydrophobic
1867 attraction and from head group repulsion, each as a
1868 function of micelle size. The difficult problem of an a
1869 priori calculation of the repulsive factor is circumvented
1870 by using experimental values of this parameter, derived
1871 from pressure-area curves of monolayers at an interface
1872 between an aqueous solution and liquid hydrocarbon. Though
1873 some parameters of the theory are still somewhat uncertain,
1874 self-consistent and physically realistic values can be
1875 assigned that lead to almost exact prediction of
1876 experimental micelle sizes and critical micelle
1877 concentrations for two distinctly different ionic
1881 @article{Tewes2001:lipid_polarity_in_bec,
1882 author = {BJ Tewes and HJ Galla},
1883 title = {Lipid polarity in brain capillary endothelial cells.},
1884 journal = {Endothelium},
1886 key = {bec, lipid polarity, lipid composition},
1890 abstract = {Brain capillary endothelial cells (BCEC) represent an
1891 epithelial like cell type with continuous tight
1892 junctions and polar distributed proteins. In this paper
1893 we investigated whether cultured BCEC show a polar
1894 distribution of membrane lipids as this was demonstrated
1895 for many epithelial cell types. Therefore we applied a
1896 high yield membrane fractionation method to isolate pure
1897 fractions of the apical and the basolateral plasma
1898 membrane (PM) domains. Using a set of methods for lipid
1899 analysis we were able to determine the total lipid
1900 composition of the whole cells and the PM
1901 fractions. Both membrane domains showed a unique lipid
1902 composition with clear differences to each other and to
1903 the whole cell composition. Three lipid species were
1904 polar distributed between the two PM
1905 domains. Phosphatidylcholine was enriched in the apical
1906 membrane whereas sphingomyelin and glucosylceramide were
1907 enriched in the basolateral membrane. The possible
1908 function of this lipid polarity for the blood-brain
1909 barrier mechanism is the generation of a suitable lipid
1910 environment for polar distributed membrane proteins and
1911 the generation of two PM domains with different
1912 biophysical properties and permeabilities.},
1915 @Article{Thomas1988:chol_transfer,
1916 author = {P D Thomas and M J Poznansky},
1917 title = {Cholesterol transfer between lipid vesicles. Effect of
1918 phospholipids and gangliosides},
1919 journal = {Biochem J},
1925 abstract = {The effect of lipid composition on the rate of cholesterol
1926 movement between cellular membranes is investigated using
1927 lipid vesicles. The separation of donor and acceptor
1928 vesicles required for rate measurement is achieved by
1929 differential centrifugation so that the lipid effect can be
1930 quantified in the absence of a charged lipid generally used
1931 for ion-exchange-based separation. The rate of cholesterol
1932 transfer from small unilamellar vesicles (SUVs) containing
1933 50 mol\% cholesterol to a common large unilamellar vesicle
1934 (LUV) acceptor containing 20 mol\% cholesterol decreases
1935 with increasing mol\% of sphingomyelin in the SUVs, while
1936 phosphatidylethanolamine and phosphatidylserine have no
1937 appreciable effect at physiologically relevant levels.
1938 There is a large decrease in rate when
1939 phosphatidylethanolamine constitutes 50 mol\% of donor
1940 phospholipids. Interestingly, gangliosides which have the
1941 same hydrocarbon moiety as sphingomyelin exert an opposite
1942 effect. The effect of spingomyelin seems to be mediated by
1943 its ability to decrease the fluidity of the lipid matrix,
1944 while that of gangliosides may arise from a weakening of
1945 phosphatidylcholine-cholesterol interactions or from a more
1946 favourable (less polar) microenvironment for the desorption
1947 of cholesterol provided by the head-group interactions
1948 involving sugar residues. If the effect of asymmetric
1949 transbilayer distribution of lipids is taken into
1950 consideration, the observed composition-dependent rate
1951 changes could partly account for the large difference in
1952 the rates of cholesterol desorption from the inner and
1953 outer layers of plasma membrane. Such rate differences may
1954 be responsible for an unequal steady-state distribution of
1955 cholesterol among various cellular membranes and
1959 @Article{Thurmond1991:area_of_pc_pe_2hnmr,
1960 author = {R L Thurmond and S W Dodd and M F Brown},
1961 title = {Molecular areas of phospholipids as determined by 2H NMR
1962 spectroscopy. Comparison of phosphatidylethanolamines and
1963 phosphatidylcholines},
1964 journal = {Biophys J},
1970 abstract = {The role of lipid diversity in biomembranes is one of the
