Assembly-driven protection from hydrolysis as key selective force during chemical evolution.
Recalcitrance
abiotic chemistry
biopolymers
chemical evolution
molecular evolution
origins of life
prebiotic chemistry
self-assembly
Journal
FEBS letters
ISSN: 1873-3468
Titre abrégé: FEBS Lett
Pays: England
ID NLM: 0155157
Informations de publication
Date de publication:
Dec 2023
Dec 2023
Historique:
revised:
07
09
2023
received:
13
07
2023
accepted:
21
09
2023
pubmed:
27
10
2023
medline:
27
10
2023
entrez:
26
10
2023
Statut:
ppublish
Résumé
The origins of biopolymers pose fascinating questions in prebiotic chemistry. The marvelous assembly proficiencies of biopolymers suggest they are winners of a competitive evolutionary process. Sophisticated molecular assembly is ubiquitous in life where it is often emergent upon polymerization. We focus on the influence of molecular assembly on hydrolysis rates in aqueous media and suggest that assembly was crucial for biopolymer selection. In this model, incremental enrichment of some molecular species during chemical evolution was partially driven by the interplay of kinetics of synthesis and hydrolysis. We document a general attenuation of hydrolysis by assembly (i.e., recalcitrance) for all universal biopolymers and highlight the likely role of assembly in the survival of the 'fittest' molecules during chemical evolution.
Identifiants
pubmed: 37884438
doi: 10.1002/1873-3468.14766
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
2879-2896Subventions
Organisme : Israel Science Foundation
ID : 1611/22
Organisme : The Azrieli Foundation Early Career Faculty Grant
Organisme : The FEBS Foundation Excellence Award
Organisme : The Minerva Foundation
Informations de copyright
© 2023 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.
Références
Matange K, Rajaei V, Capera-Aragonès P, Costner JT, Robertson A, Kim JS, Petrov AS, Bowman JC, Williams LD and Frenkel-Pinter M (2023) Evolution of complex chemical mixtures reveals combinatorial compression and population synchronicity. ChemRxiv doi: 10.26434/chemrxiv-2022-s3cr2-v2
Capera-Aragonès P, Matange K, Rajaei V, Williams LD and Frenkel-Pinter M (2023) Thermodynamic and kinetic selection in evolving chemical mixtures. ChemRxiv doi: 10.26434/chemrxiv-2023-b3glp
Bell EA, Boehnke P, Harrison TM and Mao WL (2015) Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon. Proc Natl Acad Sci USA 112, 14518-14521.
Knoll AH and Nowak MA (2017) The timetable of evolution. Sci Adv 3, e1603076.
Benton MJ and Harper DAT (2020) Introduction to Paleobiology and the Fossil Record. John Wiley & Sons, Hoboken, NJ.
Jacob F (1977) Evolution and tinkering. Science 196, 1161-1166.
Woese CR (2002) On the evolution of cells. Proc Natl Acad Sci USA 99, 8742-8747.
Orgel LE (1994) The origin of life on the earth. Sci Am 271, 76-83.
Trainer MG, Pavlov AA, DeWitt HL, Jimenez JL, McKay CP, Toon OB and Tolbert MA (2006) Organic haze on titan and the early earth. Proc Natl Acad Sci USA 103, 18035-18042.
Reed NW, Wing BA, Tolbert MA and Browne EC (2022) Trace H2S promotes organic aerosol production and organosulfur compound formation in Archean analog haze photochemistry experiments. Geophys Res Lett 49, e2021GL097032.
Zahnle KJ, Lupu R, Catling DC and Wogan N (2020) Creation and evolution of impact-generated reduced atmospheres of early earth. Planet Sci J 1, 11.
Hud NV, Cafferty BJ, Krishnamurthy R and Williams LD (2013) The origin of RNA and “my Grandfather's axe”. Chem Biol 20, 466-474.
Brack A (1987) Selective emergence and survival of early polypeptides in water. Orig Life Evol Biosph 17, 367-379.
Schneider C, Becker S, Okamura H, Crisp A, Amatov T, Stadlmeier M and Carell T (2018) Noncanonical RNA nucleosides as molecular fossils of an early earth-generation by prebiotic methylations and carbamoylations. Angew Chem Int Ed Engl 57, 5943-5946.
Deamer D (2017) The role of lipid membranes in Life's origin. Life 7, 5.
Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V and Szostak JW (2020) A model for the emergence of RNA from a Prebiotically plausible mixture of ribonucleotides, Arabinonucleotides, and 2′-Deoxynucleotides. J Am Chem Soc 142, 2317-2326.
