From e9bc959d34bfd28b3b20435832a00e8b9829ad68 Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Thu, 2 Feb 2017 17:11:15 -0800 Subject: [PATCH] include references.bib --- references.bib | 2158 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 2158 insertions(+) create mode 100644 references.bib diff --git a/references.bib b/references.bib new file mode 100644 index 0000000..8aadcf8 --- /dev/null +++ b/references.bib @@ -0,0 +1,2158 @@ +@Article{Abreu2003:fl_albumin, + author = {Magda S C Abreu and Lu\'is M B B Estronca and Maria Jo{\~{a}}o Moreno + and Winchil L C Vaz}, + title = {Binding of a fluorescent lipid amphiphile to albumin and its + transfer to lipid bilayer membranes}, + journal = {Biophys J}, + year = {2003}, + volume = {84}, + number = {1}, + pages = {386--99}, + month = {Jan}, + abstract = {Kinetics and thermodynamics of the binding of a fluorescent + lipid amphiphile, Rhodamine Green(TM)-tetradecylamide + (RG-C(14:0)), to bovine serum albumin were characterized in + an equilibrium titration and by stopped-flow fluorimetry. + The binding equilibrium of RG-C(14:0) to albumin was then + used to reduce its concentration in the aqueous phase to a + value below its critical micelle concentration. Under these + conditions, the only two species of RG-C(14:0) in the + system were the monomer in aqueous solution in equilibrium + with the protein-bound species. After previous + determination of the kinetic and thermodynamic parameters + for association of RG-C(14:0) with albumin, the kinetics of + insertion of the amphiphile into and desorption off lipid + bilayer membranes in different phases (solid, + liquid-ordered, and liquid-disordered phases, presented as + large unilamellar vesicles) were studied by stopped-flow + fluorimetry at 30 degrees C. Insertion and desorption rate + constants for association of the RG-C(14:0) monomer with + the lipid bilayers were used to obtain lipid/water + equilibrium partition coefficients for this fluorescent + amphiphile. The direct measurement of these partition + coefficients is shown to provide a new method for the + indirect determination of the equilibrium partition + coefficient of similar molecules between two defined lipid + phases if they coexist in the same membrane.}, + pmid = {12524292}, + doi = {10.1016/S0006-3495(03)74859-0}, +} +@Article{Abreu2004:kinetics_ld_lo, + author = {Magda S C Abreu and Maria Jo{\~{a}}o Moreno and Winchil L C Vaz}, + title = {Kinetics and thermodynamics of association of a phospholipid + derivative with lipid bilayers in liquid-disordered and + liquid-ordered phases}, + journal = {Biophys J}, + year = {2004}, + volume = {87}, + number = {1}, + pages = {353--65}, + month = {Jul}, + abstract = {We have measured the rates of insertion into, desorption + from, and spontaneous interlayer translocation (flip-flop) + in liquid-disordered and liquid-ordered phase lipid bilayer + membranes, of the fluorescent phospholipid derivative + NBD-dimyristoylphosphatidyl ethanolamine. This study made + use of a recently described method that exploits a detailed + knowledge of the binding kinetics of an amphiphile to + bovine serum albumin, to recover the insertion and + desorption rate constants when the albumin-bound amphiphile + is transferred through the aqueous phase to the membrane + and vice versa. The lipid bilayers, studied as large + unilamellar vesicles, were prepared from pure + 1-palmitoyl-2-oleoylphosphatidylcholine in the + liquid-disordered phase; and from two + cholesterol-containing binary lipid mixtures, + 1-palmitoyl-2-oleoylphosphatidylcholine and cholesterol + (molar ratio of 1:1), and egg sphingomyelin and cholesterol + (molar ratio of 6:4), both in the liquid-ordered phase. + Insertion, desorption, and translocation rate constants and + equilibrium constants for association of the amphiphile + monomer with the lipid bilayers were directly measured + between 15 degrees and 35 degrees C, and the standard free + energies, enthalpies, and entropies, as well as the + activation energies for these processes, were derived from + this data. The equilibrium partition coefficients for + partitioning of the amphiphile between the aqueous phase + and the different membrane phases were also derived, and + permitted the estimation of hypothetical partition + coefficients and the respective energetic parameters for + partitioning between the different lipid phases if these + were to coexist in the same membrane.}, + pmid = {15240470}, + doi = {10.1529/biophysj.104.040576}, +} +@Book{Arrhenius1908:world_in_making, + author = {Svante Arrhenius}, + title = {Worlds in the making; the evolution of the universe}, + publisher = {New York, London, Harper}, + year = 1908, + address = {http://www.archive.org/details/worldsinmakingev00arrhrich} +} + +@Article{Bachmann1992:autocatalysis_micelles, + author = {Pascale Angelica Bachmann and Pier Luigi Luisi and Jacques Lang}, + title = {Autocatalytic self-replicating micelles as models for prebiotic structures}, + journal = {Nature}, + year = 1992, + volume = 357, + pages = {57--9}, + month = {May}, + abstract = {MICELLES that can catalyse their replication have been + described recently1–3. In the previous experiments, + micelles (or bilayer vesicles4) were always present + in the initial reaction mixture—that is, the system + was presented with the bounded structures required + for autocatalysis. Here we describe a system in + which autocatalytic micelles are formed from + amphiphiles that are themselves generated from a + hydrolysis reaction in the absence of compartmental + structures. Alkaline hydrolysis of ethyl caprylate + (itself insoluble in water) yields sodium caprylate, + initially at a very slow rate; but as soon as + sufficient caprylate is formed for aggregation into + micelles to take place, there is an exponential + increase in reaction rate owing to micellar + catalysis. These self-assembling surfactant + structures may consequently provide a model system + for studies of prebiotic chemistry. The possible + relevance of this process to prebiotic chemistry is + emphasized by our observation that the micelles can + be converted into more-robust vesicles by a pH + change induced by dissolved CO2.}, + doi = {10.1038/357057a0} +} +@Article{Bai1997:lipid_movementbodipy, + author = {J Bai and R E Pagano}, + title = {Measurement of spontaneous transfer and transbilayer movement + of BODIPY-labeled lipids in lipid vesicles}, + journal = {Biochemistry}, + year = {1997}, + volume = {36}, + number = {29}, + pages = {8840--8}, + month = {Jul}, + abstract = {An assay was developed to study the spontaneous transfer + and transbilayer movement (flip-flop) of lipid analogs + labeled with the fluorescent fatty acid, 5-(5,7-dimethyl + BODIPY)-1-pentanoic acid (C5-DMB-) in large unilamellar + lipid vesicles comprised of 1-palmitoyl-2-oleoyl + phosphatidylcholine (POPC). The assay is based on the + concentration-dependent changes in fluorescence intensity + that occur when donor vesicles containing a C5-DMB-lipid + are mixed with nonfluorescent acceptor vesicles. A kinetic + model was developed to describe the time-dependent changes + in concentration of a lipid undergoing both spontaneous + transfer between unilamellar vesicles and transbilayer + movement within the vesicle membranes, and a mathematical + solution was obtained. Data were obtained using + C5-DMB-labeled analogs of sphingomyelin (C5-DMB-SM), + ceramide (C5-DMB-Cer), phosphatidylcholine (C5-DMB-PC), and + diacylglycerol (C5-DMB-DAG), and kinetic parameters for + each lipid were determined using a nonlinear least-squares + fitting program. The half-times for interbilayer transfer + of the lipids were C5-DMB-SM (21 s) < C5-DMB-PC (350 s) + approximately C5-DMB-Cer (400 s) << C5-DMB-DAG (100 h). + C5-DMB-Cer (t1/2 approximately 22 min) and C5-DMB-DAG (t1/2 + approximately 70 ms) exhibited rapid spontaneous + transbilayer movement, while C5-DMB-SM (t1/2 approximately + 3.3 h) and C5-DMB-PC (t1/2 approximately 7.5 h) moved + across the bilayer very slowly. These results provide a + basis for interpreting the behavior of these lipid analogs + in cells.}, + pmid = {9220970}, + doi = {10.1021/bi970145r}, +} +@Article{Baron2004:sm_raft_composition, + author = {Carl B Baron and Ronald F Coburn}, + title = {Smooth muscle raft-like membranes}, + journal = {J Lipid Res}, + year = {2004}, + volume = {45}, + number = {1}, + pages = {41--53}, + month = {Jan}, + abstract = {We developed a method for extracting raft-like, + liquid-ordered membranes from the particulate fraction + prepared from porcine trachealis smooth muscle. This + fraction, which contains most of the plasma membrane in + this tissue, was homogenized in the presence of cold 0.5\% + Triton X-100. After centrifugation, membranes containing + high contents of sphingomyelin (SM) and cholesterol and low + phosphatidylcholine (PC) contents remained in the pellet. + Thirty-five millimolar octyl glucoside (OG) extracted 75\% + of these membranes from the Triton X-100-resistant pellet. + These membranes had low buoyant densities and accounted for + 28\% of the particulate fraction lipid. Their lipid + composition, 22\% SM, 60\% cholesterol, 11\% + phosphatidylethanolamine, 8\% PC, <1\% + phosphatidylinositol, and coisolation with 5'-nucleotidase + and caveolin-1 suggest that they are liquid-ordered + membranes. We compared characteristics of OG and Triton + X-100 extractions of the particulate fraction. In contrast + to Triton X-100 extractions, membranes released from the + particulate fraction by OG were mainly collected in low + buoyant fractions at densities ranging from 1.05 to 1.11 + g/ml and had phospholipid and cholesterol contents + consistent with a mixture of liquid-ordered and + liquid-disordered membranes. Thus, OG extraction of + apparent liquid-ordered membranes from Triton + X-100-resistant pellets was not due to selective extraction + of these membranes. Low buoyant density appears not to be + unique for liquid-ordered membranes.