1971 major unsolved problems in biochemistry. One parameter of
1972 possible importance is the mean cross-sectional area
1973 occupied per lipid molecule, which may be related to
1974 formation of nonbilayer structures and membrane protein
1975 function. We have used 2H NMR spectroscopy to compare the
1977 1,2-diperdeuteriopalmitoyl-sn-glycero-3-phosphoethanolamine
1979 1,2-diperdeuteriopalmitoyl-sn-glycero-3-phosphocholine
1980 (DPPC-d62) in the L alpha phase. We find that DPPE has
1981 greater segmental order than DPPC, and that this increase
1982 in order is related to the smaller area per acyl chain
1983 found for DPPE. Values of the mean cross-sectional chain
1984 area are calculated using a simple diamond lattice model
1985 for the acyl chain configurational statistics, together
1986 with dilatometry data. The results obtained for the mean
1987 area per molecule are comparable with those from low angle
1988 x-ray diffraction studies.},
1990 doi = {10.1016/S0006-3495(91)82203-2},
1992 @Article{Walde1994:fa_vesicle_reproduction,
1993 author = {Peter Wlade and Roger Wick and Massimo Fresta and Annarosa Mangone and Pier Luigi Luisi},
1994 title = {Autopoetic Self-Reproduction of Fatty Acid Vesicles},
1995 journal = {J Am. Chem. Soc},
1999 pages = {11649-11654},
2000 abstract = {Conditions are described under which vesicles formed
2001 by caprylic acid and oleic acid in water are able to
2002 undergo autopoietic self-reproduction---namely an
2003 increase of their population number due to reaction
2004 which takes place within the spherical boundary of
2005 the vesicles themselves. This is acchieved by
2006 letting a certain amount of the neat water-insoluble
2007 caprylic or oleic anhydride hydrolyze at alkaline
2008 pH: the initial increase of the concentration of the
2009 released acid/carboxylate is extremely slow (several
2010 days to reach thte conditions for spontaneous
2011 vesicle formation), but afterwards, the presence of
2012 vesicles brings about a rapid second phase leading
2013 to more and more vesicles being formed in an overall
2014 autocatalystic process. THe catalytic power of the
2015 caprylic acid and oleic acid vesicles toward the
2016 hydrolysis of the correpsonding anhydride is
2017 documented in a set of indepenedent experiments. In
2018 these experiments, the hydroysis was carried out in
2019 the presence of vesicles at a pH corresponding
2020 approximately to the pK of the acid in the vesicles.
2021 The process of autopoeitc self-reproduction of
2022 caprylic acid and oleic acid vesicles is studied as
2023 a function of temperature: by increasing temperature
2024 (up to 70 C), the exponential time progress of
2025 vesicle formation tend sot become steeper while the
2026 long initial slow phase is significantly shortened.
2027 The caprylic acid and oleic acid vesicles are
2028 characterized by electron microscopy and by
2029 determining their internal volume. The question
2030 whether and to what extent these vesicles form a
2031 classic chemical equilibrium system---in which
2032 namely the free surfactant is in equilibrium with
2033 the aggregates---is also investigated.},
2034 doi = {10.1021/ja00105a004}
2036 @Article{Wimley1990:dmpc_exchange,
2037 author = {W C Wimley and T E Thompson},
2038 title = {Exchange and flip-flop of dimyristoylphosphatidylcholine in
2039 liquid-crystalline, gel, and two-component, two-phase large
2040 unilamellar vesicles},
2041 journal = {Biochemistry},
2045 pages = {1296--303},
2047 abstract = {The rate and extent of spontaneous exchange of
2048 dimyristoylphosphatidylcholine (DMPC) from large
2049 unilamellar vesicles (LUV) composed of either DMPC or
2050 mixtures of DMPC/distearoylphosphatidylcholine (DSPC) have
2051 been examined under equilibrium conditions. The phase state
2052 of the vesicles ranged from all-liquid-crystalline through
2053 mixed gel/liquid-crystalline to all-gel. The exchange rate
2054 of DMPC between liquid-crystalline DMPC LUV, measured
2055 between 25 and 55 degrees C, was found to have an Arrhenius
2056 activation energy of 24.9 +/- 1.4 kcal/mol. This activation
2057 energy and the exchange rates are very similar to those
2058 obtained for the exchange of DMPC between DMPC small
2059 unilamellar vesicles (SUV). The extent of exchange of DMPC
2060 in LUV was found to be approximately 90\%. This is in
2061 direct contrast to the situation in DMPC SUV where only the
2062 lipid in the outer monolayer is available for exchange.
2063 Thus, transbilayer movement (flip-flop) is substantially
2064 faster in liquid-crystalline DMPC LUV than in SUV.
2065 Desorption from gel-phase LUV has a much lower rate than
2066 gel-phase SUV with an activation energy of 31.7 +/- 3.7
2067 kcal/mol compared to 11.5 +/- 2 kcal/mol reported for SUV.