Frenkel-Pinter M, Haynes JW, Martin C, Petrov AS, Burcar BT, Krishnamurthy R, Hud NV, Leman LJ and Williams LD (2019) Selective incorporation of proteinaceous over nonproteinaceous cationic amino acids in model prebiotic oligomerization reactions. Proc Natl Acad Sci USA 116, 16338-16346.
Runnels CM, Lanier KA, Williams JK, Bowman JC, Petrov AS, Hud NV and Williams LD (2018) Folding, assembly, and persistence: the essential nature and origins of biopolymers. J Mol Evol 86, 598-610.
Lemmon RM (1970) Chemical evolution. Chem Rev 70, 95-109.
Cleaves HJ (2010) The origin of the biologically coded amino acids. J Theor Biol 263, 490-498.
Eschenmoser A and Eschenmoser A (2011) Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of Life's origin: a retrospective. Angew Chem Int Ed Engl 50, 12412-12472.
Vincent L, Berg M, Krismer M, Saghafi SS, Cosby J, Sankari T, Vetsigian K, Cleaves HJ and Baum DA (2019) Chemical ecosystem selection on mineral surfaces reveals long-term dynamics consistent with the spontaneous emergence of mutual catalysis. Life 9, 80.
Rodriguez-Garcia M, Surman AJ, Cooper GJT, Suárez-Marina I, Hosni Z, Lee MP and Cronin L (2015) Formation of oligopeptides in high yield under simple programmable conditions. Nat Commun 61, 1-7.
Matange K, Rajaei V, Schuster G, Hud N, Capera-Aragonès P, Frenkel-Pinter M and Williams L (2023) Origins of life: chemistry and evolution. ChemRxiv doi: 10.26434/chemrxiv-2023-1jrcq
Heames B, Buchel F, Aubel M, Tretyachenko V, Loginov D, Novák P, Lange A, Bornberg-Bauer E and Hlouchová K (2023) Experimental characterization of de novo proteins and their unevolved random-sequence counterparts. Nat Ecol Evol 7, 570-580.
Lee DH, Granja JR, Martinez JA, Severin K and Ghadiri MR (1996) A self-replicating peptide. Nature 382, 525-528.
Childers WS, Ni R, Mehta AK and Lynn DG (2009) Peptide membranes in chemical evolution. Curr Opin Chem Biol 13, 652-659.
Zozulia O, Dolan MA and Korendovych IV (2018) Catalytic peptide assemblies. Chem Soc Rev 47, 3621-3639.
Danger G, Plasson R and Pascal R (2012) Pathways for the formation and evolution of peptides in prebiotic environments. Chem Soc Rev 41, 5416-5429.
Makarov M, Sanchez Rocha AC, Krystufek R, Cherepashuk I, Dzmitruk V, Charnavets T, Faustino AM, Lebl M, Fujishima K, Fried SD et al. (2023) Early selection of the amino acid alphabet was adaptively shaped by biophysical constraints of foldability. J Am Chem Soc 145, 5320-5329.
Frenkel-Pinter M, Samanta M, Ashkenasy G and Leman LJ (2020) Prebiotic peptides: molecular hubs in the origin of life. Chem Rev 120, 4707-4765.
Berger O, Yoskovitz E, Adler-Abramovich L and Gazit E (2016) Photonic crystals: spectral transition in bio-inspired self-assembled peptide nucleic acid photonic crystals. Adv Mater 28, 2276.
Mutschler H, Taylor AI, Porebski BT, Lightowlers A, Houlihan G, Abramov M, Herdewijn P and Holliger P (2018) Random-sequence genetic oligomer pools display an innate potential for ligation and recombination. Elife 7, e43022.
Moore PB (1999) Structural motifs in RNA. Annu Rev Biochem 68, 287-300.
Bellini T, Zanchetta G, Fraccia TP, Cerbino R, Tsai E, Smith GP, Moran MJ, Walba DM and Clark NA (2012) Liquid crystal self-assembly of random-sequence DNA oligomers. Proc Natl Acad Sci USA 109, 1110-1115.
Smith GP, Fraccia TP, Todisco M, Zanchetta G, Zhu C, Hayden E, Bellini T and Clark NA (2018) Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson-crick selectivity. Proc Natl Acad Sci USA 115, E7658-E7664.
Zanchetta G, Bellini T, Nakata M and Clark NA (2008) Physical polymerization and liquid crystallization of RNA oligomers. J Am Chem Soc 130, 12864-12865.