}, + pmid = {14563832}, + doi = {10.1194/jlr.M300402-JLR200}, +} +@Article{Baumgart2003:curvature_and_line_tension, + author = {Tobias Baumgart and Samuel T Hess and Watt W Webb}, + title = {Imaging coexisting fluid domains in biomembrane models + coupling curvature and line tension}, + journal = {Nature}, + year = {2003}, + volume = {425}, + number = {6960}, + pages = {821--4}, + month = {Oct}, + abstract = {Lipid bilayer membranes--ubiquitous in biological systems + and closely associated with cell function--exhibit rich + shape-transition behaviour, including bud formation and + vesicle fission. Membranes formed from multiple lipid + components can laterally separate into coexisting liquid + phases, or domains, with distinct compositions. This + process, which may resemble raft formation in cell + membranes, has been directly observed in giant unilamellar + vesicles. Detailed theoretical frameworks link the + elasticity of domains and their boundary properties to the + shape adopted by membranes and the formation of particular + domain patterns, but it has been difficult to + experimentally probe and validate these theories. Here we + show that high-resolution fluorescence imaging using two + dyes preferentially labelling different fluid phases + directly provides a correlation between domain composition + and local membrane curvature. Using freely suspended + membranes of giant unilamellar vesicles, we are able to + optically resolve curvature and line tension interactions + of circular, stripe and ring domains. We observe long-range + domain ordering in the form of locally parallel stripes and + hexagonal arrays of circular domains, curvature-dependent + domain sorting, and membrane fission into separate vesicles + at domain boundaries. By analysing our observations using + available membrane theory, we are able to provide + experimental estimates of boundary tension between fluid + bilayer domains.}, + pmid = {14574408}, + doi = {10.1038/nature02013}, +} +@Article{Budin2010:ool_review, + author = {Itay Budin and Jack W Szostak}, + title = {Expanding roles for diverse physical phenomena during the + origin of life}, + journal = {Annu Rev Biophys}, + year = {2010}, + volume = {39}, + number = {}, + pages = {245--63}, + month = {Jun}, + abstract = {Recent synthetic approaches to understanding the origin of + life have yielded insights into plausible pathways for the + emergence of the first cells. Here we review current + experiments with implications for the origin of life, + emphasizing the ability of unexpected physical processes to + facilitate the self-assembly and self-replication of the + first biological systems. These laboratory efforts have + uncovered novel physical mechanisms for the emergence of + homochirality; the concentration and purification of + prebiotic building blocks; and the ability of the first + cells to assemble, grow, divide, and acquire greater + complexity. In the absence of evolved biochemical + capabilities, such physical processes likely played an + essential role in early biology.}, + pmid = {20192779}, + doi = {10.1146/annurev.biophys.050708.133753}, +} +@Article{Cascales1996:mds_dpps_area, + author = {J. J. L\'opez Cascales and H. J. C. Berendsen and J. Garc\'ia de la Torre}, + title = {Molecular Dynamics Simulation of Water between Two Charged Layers of Dipalmitoylphosphatidylserine}, + journal = {J. Phys. Chem.}, + year = 1996, + volume = 100, + number = 21, + pages = {8621--7}, + month = {May}, + abstract = {A molecular dynamics simulation of water between two + charged layers of dipalmitoylphosphatidylserine in + its liquid-crystalline state with atomic detail was + carried out. From an analysis of a trajectory of 184 + ps of length, we obtained information about the + dynamics and structure of water between such charged + layers. The most remarkable conclusions of this work + indicate that the presence of counterions and charge + interactions between adjacent phospholipids produce + a screening of the electric field which reduces the + strength of the lipid-water interactions. In this + way, only minor differences of the behavior of the + water compared to uncharged phospholipids were + found. This conclusion was based on the calculation + of the following properties: electric potential and + water dipole orientation across the water layer, + radial distribution function of water about lipid + atoms, and diffusion and orientational relaxation + time of water. }, + doi = {10.1021/jp9516405} +} +@Article{Chen2004:competition_model_protocells, + author = {Irene A Chen and Richard W Roberts and Jack W Szostak}, + title = {The emergence of competition between model protocells}, + journal = {Science}, + year = {2004}, + volume = {305}, + number = {5689}, + pages = {1474--6}, + month = {Sep}, + abstract = {The transition from independent molecular entities to + cellular structures with integrated behaviors was a crucial + aspect of the origin of life. We show that simple physical + principles can mediate a coordinated interaction between + genome and compartment boundary, independent of any genomic + functions beyond self-replication. RNA, encapsulated in + fatty acid vesicles, exerts an osmotic pressure on the + vesicle membrane that drives the uptake of additional + membrane components, leading to membrane growth at the + expense of relaxed vesicles, which shrink. Thus, more + efficient RNA replication could cause faster cell growth, + leading to the emergence of Darwinian evolution at the + cellular level.}, + pmid = {15353806}, + doi = {10.1126/science.1100757}, +} +@Article{Copley2007:rna_world, + author = {Shelley D Copley and Eric Smith and Harold J Morowitz}, + title = {The origin of the RNA world: co-evolution of genes and + metabolism}, + journal = {Bioorg Chem}, + year = {2007}, + volume = {35}, + number = {6}, + pages = {430--43}, + month = {Dec}, + abstract = {Discoveries demonstrating that RNA can serve genetic, + catalytic, structural, and regulatory roles have provided + strong support for the existence of an RNA World that + preceded the origin of life as we know it. Despite the + appeal of this idea, it has been difficult to explain how + macromolecular RNAs emerged from small molecules available + on the early Earth. We propose here a mechanism by which + mutual catalysis in a pre-biotic network initiated a + progression of stages characterized by ever larger and more + effective catalysts supporting a proto-metabolic network, + and the emergence of RNA as the dominant macromolecule due + to its ability to both catalyze chemical reactions and to + be copied in a template-directed manner. This model + suggests that many features of modern life, including the + biosynthetic pathways leading to simple metabolites, the + structures of organic and metal ion cofactors, + homochirality, and template-directed replication of nucleic + acids, arose long before the RNA World and were retained as + pre-biotic systems became more sophisticated.}, + pmid = {17897696}, + doi = {10.1016/j.bioorg.2007.08.001}, +} +@Article{Deamer1986:aphiphile_origin, + author = {D W Deamer}, + title = {Role of amphiphilic compounds in the evolution of membrane + structure on the early earth}, + journal = {Orig Life Evol Biosph}, + year = {1986}, + volume = {17}, + number = {1}, + pages = {3--25}, + abstract = {A variety of amphiphilic compounds have the capacity to + self-assemble into membranous structures in the form of + bilayers. The earliest cellular organisms must have + incorporated such compounds into boundary membranes, and + this review discusses amphiphilic components of the + prebiotic environment which would be candidates. One + possible source is organic material carried to the earth's + surface by meteoritic infall. To test this, we have + extracted and analysed non-polar substances from the + Murchison carbonaceous chondrite, and found that at least + some of the components can produce boundary structures + which resemble membranes. This observation suggests that + membranous boundary structures were present on the early + earth, and available to participate in the origin and + evolution of the first cellular forms of life.}, + pmid = {3796965}, +} +@Article{Deamer1989:murchison_chondrite, + author = {D W Deamer and R M Pashley}, + title = {Amphiphilic components of the Murchison carbonaceous + chondrite: surface properties and membrane formation}, + journal = {Orig Life Evol Biosph}, + year = {1989}, + volume = {19}, + number = {1}, + pages = {21--38}, + abstract = {We have investigated physicochemical properties of + amphiphilic compounds in carbonaceous meteorites. The + primary aim was to determine whether such materials + represent plausible sources of lipid-like compounds that + could have been involved as membrane components in + primitive cells. Samples of the Murchison CM2 chondrite + were extracted with chloroform-methanol, and the + chloroform-soluble material was separated by + two-dimensional thin layer chromatography. Fluorescence, + iodine stains and charring were used to identify major + components on the plates. These were then scraped and + eluted as specific fractions which were investigated by + fluorescence and absorption spectra, surface chemical + methods, gas chromatography-mass spectrometry, and electron + microscopy. Fraction 5 was strongly fluorescent, and + contained pyrene and fluoranthene, the major polycyclic + aromatic hydrocarbons of the Murchison chondrite. This + fraction was also present in extracts from the Murray and + Mighei CM2 chondrites. Fraction 3 was surface active, + forming apparent monomolecular films at air-water + interfaces. Surface force measurements suggested that + fraction 3 contained acidic groups. Fraction 1 was also + surface active, and certain components could self-assemble + into membranous vesicles which encapsulated polar solutes. + The observations reported here demonstrate that organic + compounds plausibly available on the primitive Earth + through meteoritic infall are surface active, and have the + ability to self-assemble into membranes.