2068 A defect-mediated exchange in gel-phase SUV, which is not
2069 the major pathway for exchange in LUV, is proposed on the
2070 basis of the thermodynamic parameters of the activation
2071 process. Surprisingly, the rates of DMPC exchange between
2072 DMPC/DSPC two-component LUV, measured over a wide range of
2073 compositions and temperatures, were found to exhibit very
2074 little dependence on the composition or phase configuration
2075 of the vesicles.(ABSTRACT TRUNCATED AT 250 WORDS)},
2078 @Article{Wimley1991,
2079 author = {W C Wimley and T E Thompson},
2080 title = {Phosphatidylethanolamine enhances the concentration-dependent
2081 exchange of phospholipids between bilayers},
2082 journal = {Biochemistry},
2088 abstract = {It has previously been demonstrated that lipid exchange
2089 between phosphatidylcholine vesicles, at higher
2090 concentrations, is characterized by a second-order
2091 concentration-dependent exchange process in addition to the
2092 first-order process operative at lower concentrations
2093 (Jones, J. D., & Thompson, T. E. (1989) Biochemistry 28,
2094 129-134). Furthermore, it was demonstrated that the
2095 second-order process occurs as a result of an enhancement
2096 of the first-order desorption process, possibly resulting
2097 from attractive interactions between a potentially
2098 desorbing lipid molecule and a transiently apposed bilayer
2099 (Jones, J. D., & Thompson, T. E. (1990) Biochemistry 29,
2100 1593-1600). In this work we have studied the exchange of
2101 [3H]dimyristoylphosphatidylcholine (DMPC) between large
2102 vesicles of the compositions 100\% DMPC, 70/30 (mol/mol)
2103 DMPC/dimyristoylphosphatidylethanolamine (DMPE), and
2104 68.25/30/1.75 (mol/mol/mol)
2105 DMPC/DMPE/dimyristoylphosphatidylglycerol (DMPG). The
2106 second-order exchange process is enhanced by 100-fold or
2107 more in vesicles containing 30 mol \% DMPE relative to
2108 100\% DMPC and is reduced or eliminated by the addition of
2109 1.75\% of the anionic lipid DMPG. These effects can be
2110 achieved by alterations in the equilibrium bilayer
2111 separation of 5 A or less. The results are in accord with
2112 the model of Jones and Thompson and indicate that
2113 relatively low concentrations of PE in a PC bilayer can
2114 have significant effects on bilayer surface properties and
2115 on potential interactions between bilayers.},
2118 @Article{Wimley1991:dmpc_depc_exchange,
2119 author = {W C Wimley and T E Thompson},
2120 title = {Transbilayer and interbilayer phospholipid exchange in
2121 dimyristoylphosphatidylcholine/dimyristoylphosphatidylethanolamine
2122 large unilamellar vesicles},
2123 journal = {Biochemistry},
2129 abstract = {The rates of spontaneous interbilayer and transbilayer
2130 exchange of [3H]dimyristoylphosphatidylcholine ([3H]DMPC)
2131 were examined in DMPC and
2132 DMPC/dimyristoylphosphatidylethanolamine (DMPE) large
2133 unilamellar vesicles in the liquid-crystalline-, gel-, and
2134 mixed-phase states. DMPC desorption rates from either gel
2135 or liquid-crystalline phases containing DMPE are very
2136 similar to the corresponding rates from pure DMPC gel or
2137 liquid-crystalline phases. This is not the case for DMPC
2138 desorption from distearoylphosphatidylcholine
2139 (DSPC)-containing gel phases, where the desorption rates
2140 are significantly faster than from a pure DMPC gel phase
2141 [Wimley, W. C., & Thompson, T. E. (1990) Biochemistry 29,
2142 1296-1303]. We proposed that the DMPC/DSPC behavior results
2143 from packing defects in gel phases composed of both DMPC
2144 and DSPC molecules because of the four-carbon difference in
2145 the acyl chain lengths of the two species. The present
2146 results strongly support this hypothesis because no such
2147 anomalous behavior is observed in DMPC/DMPE, which is
2148 similar to DMPC/DSPC in phase behavior but does not have
2149 the chain length difference. The inclusion of 10-30 mol \%
2150 DMPE in DMPC bilayers was also found to have a significant
2151 effect on the rate of transbilayer movement (flip-flop) of
2152 [3H]DMPC in the liquid-crystalline phase. Between 10 and 30
2153 mol \% DMPE, flip-flop of DMPC is slowed by at least
2154 10-fold relative to flip-flop in DMPC bilayers, and the
2155 entropy and enthalpy of flip-flop activation are both
2156 substantially decreased.(ABSTRACT TRUNCATED AT 250 WORDS)},
projects / ool / lipid_simulation_formalism.git / blob