Smith GP, Fraccia TP, Todisco M, Zanchetta G, Zhu C, Hayden E, Bellini T and Clark NA (2018) Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson-crick selectivity. Proc Natl Acad Sci USA 115, E7658-E7664.
Jia TZ, Bellini T, Clark N and Fraccia TP (2022) A liquid crystal world for the origins of life. Emerg Top Life Sci 6, 557-569.
Zhang C, Xue X, Luo Q, Li Y, Yang K, Zhuang X, Jiang Y, Zhang J, Liu J, Zou G et al. (2014) Self-assembled peptide nanofibers designed as biological enzymes for catalyzing ester hydrolysis. ACS Nano 8, 11715-11723.
Mendes AC, Baran ET, Reis RL and Azevedo HS (2013) Self-assembly in nature: using the principles of nature to create complex nanobiomaterials. Wiley Interdiscip Rev Nanomed Nanobiotechnol 5, 582-612.
Tian L, Liu S, Wang S and Wang L (2016) Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis. Sci Rep 6, 23605.
MacGregor EA, Janeček Š and Svensson B (2001) Relationship of sequence and structure to specificity in the α-amylase family of enzymes. Biochim Biophys Acta Protein Struct Mol Enzymol 1546, 1-20.
Sussman JL and Silman I (1992) Acetylcholinesterase: structure and use as a model for specific cation-protein interactions. Curr Opin Struct Biol 2, 721-729.
Raasakka A, Myllykoski M, Laulumaa S, Lehtimäki M, Härtlein M, Moulin M, Kursula I and Kursula P (2015) Determinants of ligand binding and catalytic activity in the myelin enzyme 2′,3′-cyclic nucleotide 3′-phosphodiesterase. Sci Rep 5, 1-15.
Adamala K and Szostak JW (2013) Competition between model protocells driven by an encapsulated catalyst. Nat Chem 5, 495-501.
Miao X, Paikar A, Lerner B, Diskin-Posner Y, Shmul G and Semenov SN (2021) Kinetic selection in the out-of-equilibrium autocatalytic reaction networks that produce macrocyclic peptides. Angew Chem Int Ed Engl 60, 20366-20375.
Akagawa K and Kudo K (2017) Development of selective peptide catalysts with secondary structural frameworks. Acc Chem Res 50, 2429-2439.
Lewandowski B and Wennemers H (2014) Asymmetric catalysis with short-chain peptides. Curr Opin Chem Biol 22, 40-46.
Metrano AJ and Miller SJ (2019) Peptide-based catalysts reach the outer sphere through remote desymmetrization and atroposelectivity. Acc Chem Res 52, 199-215.
Tena-Solsona M, Nanda J, Díaz-Oltra S, Chotera A, Ashkenasy G and Escuder B (2016) Emergent catalytic behavior of self-assembled low molecular weight peptide-based aggregates and hydrogels. Chemistry 22, 6687-6694.
Agazani O, Tulpin A and Reches M (2021) An individual amino acid as a possible prebiotic catalyst. ChemSystemsChem 3, 3-8.
Zozulia O, Dolan MA and Korendovych IV (2018) Catalytic peptide assemblies. Chem Soc Rev 47, 3621-3639.
Singh N, Kumar M, Miravet JF, Ulijn RV and Escuder B (2017) Peptide-based molecular hydrogels as supramolecular protein mimics. Chemistry 23, 981-993.
Humenik M, Scheibel T and Smith A (2011) Spider Silk: Understanding the Structure-Function Relationship of a Natural Fiber. 1st edn. Elsevier Inc, Amsterdam.
Misra R, Rudnick-Glick S and Adler-Abramovich L (2021) From folding to assembly: functional supramolecular architectures of peptides comprised of non-canonical amino acids. Macromol Biosci 21, 1-23.
Rufo CM, Moroz YS, Moroz OV, Stöhr J, Smith TA, Hu X, Degrado WF and Korendovych IV (2014) Short peptides self-assemble to produce catalytic amyloids. Nat Chem 6, 303-309.
Klussmann M, Iwamura H, Mathew SP, Wells DH, Pandya U, Armstrong A and Blackmond DG (2006) Thermodynamic control of asymmetric amplification in amino acid catalysis. Nature 441, 621-623.
Ibrahem I, Casas J and Córdova A (2004) Direct catalytic enantioselective α-aminomethylation of ketones. Angew Chem Int Ed Engl 43, 6528-6531.
Notz W, Tanaka F and Barbas CF (2004) Enamine-based organocatalysis with proline and diamines: the development of direct catalytic asymmetric aldol, Mannich, Michael, and Diels-Alder reactions. Acc Chem Res 37, 580-591.