}, + pmid = {2748144}, +} +@Article{Deamer1991:amphiphile_origin, + author = {D Deamer and S I Kuzina and A I Mikhailov and E I Maslikova + and S A Seleznev}, + title = {Origin of amphiphilic molecules and their role in primary + structure formation}, + journal = {J Evol Biochem Physiol}, + year = {1991}, + volume = {27}, + number = {3}, + pages = {212--7}, + month = {May-Jun}, + abstract = {Attempts to solve two fundamental questions are described: + the first concerns which mechanisms were responsible for + the self-assembly of membrane structures on the prebiotic + Earth, and the second concerns the routes by which + considerable amounts of membrane amphiphiles formed from + simpler hydrocarbons. The physicochemical properties of + several amphiphilic compounds extracted from the Murchison + carbonaceous chondrite were studied, using infra-red and + fluorescent spectroscopy, measurements of surface activity, + chromato-mass spectrometry, and polarization and electron + microscopy. The results supported previous observations + that amphiphilic and aromatic hydrocarbons were present in + significant quantities, and the first demonstration of + surface activity among a number of acidic derivatives of + hydrocarbons is reported. In addition, one fraction of the + surface-active compounds can form bilayer structures, + showing that membranes could have self-assembled on the + prebiotic Earth. Photochemical oxidation of hydrocarbons + is shown to be a likely source of the amphiphilic molecules + required for the self-assembly of primary membrane + structures.}, + pmid = {11538377}, +} +@Article{Demel1987:ps_area, + author = {R A Demel and F Paltauf and H Hauser}, + title = {Monolayer characteristics and thermal behavior of natural and + synthetic phosphatidylserines}, + journal = {Biochemistry}, + year = {1987}, + volume = {26}, + number = {26}, + pages = {8659--65}, + month = {Dec}, + abstract = {The monolayer properties and thermal behavior of different + phosphatidylserines are presented. At neutral pH and 22 + degrees C, saturated phosphatidylserines form condensed + monolayers while unsaturated phosphatidylserines form + liquid-expanded films. Under similar conditions, + dimyristoylphosphatidylserine undergoes a transition from + the liquid-expanded to the condensed state. At pH 4 and 22 + degrees C, the surface pressure-area isotherms are shifted + to smaller areas relative to the monolayers recorded at + neutral pH. The condensation observed at pH 4 is close to + that produced at pH 7.4 by the addition of 10 mM CaCl2. As + regards the molecular packing in monolayers and the thermal + behavior, 1,2-dipalmitoyl-sn-glycero-3-phospho-L-serine + (DPPS) and its ether analogue are similar, albeit not + identical. Below 30 mN/m, monolayers of the ether analogue + are even more condensed than those of DPPS. The + order-disorder transition of the ether analogue occurs + usually at higher temperatures than that of the diacyl + compound. Sonicated phosphatidylserine dispersions + consisting of small unilamellar vesicles show anomalous + thermal properties compared to sonicated + phosphatidylcholine dispersions. They exhibit sharp + order-disorder transitions at similar or even slightly + elevated temperatures compared to unsonicated + phosphatidylserine dispersions. This anomaly is explained + in terms of a pH gradient across the bilayer membrane of + the small unilamellar phosphatidylserine vesicle. The + internal surface pH is more acidic than the external pH, + leading to some protonation of phosphatidylserine + molecules. This in turn leads to a condensation of + phosphatidylserine molecules on the inner bilayer surface. + Such a gradient is proposed to be responsible for the + thermodynamic stability of highly curved negatively charged + bilayer vesicles.}, + pmid = {3442681}, +} +@Article{Dworkin2001:amphiphile_assembly, + author = {J Dworkin and D Deamer and S Sandford and L Allamandola}, + title = {Self-assembling amphiphilic molecules: Synthesis in simulated + interstellar/precometary ices}, + journal = {Proc Natl Acad Sci U S A}, + year = {2001}, + volume = {98}, + number = {3}, + pages = {815--9}, + month = {Jan}, + abstract = {Interstellar gas and dust constitute the primary material + from which the solar system formed. Near the end of the hot + early phase of star and planet formation, volatile, less + refractory materials were transported into the inner solar + system as comets and interplanetary dust particles. Once + the inner planets had sufficiently cooled, late + accretionary infall seeded them with complex organic + compounds [Oró, J. (1961) Nature (London) 190, 389-390; + Delsemme, A. H. (1984) Origins Life 14, 51-60; Anders, E. + (1989) Nature (London) 342, 255-257; Chyba, C. F. & Sagan, + C. (1992) Nature (London) 355, 125-131]. Delivery of such + extraterrestrial compounds may have contributed to the + organic inventory necessary for the origin of life. + Interstellar ices, the building blocks of comets, tie up a + large fraction of the biogenic elements available in + molecular clouds. In our efforts to understand their + synthesis, chemical composition, and physical properties, + we report here that a complex mixture of molecules is + produced by UV photolysis of realistic, interstellar ice + analogs, and that some of the components have properties + relevant to the origin of life, including the ability to + self-assemble into vesicular structures.}, + pmid = {11158552}, + doi = {10.1073/pnas.98.3.815}, +} +@Article{Estronca2007:dhe_kinetics, + author = {Lu\'is M B B Estronca and Maria Jo{\~{a}}o Moreno and Winchil L C + Vaz}, + title = {Kinetics and thermodynamics of the association of + dehydroergosterol with lipid bilayer membranes}, + journal = {Biophys J}, + year = {2007}, + volume = {93}, + number = {12}, + pages = {4244--53}, + month = {Dec}, + abstract = {We have examined the detailed kinetics and thermodynamics + of the association of Ergosta-5,7,9(11),22-tetraen-3beta-ol + (dehydroergosterol, DHE) with lipid bilayers prepared from + 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), a 1:1 + binary mixture of POPC and cholesterol (Chol), and a 6:4 + binary mixture of egg sphingomyelin (SpM) and Chol. + Association of DHE with all three membranes was shown to be + entropically driven, most so in the case of SpM-Chol + bilayers. Equilibrium partition coefficients for + partitioning of DHE between the lipid phase and the aqueous + phase were shown to be similar for POPC and POPC-Chol + bilayers between 15 and 35 degrees C. Partitioning into the + SpM-Chol bilayer is favored at higher temperatures and + there is a crossover in solubility preference at + approximately 25 degrees C. Insertion (k(+)) and desorption + (k(-)) rate constants were shown to be very similar for + POPC and POPC-Chol bilayer membranes, but were lower for + SpM-Chol bilayers. Similar results were previously reported + by us for the association of other amphiphiles with these + membranes. We propose a model for the microscopic structure + of a POPC-Chol (1:1) bilayer membrane that is consistent + with these observations.}, + pmid = {17766353}, + doi = {10.1529/biophysj.107.112847}, +} +@Article{Ferris1987:prebiotic_synthesis, + author = {J P Ferris}, + title = {Prebiotic synthesis: problems and challenges}, + journal = {Cold Spring Harb Symp Quant Biol}, + year = {1987}, + volume = {52}, + pages = {29--35}, + pmid = {2456880}, +} +@Article{Gaus2005:macrophage_lipid_distribution, + author = {Katharina Gaus and Macarena Rodriguez and Kalani R Ruberu and + Ingrid Gelissen and Timothy M Sloane and Leonard Kritharides + and Wendy Jessup}, + title = {Domain-specific lipid distribution in macrophage plasma + membranes}, + journal = {J. Lipid Res.}, + year = {2005}, + volume = {46}, + number = {7}, + pages = {1526--38}, + month = {Jul}, + abstract = {Lipid rafts, defined as cholesterol- and sphingolipid-rich + domains, provide specialized lipid environments understood + to regulate the organization and function of many plasma + membrane proteins. Growing evidence of their existence, + protein cargo, and regulation is based largely on the study + of isolated lipid rafts; however, the consistency and + validity of common isolation methods is controversial. + Here, we provide a detailed and direct comparison of the + lipid and protein composition of plasma membrane "rafts" + prepared from human macrophages by different methods, + including several detergent-based isolations and a + detergent-free method. We find that detergent-based and + detergent-free methods can generate raft fractions with + similar lipid contents and a biophysical structure close to + that previously found on living cells, even in cells not + expressing caveolin-1, such as primary human macrophages. + However, important differences between isolation methods + are demonstrated. Triton X-100-resistant rafts are less + sensitive to cholesterol or sphingomyelin depletion than + those prepared by detergent-free methods. Moreover, we show + that detergent-based methods can scramble membrane lipids + during the isolation process, reorganizing lipids + previously in sonication-derived nonraft domains to + generate new detergent-resistant rafts. The role of rafts + in regulating the biological activities of macrophage + plasma membrane proteins may require careful reevaluation + using multiple isolation procedures, analyses of lipids, + and microscopic techniques.