Zheng X and Wang Y (2008) Proline-catalyzed asymmetric reactions. Prog Chem 20, 1675-1686.
Reches M and Gazit E (2003) Casting metal nanowires within discrete self-assembled peptide nanotubes. Science 300, 625-627.
Davie EAC, Mennen SM, Xu Y and Miller SJ (2007) Asymmetric catalysis mediated by synthetic peptides. Chem Rev 107, 5759-5812.
Zhang S (2012) Lipid-like self-assembling peptides. Acc Chem Res 45, 2142-2150.
Egel R (2009) Peptide-dominated membranes preceding the genetic takeover by RNA: latest thinking on a classic controversy. Bioessays 31, 1100-1109.
Poudyal RR, Pir Cakmak F, Keating CD and Bevilacqua PC (2018) Physical principles and extant biology reveal roles for RNA-containing Membraneless compartments in origins of life chemistry. Biochemistry 57, 2509-2519.
Markovitch O and Lancet D (2012) Excess mutual catalysis is required for effective evolvability. Artif Life 18, 243-266.
Segré D, Ben-Eli D and Lancet D (2000) Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies. Proc Natl Acad Sci USA 97, 4112-4117.
Fittolani G, Seeberger PH and Delbianco M (2020) Helical polysaccharides. Pept Sci 112, e24124.
Du B, Nie S, Peng F, Yang Y and Xu B (2022) A narrative review on conformational structure characterization of natural polysaccharides. Food Front 3, 631-640.
Boddohi S and Kipper MJ (2010) Engineering nanoassemblies of polysaccharides. Adv Mater 22, 2998-3016.
Ioelovich M and Morag E (2011) Effect of cellulose structure on enzymatic hydrolysis. BioResources 6, 2818-2835.
Matthews JF, Skopec CE, Mason PE, Zuccato P, Torget RW, Sugiyama J, Himmel ME and Brady JW (2006) Computer simulation studies of microcrystalline cellulose Ibeta. Carbohydr Res 341, 138-152.
Nishiyama Y, Langan P and Chanzy H (2002) Crystal structure and hydrogen-bonding system in cellulose Iβ from synchrotron X-ray and neutron fiber diffraction. J Am Chem Soc 124, 9074-9082.
Tseng SL, Valente A and Gray DG (1981) Cholesteric liquid crystalline phases based on (Acetoxypropyl) cellulose. Macromolecules 14, 715-719.
Pawlowski WP, Gilbert RD, Fornes RE and Purrington ST (1987) The thermotropic and lyotropic liquid-crystalline properties of acetoacetoxypropyl cellulose. J Polym Sci B Polym Phys 25, 2293-2301.
Werbowyj RS and Gray DG (2007) Liquid crystalline structure in aqueous hydroxypropyl cellulose solutions. Mol Cryst Liq Cryst 34, 97-103.
Gray DG (1985) Chemical characteristics of cellulosic liquid crystals. Faraday Discuss Chem Soc 79, 257-264.
Chanzy H, Peguy A, Chaunis S and Monzie P (1980) Oriented cellulose films and fibers from a mesophase system. J Polym Sci Polym Phys Ed 18, 1137-1144.
Creek JA, Ziegler GR and Runt J (2006) Amylose crystallization from concentrated aqueous solution. Biomacromolecules 7, 761-770.
Sato T, Norisuye T and Fujita H (1984) Double-stranded helix of xanthan in dilute solution: evidence from light scattering. Polym J 164, 341-350.
Kiatponglarp W, Rugmai S, Rolland-Sabaté A, Buléon A and Tongta S (2016) Spherulitic self-assembly of debranched starch from aqueous solution and its effect on enzyme digestibility. Food Hydrocoll 55, 235-243.
Watson H (2015) Biological membranes. Essays Biochem 59, 43-69.
Tanford C (1978) The hydrophobic effect and the organization of living matter. Science 200, 1012-1018.
Tanford C (1979) Interfacial free energy and the hydrophobic effect. Proc Natl Acad Sci USA 76, 4175-4176.
Cistola DP, Atkinson D, Hamilton JA and Small DM (1986) Phase behavior and bilayer properties of fatty acids: hydrated 1:1 acid-soaps. Biochemistry 25, 2804-2812.
Lewis RNAH, Mannock DA, McElhaney RN, Turner DC and Gruner SM (1989) Effect of fatty acyl chain length and structure on the lamellar gel to liquid-crystalline and lamellar to reversed hexagonal phase transitions of aqueous phosphatidylethanolamine dispersions. Biochemistry 28, 541-548.
Platz G, Poelike J, Thunig C, Hofmann R, Nickel D and von Rybinski W (1995) Phase behavior, Lyotropic phases, and flow properties of alkyl glycosides in aqueous solution. Langmuir 11, 4250-4255.
Douliez JP, Houssou BH, Fameau AL, Navailles L, Nallet F, Grélard A, Dufourc EJ and Gaillard C (2016) Self-assembly of bilayer vesicles made of saturated long chain fatty acids. Langmuir 32, 401-410.
Monnard PA and Deamer DW (2003) Preparation of vesicles from nonphospholipid amphiphiles. Methods Enzymol 372, 133-151.
Gustafsson J, Nylander T and Almgren M (1999) Phase behavior and aggregate structure in aqueous mixtures of sodium cholate and glycerol monooleate. J Colloid Interface Sci 211, 326-335.
Hargreaves WR and Deamer DW (1978) Liposomes from ionic, single-chain Amphiphiles. Biochemistry 17, 3759-3768.
Paul A, Jacoby G, Laor Bar-Yosef D, Beck R, Gazit E and Segal D (2021) Glucosylceramide associated with Gaucher disease forms amyloid-like twisted ribbon fibrils that induce α-Synuclein aggregation. ACS Nano 15, 11854-11868.
Israelachvili JN, Mitchell DJ and Ninham BW (1976) Theory of self-assembly of hydrocarbon amphiphiles into micelles and bilayers. J Chem Soc Faraday Trans 2, 1525.
Israelachvili JN, Mitchell DJ and Ninham BW (1977) Theory of self-assembly of lipid bilayers and vesicles. Biochim Biophys Acta 470, 185-201.
May S and Ben-Shaul A (1995) Spontaneous curvature and thermodynamic stability of mixed amphiphilic layers. J Chem Phys 103, 3839-3848.
Jewell SA (2011) Living systems and liquid crystals. Liq Cryst 38, 1699-1714.
Deng Y, Marko M, Buttle KF, Leith A, Mieczkowski M and Mannella CA (1999) Cubic membrane structure in amoeba (Chaos carolinensis) mitochondria determined by electron microscopic tomography. J Struct Biol 127, 231-239.
Westheimer FH (1987) Why nature chose phosphates. Science 235, 1173-1178.
Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362, 709-715.
Peller L (1976) On the free-energy changes in the synthesis and degradation of nucleic acids. Biochemistry 15, 141-146.
Martin RB (1998) Free energies and equilibria of peptide bond hydrolysis and formation. Biopolymers 45, 351-353.
Ross DS and Deamer D (2016) Dry/wet cycling and the thermodynamics and kinetics of prebiotic polymer synthesis. Life 6, 28.
Wolfenden R, Lu X and Young G (1998) Spontaneous hydrolysis of glycosides. J Am Chem Soc 120, 6814-6815.
Radzicka A and Wolfenden R (1995) A proficient enzyme. Science 267, 90-93.
Radzicka A and Wolfenden R (1996) Rates of Uncatalyzed peptide bond hydrolysis in neutral solution and the transition state affinities of proteases. J Am Chem Soc 118, 6105-6109.
McKinley MP, Bolton DC and Prusiner SB (1983) A protease-resistant protein is a structural component of the scrapie prion. Cell 35, 57-62.
Kjaer KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, Sand KK, Jelavić S, Ruter AH, Schmidt AMA et al. (2022) A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 612, 283-291.
Usher DA and McHale AH (1976) Hydrolytic stability of helical RNA: a selective advantage for the natural 3′,5′-bond. Proc Natl Acad Sci USA 73, 1149-1153.
Rohatgi R, Bartel DP and Szostak JW (1996) Nonenzymatic, template-directed ligation of oligoribonucleotides is highly regioselective for the formation of 3′-5′ phosphodiester bonds. J Am Chem Soc 118, 3340-3344.
Lutay AV, Chernolovskaya EL, Zenkova MA and Vlassov VV (2006) The nonenzymatic template-directed ligation of oligonucleotides. Biogeosciences 3, 243-249.
Kavita K and Breaker RR (2023) Discovering riboswitches: the past and the future. Trends Biochem Sci 48, 119-141.
Guth-Metzler R, Mohyeldin Mohamed A, Cowan ET, Frankel-Pinter M, Wartell RM, Glass JB and Dean Williams L (2021) RNA and the Goldilocks zone: where Mg2+ concentration is just right. Nucleic Acids Res 51, 3529-3539.