}, + pmid = {15863834}, + doi = {10.1194/jlr.M500103-JLR200}, +} +@Article{Hanczyc2003:protocell_model, + author = {Martin M Hanczyc and Shelly M Fujikawa and Jack W Szostak}, + title = {Experimental models of primitive cellular compartments: + encapsulation, growth, and division}, + journal = {Science}, + year = {2003}, + volume = {302}, + number = {5645}, + pages = {618--22}, + month = {Oct}, + abstract = {The clay montmorillonite is known to catalyze the + polymerization of RNA from activated ribonucleotides. Here + we report that montmorillonite accelerates the spontaneous + conversion of fatty acid micelles into vesicles. Clay + particles often become encapsulated in these vesicles, thus + providing a pathway for the prebiotic encapsulation of + catalytically active surfaces within membrane vesicles. In + addition, RNA adsorbed to clay can be encapsulated within + vesicles. Once formed, such vesicles can grow by + incorporating fatty acid supplied as micelles and can + divide without dilution of their contents by extrusion + through small pores. These processes mediate vesicle + replication through cycles of growth and division. The + formation, growth, and division of the earliest cells may + have occurred in response to similar interactions with + mineral particles and inputs of material and energy.}, + pmid = {14576428}, + doi = {10.1126/science.1089904}, +} +@Article{Hargreaves1977:pl_synthesis, + author = {W R Hargreaves and S J Mulvihill and D W Deamer}, + title = {Synthesis of phospholipids and membranes in prebiotic + conditions}, + journal = {Nature}, + year = {1977}, + volume = {266}, + number = {5597}, + pages = {78--80}, + month = {Mar}, + pmid = {840303}, +} +@Article{Hargreaves1978:liposome_from_aphiphiles, + author = {W R Hargreaves and D W Deamer}, + title = {Liposomes from ionic, single-chain amphiphiles}, + journal = {Biochemistry}, + year = {1978}, + volume = {17}, + number = {18}, + pages = {3759--68}, + month = {Sep}, + abstract = {In studies of the minimum physiochemical requirements for + lipid membrane formation, we have made liposomes from + dilute, aqueous dispersions of C(8)-C(18) single-chain + amphiphiles. In general, membrane formation from ionic + soaps and detergents requires the presence of uncharged + amphiphiles. Vesicles were characterized by phase-contrast + microscopy, by trapping of ionic dyes, as well as by + negativestain and freez-frature electron microscopy. They + were typically heterogeneous in size, but the average + diameter could be experimentally varied in some cases over + the range of 1 to 100 micrometer. Uni-, oligo-, and + multilamellar vesicles were observed. Membrane permeability + to various solutes was determined in part by a new + technique which utilized phase-contract microscopy; when + impermeable vesciles exclude added solutes such as sucrose, + refractive index differences are created between vesicle + contents and surrounding medium, so that the vesicles + appear bright in the phase microscope. Permeant solutes do + not produce this effect. Spectrophotometric permeability + determinations confirmed the results of this technique and + provided quantitative measures of permeability. Monoalkyl + liposomes have potential uses as models of biomembranes and + in drug delivery. They are also relevant to the prebiotic + origin of biomembranes.}, + pmid = {698196}, +} +@Article{Huang1999:chol_solubility_model, + author = {J Huang and G W Feigenson}, + title = {A microscopic interaction model of maximum solubility of + cholesterol in lipid bilayers}, + journal = {Biophys. J}, + year = {1999}, + volume = {76}, + number = {4}, + pages = {2142--57}, + month = {Apr}, + abstract = {We recently reported the equilibrium maximum solubility of + cholesterol in a lipid bilayer, chi*chol, to be 0.66 in + four different phosphatidylcholines, and 0.51 in a + phosphatidylethanolamine (Huang, J.,J.T. Buboltz, and G. W. + Feigenson. 1999. Biochim. Biophys. Acta. in press). Here we + present a model of cholesterol-phospholipid mixing that + explains these observed values of chi*chol. Monte Carlo + simulations show that pairwise-additivity of + nearest-neighbor interactions is inadequate to describe all + the chi*chol values. Instead, if cholesterol multibody + interactions are assigned highly unfavorable energy, then + jumps occur in cholesterol chemical potential that lead to + its precipitation from the bilayer. Cholesterol + precipitation is most likely to occur near three discrete + values of cholesterol mole fraction, 0.50, 0.57, and 0.67, + which correspond to cholesterol/phospholipid mole ratios of + 1/1, 4/3, and 2/1, respectively. At these solubility + limits, where cholesterol chemical potential jumps, the + cholesterol-phospholipid bilayer mixture forms highly + regular lipid distributions in order to minimize + cholesterol-cholesterol contacts. This treatment shows that + dramatic structural and thermodynamic changes can occur at + particular cholesterol mole fractions without any + stoichiometric complex formation. The physical origin of + the unfavorable cholesterol multibody interaction is + explained by an "umbrella model": in a bilayer, nonpolar + cholesterol relies on polar phospholipid headgroup coverage + to avoid the unfavorable free energy of cholesterol contact + with water. Thus, at high cholesterol mole fraction, this + unfavorable free energy, not any favorable + cholesterol-phospholipid interaction, dominates the mixing + behavior. This physical origin also explains the + "cholesterol condensing effect" and the increase in acyl + chain order parameter in cholesterol-phospholipid + mixtures.}, + pmid = {10096908}, +} +@Article{Huang1999:cholesterol_solubility, + author = {J Huang and J T Buboltz and G W Feigenson}, + title = {Maximum solubility of cholesterol in phosphatidylcholine and + phosphatidylethanolamine bilayers}, + year = {1999}, + volume = {1417}, + number = {1}, + journal = {Biochim. Biophys. Acta}, + pages = {89--100}, + month = {Feb}, + abstract = {In any lipid bilayer membrane, there is an upper limit on + the cholesterol concentration that can be accommodated + within the bilayer structure; excess cholesterol will + precipitate as crystals of pure cholesterol monohydrate. + This cholesterol solubility limit is a well-defined + quantity. It is a first-order phase boundary in the + phospholipid/cholesterol phase diagram. There are many + different solubility limits in the literature, but no clear + picture has emerged that can unify the disparate results. + We have studied the effects that different sample + preparation methods can have on the apparent experimental + solubility limit. We find that artifactual demixing of + cholesterol can occur during conventional sample + preparation and that this demixed cholesterol may produce + artifactual cholesterol crystals. Therefore, + phospholipid/cholesterol suspensions which are prepared by + conventional methods may manifest variable, falsely low + cholesterol solubility limits. We have developed two novel + preparative methods which are specifically designed to + prevent demixing during sample preparation. For detection + of the cholesterol crystals, X-ray diffraction has proven + to be quantitative and highly sensitive. Experiments based + on these methods yield reproducible and precise cholesterol + solubility limits: 66 mol\% for phosphatidylcholine (PC) + bilayers and 51 mol\% for phosphatidylethanolamine (PE) + bilayers. We present evidence that these are true, + equilibrium values. In contrast to the dramatic headgroup + effect (PC vs. PE), acyl chain variations had no effect on + the cholesterol solubility limit in four different + PC/cholesterol mixtures.}, + pmid = {10076038}, +} +@Article{Inger2009:gard_mutations, + author = {Aron Inger and Ariel Solomon and Barak Shenhav and Tsviya + Olender and Doron Lancet}, + title = {Mutations and lethality in simulated prebiotic networks}, + journal = {J Mol Evol}, + year = {2009}, + volume = {69}, + number = {5}, + pages = {568--78}, + month = {Nov}, + abstract = {The Graded Autocatalysis Replication Domain (GARD) model + describes an origin of life scenario which involves + non-covalent compositional assemblies, made of monomeric + mutually catalytic molecules. GARD constitutes an + alternative to informational biopolymers as a mechanism of + primordial inheritance. In the present work, we examined + the effect of mutations, one of the most fundamental + mechanisms for evolution, in the context of the networks of + mutual interaction within GARD prebiotic assemblies. We + performed a systematic analysis analogous to single and + double gene deletions within GARD. While most deletions + have only a small effect on both growth rate and molecular + composition of the assemblies, $\approx$10\% of the deletions + caused lethality, or sometimes showed enhanced fitness. + Analysis of 14 different network properties on 2,000 + different GARD networks indicated that lethality usually + takes place when the deleted node has a high molecular + count, or when it is a catalyst for such node. A + correlation was also found between lethality and node + degree centrality, similar to what is seen in real + biological networks. Addressing double knockout mutations, + our results demonstrate the occurrence of both synthetic + lethality and extragenic suppression within GARD networks, + and convey an attempt to correlate synthetic lethality to + network node-pair properties. The analyses presented help + establish GARD as a workable alternative prebiotic + scenario, suggesting that life may have begun with large + molecular networks of low fidelity, that later underwent + evolutionary compaction and fidelity augmentation.}, + pmid = {19787385}, + doi = {10.1007/s00239-009-9281-y}, +} +@Article{Israelachvili1975:amphiphile_self_assembly, + author = {Jacob N Israelachvili and D John Mitchell and Barry W Ninham}, + title = {Theory of Self-Assembly of Hydrocarbon Amphiphiles + into Micelles and Bilayers}, + journal = {J. Chem. Soc., Faraday Trans. 2,}, + year = 1976, + volume = 72, + pages = 1525, + abstract = {A simple theory is developed that accounts for many of + the observed physical properties of micelles, both + globular and rod-like, and of bilayer vesicles + composed of ionic or zwitterionic amphiphiles. The + main point of departure from previous theories lies + in the recognition and elucidation of the role of + geometric constraints in self-assembly. The linking + together of thermodynamics, interaction free + energies and geometry results in a general framework + which permits extension to more complicated + self-assembly problems.}, + doi = {10.1039/F29767201525} +} + +@Article{Janas2004:rna_membrane_transporter, + author = {Teresa Janas and Tadeusz Janas and Michael Yarus}, + title = {A membrane transporter for tryptophan composed of RNA}, + journal = {RNA}, + year = {2004}, + volume = {10}, + number = {10}, + pages = {1541--9}, + month = {Oct}, + abstract = {We have incorporated an RNA binding site for the biological + amino acid tryptophan within an RNA complex with affinity + for phospholipid bilayer membranes. The resulting RNA + (9:10Trp) creates a selective route through the bilayer for + the amino acid. Binding and enhanced tryptophan + permeability are nonlinear in RNA concentration, suggesting + that RNA aggregation is required for both. Tryptophan + permeability saturates with increased concentration, though + at approximately 1000-fold greater level than when binding + a free aptamer. The RNA (9:10Trp) complex, bound at a mean + of two per liposome, halves the activation energy for + tryptophan transport (to 46 kJ/mole), specifically + increasing tryptophan entry to a maximal velocity of 0.5 + sec(-1) per liposome with little or no accompanying + increase in general permeability. Individual RNAs turn over + tens of thousands of times at high tryptophan + concentration. Thus, a specific passive membrane + transporter whose properties overlap those of + single-molecule transporter proteins, can be made of RNA + alone. Permeability changes probably rely on disturbances + in lipid conformation as well as on an advantageous low + free energy position for tryptophan at the membrane. Other + RNA activities may yield other RNA-membrane nanosystems via + this route.}, + pmid = {15383677}, + doi = {10.1261/rna.7112704}, +} +@Article{Jones1990:lipid_transfer, + author = {J D Jones and T E Thompson}, + title = {Mechanism of spontaneous, concentration-dependent phospholipid + transfer between bilayers}, + journal = {Biochemistry}, + year = {1990}, + volume = {29}, + number = {6}, + pages = {1593--600}, + month = {Feb}, + abstract = {We have previously demonstrated that spontaneous + phospholipid transfer between bilayer vesicles at higher + vesicle concentrations is characterized not only by a + first-order desorption rate but also by a second-order + process dependent on vesicle concentration (Jones & + Thompson, 1989b). We have extended our studies to examine + the mechanism of this second-order process by investigating + transfer as a function of lipid type, temperature, aqueous + medium composition, and vesicle size. The results suggest a + mechanism of concentration-dependent transfer in which the + rate of lipid monomer desorption from vesicle bilayers is + enhanced in transient vesicle-vesicle complexes.}, + pmid = {2334718}, +} +@Article{Joyce2002:rna_world, + author = {Gerald F Joyce}, + title = {The antiquity of RNA-based evolution}, + journal = {Nature}, + year = {2002}, + volume = {418}, + number = {6894}, + pages = {214--21}, + month = {Jul}, + abstract = {All life that is known to exist on Earth today and all life + for which there is evidence in the geological record seems + to be of the same form--one based on DNA genomes and + protein enzymes. Yet there are strong reasons to conclude + that DNA- and protein-based life was preceded by a simpler + life form based primarily on RNA. This earlier era is + referred to as the 'RNA world', during which the genetic + information resided in the sequence of RNA molecules and + the phenotype derived from the catalytic properties of + RNA.}, + pmid = {12110897}, + doi = {10.1038/418214a}, +} +@Article{Kafri2010:enantiomer_gard, + author = {Ran Kafri and Omer Markovitch and Doron Lancet}, + title = {Spontaneous chiral symmetry breaking in early molecular + networks}, + journal = {Biol Direct}, + year = {2010}, + volume = {5}, + pages = {38}, + pmid = {20507625}, + doi = {10.1186/1745-6150-5-38}, +} +@Article{Katz1988:pl_packing_chol, + author = {S Lund-Katz and H M Laboda and L R McLean and M C Phillips}, + title = {Influence of molecular packing and phospholipid type on rates + of cholesterol exchange}, + journal = {Biochemistry}, + year = {1988}, + volume = {27}, + number = {9}, + pages = {3416--23}, + month = {May}, + abstract = {The rates of [14C]cholesterol transfer from small + unilamellar vesicles containing cholesterol dissolved in + bilayers of different phospholipids have been determined to + examine the influence of phospholipid-cholesterol + interactions on the rate of cholesterol desorption from the + lipid-water interface. The phospholipids included + unsaturated phosphatidylcholines (PC's) (egg PC, + dioleoyl-PC, and soybean PC), saturated PC (dimyristoyl-PC + and dipalmitoyl-PC), and sphingomyelins (SM's) (egg SM, + bovine brain SM, and N-palmitoyl-SM). At 37 degrees C, for + vesicles containing 10 mol\% cholesterol, the half-times + for exchange are about 1, 13, and 80 h, respectively, for + unsaturated PC, saturated PC, and SM. In order to probe how + differences in molecular packing in the bilayers cause the + rate constants for cholesterol desorption to be in the + order unsaturated PC greater than saturated PC greater than + SM, nuclear magnetic resonance (NMR) and monolayer methods + were used to evaluate the cholesterol physical state and + interactions with phospholipid. The NMR relaxation + parameters for [4-13C]cholesterol reveal no differences in + molecular dynamics in the above bilayers. Surface pressure + (pi)-molecular area isotherms for mixed monolayers of + cholesterol and the above phospholipids reveal that SM + lateral packing density is greater than that of the PC with + the same acyl chain saturation and length (e.g., at pi = 5 + mN/m, where both monolayers are in the same physical state, + dipalmitoyl-PC and palmitoyl-SM occupy 87 and 81 + A2/molecule, respectively).(ABSTRACT TRUNCATED AT 250 + WORDS)}, + pmid = {3390441}, +} +@Article{Kumar1991:lipid_packing, + author = {V V Kumar}, + title = {Complementary molecular shapes and additivity of the packing + parameter of lipids}, + journal = {Proc Natl Acad Sci U S A}, + year = {1991}, + volume = {88}, + number = {2}, + pages = {444--8}, + month = {Jan}, + abstract = {Physical dimensions of a membrane component influence its + phase preference upon hydration. A dimensionless packing + parameter, S, given by S = V/al, where V is the hydrocarbon + volume, a is the area of the head group, and l is the + critical length of the hydrocarbon chain, is useful in + determining the phase preference of a lipid, and the value + of S usually lies between 0.5 and 1 for bilayers. Here, the + value of S is calculated for phosphatidylcholine (PC) and + lysophosphatidylcholine (lysoPC) as a function of chain + length, and it is shown that diacylPC having an S value of + less than 0.74 does not form bilayers. For example, + diacylPC, up to a chain length of eight carbon atoms, forms + only micelles, whereas higher homologs with S greater than + 0.74 form bilayers. It is also shown that when lipid + molecules having complementary shapes associate, the value + of S becomes additive. Using the additivity of S, a number + of experimental results for lipid mixtures can be + explained. For example, lysoPC and cholesterol form + lamellar structures between 45 and approximately 80 mol\% + cholesterol, and the additive value of S for this region is + between 0.74 and 1. Similarly, the additivity of S shows + that the maximum amount of cholesterol that can be + incorporated into PC bilayers is 50 mol\%, in agreement + with experimental studies.}, + pmid = {1988944}, +} +@Article{Lange1983:chol_distribution, + author = {Y Lange and B V Ramos}, + title = {Analysis of the distribution of cholesterol in the intact + cell}, + journal = {J. Biol. Chem.