Jain SS and Tullius TD (2008) Footprinting protein-DNA complexes using the hydroxyl radical. Nat Protoc 3, 1092-1100.
Deigan KE, Li TW, Mathews DH and Weeks KM (2009) Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci USA 106, 97-102.
Fontana A, de Laureto PP, Spolaore B, Frare E, Picotti P and Zambonin M (2004) Probing protein structure by limited proteolysis. Acta Biochim pol 51, 299-321.
Suskiewicz MJ, Sussman JL, Silman I and Shaul Y (2011) Context-dependent resistance to proteolysis of intrinsically disordered proteins. Protein Sci 20, 1285-1297.
Fontana A, Polverino de Laureto P, Spolaore B, Frare E and Zambonin M (2010) Detecting disordered regions in proteins by limited proteolysis. In Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation (Uversky VN and Longhi S, eds), pp. 569-626. Wiley, New York, NY.
Pace CN and Barrett AJ (1984) Kinetics of tryptic hydrolysis of the arginine-valine bond in folded and unfolded ribonuclease T1. Biochem J 219, 411-417.
Umamaheswaran R, Dutta S, Prasad GVR, Khan MA, Kumar S, Bera S and Patnaik R (2023) The diagenetic fate of collagen as revealed by analytical pyrolysis of fossil fish scales from deep time. Geobiology 21, 378-389.
Lambeth TR and Julian RR (2021) Proteolysis of amyloid β by lysosomal enzymes as a function of fibril morphology. ACS Omega 6, 31520-31527.
Schönfelder J, Pfeiffer PB, Pradhan T, Bijzet J, Hazenberg BPC, Schönland SO, Hegenbart U, Reif B, Haupt C and Fändrich M (2021) Protease resistance of ex vivo amyloid fibrils implies the proteolytic selection of disease-associated fibril morphologies. Amyloid 28, 243-251.
Söderberg L, Dahlqvist C, Kakuyama H, Thyberg J, Ito A, Winblad B, Näslund J and Tjernberg LO (2005) Collagenous Alzheimer amyloid plaque component assembles amyloid fibrils into protease resistant aggregates. FEBS J 272, 2231-2236.
Benetti F, Biarnés X, Attanasio F, Giachin G, Rizzarelli E and Legname G (2014) Structural determinants in prion protein folding and stability. J Mol Biol 426, 3796-3810.
Chiti F and Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75, 333-366.
Zhou Z and Xiao G (2013) Conformational conversion of prion protein in prion diseases. Acta Biochim Biophys Sin (Shanghai) 45, 465-476.
Maury CPJ (2018) Amyloid and the origin of life: self-replicating catalytic amyloids as prebiotic informational and protometabolic entities. Cell Mol Life Sci 75, 1499-1507.
Greenwald J, Friedmann MP and Riek R (2016) Amyloid aggregates arise from amino acid condensations under prebiotic conditions. Angew Chem Int Ed Engl 55, 11609-11613.
Rubinov B, Wagner N, Matmor M, Regev O, Ashkenasy N and Ashkenasy G (2012) Transient fibril structures facilitating nonenzymatic self-replication. ACS Nano 6, 7893-7901.
Saghatelian A, Yokobayashi Y, Soltani K and Ghadiri MR (2001) A chiroselective peptide replicator. Nature 409, 797-801.
Brack A (1987) Selective emergence and survival of early polypeptides in water. Orig Life Evol Biosph J Int Soc Study Orig Life 17, 367-379.
Tian YF, Hudalla GA, Han H and Collier JH (2013) Controllably degradable β-sheet nanofibers and gels from self-assembling depsipeptides. Biomater Sci 1, 1037-1045.
Zhang S, Lockshin C, Cook R and Rich A (1994) Unusually stable β-sheet formation in an ionic self-complementary oligopeptide. Biopolymers 34, 663-672.
Zhang S, Holmes T, Lockshin C and Rich A (1993) Spontaneous assembly of a self-complementary oligopeptide to form a stable macroscopic membrane. Proc Natl Acad Sci USA 90, 3334-3338.
Abkevich VI, Gutin AM and Shakhnovich EI (1996) How the first biopolymers could have evolved. Proc Natl Acad Sci USA 93, 839-844.
Mukherjee R, Cohen-Luria R, Wagner N and Ashkenasy G (2015) A Bistable switch in dynamic Thiodepsipeptide folding and template-directed ligation. Angew Chem Int Ed Engl 54, 12452-12456.