}, + year = {1983}, + volume = {258}, + number = {24}, + pages = {15130--4}, + month = {Dec}, + abstract = {We have used the enzyme cholesterol oxidase, which + catalyzes the oxidation of cholesterol to + cholest-4-en-3-one, to examine the distribution of + cholesterol in cultured fibroblasts, Chinese hamster ovary + cells, and isolated rat liver hepatocytes. While the plasma + membrane normally was not attacked by cholesterol oxidase, + we found that treating cells with low ionic strength buffer + and glutaraldehyde rendered their cholesterol highly + susceptible to oxidation. Most of the cholesterol was + oxidized in all three cell types: 94\% in fibroblasts, 92\% + in Chinese hamster ovary cells, and 80\% in hepatocytes. + Given that the enzyme had access only to the outer surface + of the cells and cholesterol can move rapidly across the + fixed plasma membrane, these values are taken to reflect + the fraction of cellular cholesterol present in the plasma + membrane. Additional experiments confirmed this + interpretation. Fibroblasts were labeled with + [3H]cholesterol by brief exposure to exogenous radiolabel + and incubated with [14C]mevalonic acid to label cholesterol + biosynthetically. Cholesterol oxidase attacked at least + 97\% of the exogenous label but as little as 10\% of the + biosynthetically labeled cholesterol. These data suggest + that the cholesterol oxidase did not reach the + intracellular pool and that cholesterol in the plasma + membrane is not in rapid equilibrium with internal + membranes. A study of the transfer of cholesterol to plasma + from cells labeled biosynthetically with [3H]cholesterol + and exogenously with [14C]cholesterol confirmed the + different subcellular distribution of the two labels. These + studies demonstrate that an unexpectedly high proportion of + cell cholesterol is associated with plasma membranes and + that this cholesterol pool can be rapidly and selectively + labeled and oxidized. These features make cholesterol a + useful specific marker for the plasma membrane.}, + pmid = {6418742}, +} +@Article{Leirer2009:vesicle_fission, + author = {C Leirer and B Wunderlich and V M Myles and M F Schneider}, + title = {Phase transition induced fission in lipid vesicles}, + journal = {Biophys Chem}, + year = {2009}, + volume = {143}, + number = {1-2}, + pages = {106--9}, + month = {Jul}, + abstract = {In this work we demonstrate how the first order phase + transition in giant unilamellar vesicles (GUVs) can + function as a trigger for membrane fission. When driven + through their gel-fluid phase transition GUVs exhibit + budding or pearl formation. These buds remain connected to + the mother vesicle presumably by a small neck. Cooling + these vesicles from the fluid phase (T>T(m)) through the + phase transition into the gel state (T50\% + upon addition of equimolar CHOL to POPE-d(31)/SM (1:1 mol) + bilayers. Close proximity of CHOL to POPE even in the + presence of SM is indicated. Chemical shift anisotropy + (Deltasigma(csa)) measured from (1)H-decoupled (31)P NMR + spectra also implied intimate lipid mixing in POPE/SM/CHOL + (1:1:1 mol). In contrast, pi-A isotherms and corroborating + DSC studies of PDPE/SM (1:1 mol) indicate phase separation + between SM and PDPE, which was maintained in the presence + of CHOL. The cholesterol-associated increase in order of + the perdeuterated sn-1 chain of PDPE determined by (2)H NMR + was 2-fold less for PDPE-d(31)/SM/CHOL (1:1:1 mol) than + POPE-d(31)/SM/CHOL (1:1:1 mol). Our findings support the + notion that acyl chain dependent lateral phase separation + occurs in the presence of a docosahexaenoic acid + (DHA)-containing phospholipid (PDPE), but not an oleic + acid-containing phospholipid (POPE). We propose that + monounsaturated lipids do not promote formation of stable + lipid rafts and that polyunsaturation may be important for + raft stability.}, + pmid = {12186543}, +} +@Article{Shenhav2005:pgard, + author = {Barak Shenhav and Arren Bar-Even and Ran Kafri and Doron + Lancet}, + title = {Polymer GARD: computer simulation of covalent bond formation + in reproducing molecular assemblies}, + journal = {Orig Life Evol Biosph}, + year = {2005}, + volume = {35}, + number = {2}, + pages = {111--33}, + month = {Apr}, + abstract = {The basic Graded Autocatalysis Replication Domain (GARD) + model consists of a repertoire of small molecules, + typically amphiphiles, which join and leave a non-covalent + micelle-like assembly. Its replication behavior is due to + occasional fission, followed by a homeostatic growth + process governed by the assembly's composition. Limitations + of the basic GARD model are its small finite molecular + repertoire and the lack of a clear path from a 'monomer + world' towards polymer-based living entities. We have now + devised an extension of the model (polymer GARD or P-GARD), + where a monomer-based GARD serves as a 'scaffold' for + oligomer formation, as a result of internal chemical rules. + We tested this concept with computer simulations of a + simple case of monovalent monomers, whereby more complex + molecules (dimers) are formed internally, in a manner + resembling biosynthetic metabolism. We have observed events + of dimer 'take-over' - the formation of compositionally + stable, replication-prone quasi stationary states + (composomes) that have appreciable dimer content. The + appearance of novel metabolism-like networks obeys a + time-dependent power law, reminiscent of evolution under + punctuated equilibrium. A simulation under constant + population conditions shows the dynamics of takeover and + extinction of different composomes, leading to the + generation of different population distributions. The + P-GARD model offers a scenario whereby biopolymer formation + may be a result of rather than a prerequisite for early + life-like processes.}, + pmid = {16010993}, +} +@Article{Shenhav2007:comp_protocells, + author = {Barak Shenhav and Aia Oz and Doron Lancet}, + title = {Coevolution of compositional protocells and their + environment}, + journal = {Philos Trans R Soc Lond B Biol Sci}, + year = {2007}, + volume = {362}, + number = {1486}, + pages = {1813--9}, + month = {Oct}, + abstract = {The coevolution of environment and living organisms is well + known in nature. Here, it is suggested that similar + processes can take place before the onset of life, where + protocellular entities, rather than full-fledged living + systems, coevolve along with their surroundings. + Specifically, it is suggested that the chemical composition + of the environment may have governed the chemical + repertoire generated within molecular assemblies, + compositional protocells, while compounds generated within + these protocells altered the chemical composition of the + environment. We present an extension of the graded + autocatalysis replication domain (GARD) model--the + environment exchange polymer GARD (EE-GARD) model. In the + new model, molecules, which are formed in a protocellular + assembly, may be exported to the environment that surrounds + the protocell. Computer simulations of the model using an + infinite-sized environment showed that EE-GARD assemblies + may assume several distinct quasi-stationary compositions + (composomes), similar to the observations in previous + variants of the GARD model. A statistical analysis + suggested that the repertoire of composomes manifested by + the assemblies is independent of time. In simulations with + a finite environment, this was not the case. Composomes, + which were frequent in the early stages of the simulation + disappeared, while others emerged. The change in the + frequencies of composomes was found to be correlated with + changes induced on the environment by the assembly. The + EE-GARD model is the first GARD model to portray a possible + time evolution of the composomes repertoire.}, + pmid = {17510019}, + doi = {10.1098/rstb.2007.2073}, +} +@Article{Smaby1997:pc_area_with_chol, + author = {J M Smaby and M M Momsen and H L Brockman and R E Brown}, + title = {Phosphatidylcholine acyl unsaturation modulates the decrease + in interfacial elasticity induced by cholesterol}, + journal = {Biophys J}, + year = {1997}, + volume = {73}, + number = {3}, + pages = {1492--505}, + month = {Sep}, + abstract = {The effect of cholesterol on the interfacial elastic + packing interactions of various molecular species of + phosphatidylcholines (PCs) has been investigated by using a + Langmuir-type film balance and analyzing the elastic area + compressibility moduli (Cs(-1)) as a function of average + cross-sectional molecular area. Emphasis was on the high + surface pressure regions (pi > or = 30 mN/m) which are + thought to mimic biomembrane conditions. Increasing levels + of cholesterol generally caused the in-plane elasticity of + the mixed monolayers to decrease. Yet, the magnitude of the + cholesterol-induced changes was markedly dependent upon PC + hydrocarbon structure. Among PC species with a saturated + sn-1 chain but different sn-2 chain cis unsaturation levels + [e.g., myristate (14:0), oleate (18:1delta9(c), linoleate + (18:2delta9,12(c), arachidonate (20:4delta5,8,11,14(c), or + docosahexenoate (22:6delta4,7,10,13,16,19(c)], the in-plane + elasticity moduli of PC species with higher sn-2 + unsaturation levels were less affected by high cholesterol + mol fractions (e.g., >30 mol \%) than were the more + saturated PC species. The largest cholesterol-induced + decreases in the in-plane elasticity were observed when + both chains of PC were saturated (e.g., di-14:0 PC). When + both acyl chains were identically unsaturated, the + resulting PCs were 20-25\% more elastic in the presence of + cholesterol than when their sn-1 chains were long and + saturated (e.g., palmitate). The mixing of cholesterol with + PC was found to diminish the in-plane elasticity of the + films beyond what was predicted from the additive behavior + of the individual lipid components apportioned by mole and + area fraction. Deviations from additivity were greatest for + di-14:0 PC and were least for diarachidonoyl PC and + didocosahexenoyl PC. In contrast to Cs(-1) analyses, + sterol-induced area condensations were relatively + unresponsive to subtle structural differences in the PCs at + high surface pressures. Cs(-1) versus average area plots + also indicated the presence of cholesterol + concentration-dependent, low-pressure (<14 mN/m) phase + boundaries that became more prominent as PC acyl chain + unsaturation increased. Hence, area condensations measured + at low surface pressures often do not accurately portray + which lipid structural features are important in the + lipid-sterol interactions that occur at high membrane-like + surface pressures.}, + pmid = {9284316}, +} +@Article{Stano2010:vesicle_self_reproduction, + author = {Pasquale Stano and Pier Luigi Luisi}, + title = {Achievements and open questions in the self-reproduction of + vesicles and synthetic minimal cells}, + journal = {Chem Commun (Camb)}, + year = {2010}, + volume = {46}, + number = {21}, + pages = {3639--53}, + month = {Jun}, + abstract = {Supramolecular chemistry was enriched, about twenty years + ago, by the discovery of the self-reproduction of micelles + and vesicles. The dynamic aspects and complexity of these + systems makes them good models for biological compartments. + For example, the self-reproduction of vesicles suggests + that the growth in size and number of a vesicle population + resembles the pattern of living cells in several aspects, + but it take place solely due to physical forces. Several + reports demonstrate that reverse micelles, micelles, + sub-micrometric and giant vesicles can self-reproduce, + generating new particles at the expenses of a suitable + precursor. Recently, similar studies are in progress on + more complex vesicle-based systems, namely semi-synthetic + minimal cells. These are artificial cell-like compartments + that are built by filling liposomes with the minimal number + of biomolecules, such as DNA, ribosomes, enzymes, etc., in + order to construct a living cell in the laboratory. This + approach aims to investigate the minimal requirements for + molecular systems in order to display some living + properties, while it finds relevance in origins of life + studies and in synthetic (constructive) biology.}, + pmid = {20442914}, + doi = {10.1039/b913997d}, +} +@Article{Svetina2009:vesicle_budding, + author = {Sasa Svetina}, + title = {Vesicle budding and the origin of cellular life}, + journal = {Chemphyschem}, + year = {2009}, + volume = {10}, + number = {16}, + pages = {2769--76}, + month = {Nov}, + abstract = {This Minireview provides an appropriate opportunity to + demonstrate the connection between the results of some + early experimental and theoretical investigations of + vesicle budding and the more recent application of the + concepts developed there to the process of vesicle + self-reproduction. Herein, we also explain why vesicle + budding could have preceded the establishment of cellular + life.}, + pmid = {19774545}, + doi = {10.1002/cphc.200900577}, +} +@Article{Szostak2001:synthesizing_life, + author = {J W Szostak and D P Bartel and P L Luisi}, + title = {Synthesizing life}, + journal = {Nature}, + year = {2001}, + volume = {409}, + number = {6818}, + pages = {387--90}, + month = {Jan}, + pmid = {11201752}, + doi = {10.1038/35053176}, +} +@Article{Tamulis2011:lipid_world_evolution, + author = {Arvydas Tamulis and Mantas Grigalavicius}, + title = {The emergence and evolution of life in a "fatty acid world" + based on quantum mechanics}, + journal = {Orig Life Evol Biosph}, + year = {2011}, + volume = {41}, + number = {1}, + pages = {51--71}, + month = {Feb}, + abstract = {Quantum mechanical based electron correlation interactions + among molecules are the source of the weak hydrogen and Van + der Waals bonds that are critical to the self-assembly of + artificial fatty acid micelles. Life on Earth or elsewhere + could have emerged in the form of self-reproducing + photoactive fatty acid micelles, which gradually evolved + into nucleotide-containing micelles due to the enhanced + ability of nucleotide-coupled sensitizer molecules to + absorb visible light. Comparison of the calculated + absorption spectra of micelles with and without nucleotides + confirmed this idea and supports the idea of the emergence + and evolution of nucleotides in minimal cells of a + so-called Fatty Acid World. Furthermore, the + nucleotide-caused wavelength shift and broadening of the + absorption pattern potentially gives these molecules an + additional valuable role, other than a purely genetic one + in the early stages of the development of life. From the + information theory point of view, the nucleotide sequences + in such micelles carry positional information providing + better electron transport along the nucleotide-sensitizer + chain and, in addition, providing complimentary copies of + that information for the next generation. Nucleotide + sequences, which in the first period of evolution of fatty + acid molecules were useful just for better absorbance of + the light in the longer wavelength region, later in the PNA + or RNA World, took on the role of genetic information + storage.}, + pmid = {20443139}, + doi = {10.1007/s11084-010-9211-4}, +} +@Article{Tanford1974:micelle_formation_thermodynamics, + author = {C Tanford}, + title = {Thermodynamics of micelle formation: prediction of micelle + size and size distribution}, + journal = {Proc Natl Acad Sci U S A}, + year = {1974}, + volume = {71}, + number = {5}, + pages = {1811--5}, + month = {May}, + abstract = {This paper presents a simple theory for the calculation of + micelle size and other properties of micelleforming + systems. The theory is based on the separate estimation of + the components of the free energy arising from hydrophobic + attraction and from head group repulsion, each as a + function of micelle size. The difficult problem of an a + priori calculation of the repulsive factor is circumvented + by using experimental values of this parameter, derived + from pressure-area curves of monolayers at an interface + between an aqueous solution and liquid hydrocarbon. Though + some parameters of the theory are still somewhat uncertain, + self-consistent and physically realistic values can be + assigned that lead to almost exact prediction of + experimental micelle sizes and critical micelle + concentrations for two distinctly different ionic + detergents.}, + pmid = {4525294}, +} +@article{Tewes2001:lipid_polarity_in_bec, + author = {BJ Tewes and HJ Galla}, + title = {Lipid polarity in brain capillary endothelial cells.}, + journal = {Endothelium}, + year = 2001, + key = {bec, lipid polarity, lipid composition}, + volume = 8, + number = 3, + pages = {207--220}, + abstract = {Brain capillary endothelial cells (BCEC) represent an + epithelial like cell type with continuous tight + junctions and polar distributed proteins. In this paper + we investigated whether cultured BCEC show a polar + distribution of membrane lipids as this was demonstrated + for many epithelial cell types. Therefore we applied a + high yield membrane fractionation method to isolate pure + fractions of the apical and the basolateral plasma + membrane (PM) domains. Using a set of methods for lipid + analysis we were able to determine the total lipid + composition of the whole cells and the PM + fractions. Both membrane domains showed a unique lipid + composition with clear differences to each other and to + the whole cell composition. Three lipid species were + polar distributed between the two PM + domains. Phosphatidylcholine was enriched in the apical + membrane whereas sphingomyelin and glucosylceramide were + enriched in the basolateral membrane. The possible + function of this lipid polarity for the blood-brain + barrier mechanism is the generation of a suitable lipid + environment for polar distributed membrane proteins and + the generation of two PM domains with different + biophysical properties and permeabilities.}, + pmid = 11824473 +} +@Article{Thomas1988:chol_transfer, + author = {P D Thomas and M J Poznansky}, + title = {Cholesterol transfer between lipid vesicles. Effect of + phospholipids and gangliosides}, + journal = {Biochem J}, + year = {1988}, + volume = {251}, + number = {1}, + pages = {55--61}, + month = {Apr}, + abstract = {The effect of lipid composition on the rate of cholesterol + movement between cellular membranes is investigated using + lipid vesicles. The separation of donor and acceptor + vesicles required for rate measurement is achieved by + differential centrifugation so that the lipid effect can be + quantified in the absence of a charged lipid generally used + for ion-exchange-based separation. The rate of cholesterol + transfer from small unilamellar vesicles (SUVs) containing + 50 mol\% cholesterol to a common large unilamellar vesicle + (LUV) acceptor containing 20 mol\% cholesterol decreases + with increasing mol\% of sphingomyelin in the SUVs, while + phosphatidylethanolamine and phosphatidylserine have no + appreciable effect at physiologically relevant levels. + There is a large decrease in rate when + phosphatidylethanolamine constitutes 50 mol\% of donor + phospholipids. Interestingly, gangliosides which have the + same hydrocarbon moiety as sphingomyelin exert an opposite + effect. The effect of spingomyelin seems to be mediated by + its ability to decrease the fluidity of the lipid matrix, + while that of gangliosides may arise from a weakening of + phosphatidylcholine-cholesterol interactions or from a more + favourable (less polar) microenvironment for the desorption + of cholesterol provided by the head-group interactions + involving sugar residues. If the effect of asymmetric + transbilayer distribution of lipids is taken into + consideration, the observed composition-dependent rate + changes could partly account for the large difference in + the rates of cholesterol desorption from the inner and + outer layers of plasma membrane. Such rate differences may + be responsible for an unequal steady-state distribution of + cholesterol among various cellular membranes and + lipoproteins.