Jia TZ, Chandru K, Hongo Y, Afrin R, Usui T, Myojo K and James Cleaves H (2019) Membraneless polyester microdroplets as primordial compartments at the origins of life. Proc Natl Acad Sci USA 116, 15830-15835.
Jia TZ, Bapat NV, Verma A, Mamajanov I, Cleaves HJ and Chandru K (2021) Incorporation of basic α-Hydroxy acid residues into primitive polyester microdroplets for RNA segregation. Biomacromolecules 22, 1484-1493.
Colomb-Delsuc M, Mattia E, Sadownik JW and Otto S (2015) Exponential self-replication enabled through a fibre elongation/breakage mechanism. Nat Commun 6, 7427.
Jia TZ and Chandru K (2023) Recent progress in primitive polyester synthesis and membraneless microdroplet assembly. Biophys Physicobiology 20, e200012.
Afrin R, Chen C, Sarpa D, Sithamparam M, Yi R, Giri C, Mamajanov I, Cleaves HJ, Chandru K and Jia TZ (2022) The effects of dehydration temperature and monomer chirality on primitive polyester synthesis and microdroplet assembly. Macromol Chem Phys 223, 1-10.
Frenkel-Pinter M, Bouza M, Fernández FM, Leman LJ, Williams LD, Hud NV and Guzman-Martinez A (2022) Thioesters provide a plausible prebiotic path to proto-peptides. Nat Commun 13, 2569.
Bracher PJ, Snyder PW, Bohall BR and Whitesides GM (2011) The relative rates of thiol-thioester exchange and hydrolysis for alkyl and aryl Thioalkanoates in water. Orig Life Evol Biosph 41, 399-412.
Dadon Z, Samiappan M, Shahar A, Zarivach R and Ashkenasy G (2013) A high-resolution structure that provides insight into coiled-coil thiodepsipeptide dynamic chemistry. Angew Chem Int Ed Engl 52, 9944-9947.
Dadon Z, Samiappan M, Wagner N and Ashkenasy G (2012) Chemical and light triggering of peptide networks under partial thermodynamic control. Chem Commun 48, 1419-1421.
Dadon Z, Wagner N, Alasibi S, Samiappan M, Mukherjee R and Ashkenasy G (2015) Competition and cooperation in dynamic replication networks. Chemistry 21, 648-654.
Nanda J, Rubinov B, Ivnitski D, Mukherjee R, Shtelman E, Motro Y, Miller Y, Wagner N, Cohen-Luria R and Ashkenasy G (2017) Emergence of native peptide sequences in prebiotic replication networks. Nat Commun 8, 1-8.
Rubinov B, Wagner N, Rapaport H and Ashkenasy G (2009) Self-replicating amphiphilic β-sheet peptides. Angew Chem Int Ed Engl 48, 6683-6686.
Fialho DM, Karunakaran SC, Greeson KW, Martínez I, Schuster GB, Krishnamurthy R and Hud NV (2021) Depsipeptide nucleic acids: prebiotic formation, oligomerization, and self-assembly of a new proto-nucleic acid candidate. J Am Chem Soc 143, 13525-13537.
Beckham GT, Matthews JF, Peters B, Bomble YJ, Himmel ME and Crowley MF (2011) Molecular-level origins of biomass recalcitrance: decrystallization free energies for four common cellulose polymorphs. J Phys Chem B 115, 4118-4127.
Mustoe GE (2018) Non-mineralized fossil wood. Geosciences 8, 223.
Griffith JD, Willcox S, Powers DW, Nelson R and Baxter BK (2008) Discovery of abundant cellulose microfibers encased in 250 ma permian halite: a macromolecular target in the search for life on other planets. Astrobiology 8, 215-228.
Klug C, Davesne D, Fuchs D and Argyriou T (2020) First record of non-mineralized cephalopod jaws and arm hooks from the latest cretaceous of Eurytania, Greece. Swiss J Palaeontol 139, 1-13.
Kepsil CR and Dennis EA (1981) Alkaline hydrolysis of phospholipids in model membranes and the dependence on their state of aggregation. Biochemistry 20, 6079-6085.
Briuglia M-L, Rotella C, McFarlane A and Lamprou DA (2015) Influence of cholesterol on liposome stability and on in vitro drug release. Drug Deliv Transl Res 5, 231-242.
Fernández-García C and Powner MW (2017) Selective acylation of nucleosides, nucleotides, and Glycerol-3-phosphocholine in water. Synlett 28, 78-83.
Koga Y (2014) From promiscuity to the lipid divide: on the evolution of distinct membranes in archaea and bacteria. J Mol Evol 78, 234-242.