}, + pmid = {3390160}, +} +@Article{Thurmond1991:area_of_pc_pe_2hnmr, + author = {R L Thurmond and S W Dodd and M F Brown}, + title = {Molecular areas of phospholipids as determined by 2H NMR + spectroscopy. Comparison of phosphatidylethanolamines and + phosphatidylcholines}, + journal = {Biophys J}, + year = {1991}, + volume = {59}, + number = {1}, + pages = {108--13}, + month = {Jan}, + abstract = {The role of lipid diversity in biomembranes is one of the + major unsolved problems in biochemistry. One parameter of + possible importance is the mean cross-sectional area + occupied per lipid molecule, which may be related to + formation of nonbilayer structures and membrane protein + function. We have used 2H NMR spectroscopy to compare the + properties of + 1,2-diperdeuteriopalmitoyl-sn-glycero-3-phosphoethanolamine + (DPPE-d62) and + 1,2-diperdeuteriopalmitoyl-sn-glycero-3-phosphocholine + (DPPC-d62) in the L alpha phase. We find that DPPE has + greater segmental order than DPPC, and that this increase + in order is related to the smaller area per acyl chain + found for DPPE. Values of the mean cross-sectional chain + area are calculated using a simple diamond lattice model + for the acyl chain configurational statistics, together + with dilatometry data. The results obtained for the mean + area per molecule are comparable with those from low angle + x-ray diffraction studies.}, + pmid = {2015377}, + doi = {10.1016/S0006-3495(91)82203-2}, +} +@Article{Walde1994:fa_vesicle_reproduction, + author = {Peter Wlade and Roger Wick and Massimo Fresta and Annarosa Mangone and Pier Luigi Luisi}, + title = {Autopoetic Self-Reproduction of Fatty Acid Vesicles}, + journal = {J Am. Chem. Soc}, + year = 1994, + volume = 116, + number = 26, + pages = {11649-11654}, + abstract = {Conditions are described under which vesicles formed + by caprylic acid and oleic acid in water are able to + undergo autopoietic self-reproduction---namely an + increase of their population number due to reaction + which takes place within the spherical boundary of + the vesicles themselves. This is acchieved by + letting a certain amount of the neat water-insoluble + caprylic or oleic anhydride hydrolyze at alkaline + pH: the initial increase of the concentration of the + released acid/carboxylate is extremely slow (several + days to reach thte conditions for spontaneous + vesicle formation), but afterwards, the presence of + vesicles brings about a rapid second phase leading + to more and more vesicles being formed in an overall + autocatalystic process. THe catalytic power of the + caprylic acid and oleic acid vesicles toward the + hydrolysis of the correpsonding anhydride is + documented in a set of indepenedent experiments. In + these experiments, the hydroysis was carried out in + the presence of vesicles at a pH corresponding + approximately to the pK of the acid in the vesicles. + The process of autopoeitc self-reproduction of + caprylic acid and oleic acid vesicles is studied as + a function of temperature: by increasing temperature + (up to 70 C), the exponential time progress of + vesicle formation tend sot become steeper while the + long initial slow phase is significantly shortened. + The caprylic acid and oleic acid vesicles are + characterized by electron microscopy and by + determining their internal volume. The question + whether and to what extent these vesicles form a + classic chemical equilibrium system---in which + namely the free surfactant is in equilibrium with + the aggregates---is also investigated.}, + doi = {10.1021/ja00105a004} +} +@Article{Wimley1990:dmpc_exchange, + author = {W C Wimley and T E Thompson}, + title = {Exchange and flip-flop of dimyristoylphosphatidylcholine in + liquid-crystalline, gel, and two-component, two-phase large + unilamellar vesicles}, + journal = {Biochemistry}, + year = {1990}, + volume = {29}, + number = {5}, + pages = {1296--303}, + month = {Feb}, + abstract = {The rate and extent of spontaneous exchange of + dimyristoylphosphatidylcholine (DMPC) from large + unilamellar vesicles (LUV) composed of either DMPC or + mixtures of DMPC/distearoylphosphatidylcholine (DSPC) have + been examined under equilibrium conditions. The phase state + of the vesicles ranged from all-liquid-crystalline through + mixed gel/liquid-crystalline to all-gel. The exchange rate + of DMPC between liquid-crystalline DMPC LUV, measured + between 25 and 55 degrees C, was found to have an Arrhenius + activation energy of 24.9 +/- 1.4 kcal/mol. This activation + energy and the exchange rates are very similar to those + obtained for the exchange of DMPC between DMPC small + unilamellar vesicles (SUV). The extent of exchange of DMPC + in LUV was found to be approximately 90\%. This is in + direct contrast to the situation in DMPC SUV where only the + lipid in the outer monolayer is available for exchange. + Thus, transbilayer movement (flip-flop) is substantially + faster in liquid-crystalline DMPC LUV than in SUV. + Desorption from gel-phase LUV has a much lower rate than + gel-phase SUV with an activation energy of 31.7 +/- 3.7 + kcal/mol compared to 11.5 +/- 2 kcal/mol reported for SUV. + A defect-mediated exchange in gel-phase SUV, which is not + the major pathway for exchange in LUV, is proposed on the + basis of the thermodynamic parameters of the activation + process. Surprisingly, the rates of DMPC exchange between + DMPC/DSPC two-component LUV, measured over a wide range of + compositions and temperatures, were found to exhibit very + little dependence on the composition or phase configuration + of the vesicles.(ABSTRACT TRUNCATED AT 250 WORDS)}, + pmid = {2322564}, +} +@Article{Wimley1991, + author = {W C Wimley and T E Thompson}, + title = {Phosphatidylethanolamine enhances the concentration-dependent + exchange of phospholipids between bilayers}, + journal = {Biochemistry}, + year = {1991}, + volume = {30}, + number = {17}, + pages = {4200--4}, + month = {Apr}, + abstract = {It has previously been demonstrated that lipid exchange + between phosphatidylcholine vesicles, at higher + concentrations, is characterized by a second-order + concentration-dependent exchange process in addition to the + first-order process operative at lower concentrations + (Jones, J. D., & Thompson, T. E. (1989) Biochemistry 28, + 129-134). Furthermore, it was demonstrated that the + second-order process occurs as a result of an enhancement + of the first-order desorption process, possibly resulting + from attractive interactions between a potentially + desorbing lipid molecule and a transiently apposed bilayer + (Jones, J. D., & Thompson, T. E. (1990) Biochemistry 29, + 1593-1600). In this work we have studied the exchange of + [3H]dimyristoylphosphatidylcholine (DMPC) between large + vesicles of the compositions 100\% DMPC, 70/30 (mol/mol) + DMPC/dimyristoylphosphatidylethanolamine (DMPE), and + 68.25/30/1.75 (mol/mol/mol) + DMPC/DMPE/dimyristoylphosphatidylglycerol (DMPG). The + second-order exchange process is enhanced by 100-fold or + more in vesicles containing 30 mol \% DMPE relative to + 100\% DMPC and is reduced or eliminated by the addition of + 1.75\% of the anionic lipid DMPG. These effects can be + achieved by alterations in the equilibrium bilayer + separation of 5 A or less. The results are in accord with + the model of Jones and Thompson and indicate that + relatively low concentrations of PE in a PC bilayer can + have significant effects on bilayer surface properties and + on potential interactions between bilayers.}, + pmid = {2021612}, +} +@Article{Wimley1991:dmpc_depc_exchange, + author = {W C Wimley and T E Thompson}, + title = {Transbilayer and interbilayer phospholipid exchange in + dimyristoylphosphatidylcholine/dimyristoylphosphatidylethanolamine + large unilamellar vesicles}, + journal = {Biochemistry}, + year = {1991}, + volume = {30}, + number = {6}, + pages = {1702--9}, + month = {Feb}, + abstract = {The rates of spontaneous interbilayer and transbilayer + exchange of [3H]dimyristoylphosphatidylcholine ([3H]DMPC) + were examined in DMPC and + DMPC/dimyristoylphosphatidylethanolamine (DMPE) large + unilamellar vesicles in the liquid-crystalline-, gel-, and + mixed-phase states. DMPC desorption rates from either gel + or liquid-crystalline phases containing DMPE are very + similar to the corresponding rates from pure DMPC gel or + liquid-crystalline phases. This is not the case for DMPC + desorption from distearoylphosphatidylcholine + (DSPC)-containing gel phases, where the desorption rates + are significantly faster than from a pure DMPC gel phase + [Wimley, W. C., & Thompson, T. E. (1990) Biochemistry 29, + 1296-1303]. We proposed that the DMPC/DSPC behavior results + from packing defects in gel phases composed of both DMPC + and DSPC molecules because of the four-carbon difference in + the acyl chain lengths of the two species. The present + results strongly support this hypothesis because no such + anomalous behavior is observed in DMPC/DMPE, which is + similar to DMPC/DSPC in phase behavior but does not have + the chain length difference. The inclusion of 10-30 mol \% + DMPE in DMPC bilayers was also found to have a significant + effect on the rate of transbilayer movement (flip-flop) of + [3H]DMPC in the liquid-crystalline phase. Between 10 and 30 + mol \% DMPE, flip-flop of DMPC is slowed by at least + 10-fold relative to flip-flop in DMPC bilayers, and the + entropy and enthalpy of flip-flop activation are both + substantially decreased.(ABSTRACT TRUNCATED AT 250 WORDS)}, + pmid = {1993185}, +} -- 2.39.2