Bonfio C, Caumes C, Duffy CD, Patel BH, Percivalle C, Tsanakopoulou M and Sutherland JD (2019) Length-selective synthesis of Acylglycerol-phosphates through energy-dissipative cycling. J Am Chem Soc 141, 3934-3939.
Xia Y and Levitt M (2004) Simulating protein evolution in sequence and structure space. Curr Opin Struct Biol 14, 202-207.
Britten AG and Eldefrawi AT (1971) Section of neurobiology ribosome-catalyzed polyester formation. Science 173, 340-343.
Frenkel-Pinter M, Haynes JW, Mohyeldin AM, Martin C, Sargon AB, Petrov AS, Krishnamurthy R, Hud NV, Williams LD and Leman LJ (2020) Mutually stabilizing interactions between proto-peptides and RNA. Nat Commun 11, 1-14.
Yu Z, Erbas A, Tantakitti F, Palmer LC, Jackman JA, De La Cruz MO, Cho NJ and Stupp SI (2017) Co-assembly of peptide amphiphiles and lipids into supramolecular nanostructures driven by Anion-π interactions. J Am Chem Soc 139, 7823-7830.
Jiang T, Meyer TA, Modlin C, Zuo X, Conticello VP and Ke Y (2017) Structurally ordered nanowire formation from co-assembly of DNA origami and collagen-mimetic peptides. J Am Chem Soc 139, 14025-14028.
Bomba R, Kwiatkowski W, Sánchez-Ferrer A, Riek R and Greenwald J (2018) Cooperative induction of ordered peptide and fatty acid aggregates. Biophys J 115, 2336-2347.
Koga S, Williams DS, Perriman AW and Mann S (2011) Peptide-nucleotide microdroplets as a step towards a membrane-free protocell model. Nat Chem 3, 720-724.
Kahana A, Maslov S and Lancet D (2021) Dynamic lipid aptamers: non-polymeric chemical path to early life. Chem Soc Rev 50, 11741-11746.
Ryu J and Park CB (2010) High stability of self-assembled peptide nanowires against thermal, chemical, and proteolytic attacks. Biotechnol Bioeng 105, 221-230.
Rieß B, Wanzke C, Tena-Solsona M, Grötsch RK, Maity C and Boekhoven J (2018) Dissipative assemblies that inhibit their deactivation. Soft Matter 14, 4852-4859.
Kriebisch BAK, Kriebisch CME, Bergmann AM, Wanzke C, Tena-Solsona M and Boekhoven J (2023) Tuning the kinetic trapping in chemically fueled self-assembly. ChemSystemsChem 5, 1-7.
Brack A and Spach G (1979) Beta-structures of polypeptides with L-and D-residues. Part I. Synthesis and conformational studies. J Mol Evol 13, 35-46.
Basak S, Singh I, Ferranco A, Syed J and Kraatz HB (2017) On the role of chirality in guiding the self-assembly of peptides. Angew Chem Int Ed Engl 56, 13288-13292.
Marchesan S, Styan KE, Easton CD, Waddington L and Vargiu AV (2015) Higher and lower supramolecular orders for the design of self-assembled heterochiral tripeptide hydrogel biomaterials. J Mater Chem B 3, 8123-8132.
Singh V, Rai RK, Arora A, Sinha N and Thakur AK (2014) Therapeutic implication of L-phenylalanine aggregation mechanism and its modulation by D-phenylalanine in phenylketonuria. Sci Rep 4, 3875.
Sakurai K, Mizu M and Shinkai S (2001) Polysaccharide−polynucleotide complexes. 2. Complementary polynucleotide mimic behavior of the natural polysaccharide Schizophyllan in the macromolecular complex with single-stranded RNA and DNA. Biomacromolecules 2, 641-650.
Kassem S, McPhee SA, Berisha N and Ulijn RV (2023) Emergence of cooperative glucose-binding networks in adaptive peptide systems. J Am Chem Soc 145, 9800-9807.
Giacobelli VG, Fujishima K, Lepšík M, Tretyachenko V, Kadavá T, Makarov M, Bednárová L, Novák P and Hlouchová K (2022) In vitro evolution reveals noncationic protein-RNA interaction mediated by metal ions. Mol Biol Evol 39, msac032.
Fried SD, Fujishima K, Makarov M, Cherepashuk I and Hlouchova K (2022) Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids. J R Soc Interface 19, 20210641.
Frenkel-Pinter M, Rajaei V, Glass JB, Hud NV and Williams LD (2021) Water and life: the medium is the message. J Mol Evol 89, 2-11.