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Šponer JE, Coulon R, Otyepka M, Šponer J, Siegle AF, Trapp O, Ślepokura K, Zdráhal Z, Šedo O. Phosphoric acid salts of amino acids as a source of oligopeptides on the early Earth. Commun Chem 2024; 7:185. [PMID: 39174757 DOI: 10.1038/s42004-024-01264-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/30/2024] [Indexed: 08/24/2024] Open
Abstract
Because of their unique proton-conductivity, chains of phosphoric acid molecules are excellent proton-transfer catalysts. Here we demonstrate that this property could have been exploited for the prebiotic synthesis of the first oligopeptide sequences on our planet. Our results suggest that drying highly diluted solutions containing amino acids (like glycine, histidine and arginine) and phosphates in comparable concentrations at elevated temperatures (ca. 80 °C) in an acidic environment could lead to the accumulation of amino acid:phosphoric acid crystalline salts. Subsequent heating of these materials at 100 °C for 1-3 days results in the formation of oligoglycines consisting of up to 24 monomeric units, while arginine and histidine form shorter oligomers (up to trimers) only. Overall, our results suggest that combining the catalytic effect of phosphate chains with the crystalline order present in amino acid:phosphoric acid salts represents a viable solution that could be utilized to generate the first oligopeptide sequences in a mild acidic hydrothermal field scenario. Further, we propose that crystallization could help overcoming cyclic oligomer formation that is a generally known bottleneck of prebiotic polymerization processes preventing further chain growth.
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Affiliation(s)
- Judit E Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, Czech Republic.
- CATRIN-Regional Centre of Advanced Technologies and Materials, Šlechtitelů 27, Olomouc, Czech Republic.
| | - Rémi Coulon
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, Czech Republic
- CATRIN-Regional Centre of Advanced Technologies and Materials, Šlechtitelů 27, Olomouc, Czech Republic
- Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, Olomouc, Czech Republic
| | - Michal Otyepka
- CATRIN-Regional Centre of Advanced Technologies and Materials, Šlechtitelů 27, Olomouc, Czech Republic
- IT4Innovations, VSB-Technical University of Ostrava, 17. listopadu 2172/15, 708 00, Ostrava, Poruba, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, Czech Republic
- CATRIN-Regional Centre of Advanced Technologies and Materials, Šlechtitelů 27, Olomouc, Czech Republic
| | - Alexander F Siegle
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, Germany
| | - Oliver Trapp
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, Germany
| | - Katarzyna Ślepokura
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, Wrocław, Poland
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, Brno, Czech Republic
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, Brno, Czech Republic.
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2
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Hlouchová K. Peptides En Route from Prebiotic to Biotic Catalysis. Acc Chem Res 2024; 57:2027-2037. [PMID: 39016062 PMCID: PMC11308367 DOI: 10.1021/acs.accounts.4c00137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/24/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
ConspectusIn the quest to understand prebiotic catalysis, different molecular entities, mainly minerals, metal ions, organic cofactors, and ribozymes, have been implied as key players. Of these, inorganic and organic cofactors have gained attention for their ability to catalyze a wide array of reactions central to modern metabolism and frequently participate in these reactions within modern enzymes. Nevertheless, bridging the gap between prebiotic and modern metabolism remains a fundamental question in the origins of life.In this Account, peptides are investigated as a potential bridge linking prebiotic catalysis by minerals/cofactors to enzymes that dominate modern life's chemical reactions. Before ribosomal synthesis emerged, peptides of random sequences were plausible on early Earth. This was made possible by different sources of amino acid delivery and synthesis, as well as their condensation under a variety of conditions. Early peptides and proteins probably exhibited distinct compositions, enriched in small aliphatic and acidic residues. An increase in abundance of amino acids with larger side chains and canonical basic groups was most likely dependent on the emergence of their more challenging (bio)synthesis. Pressing questions thus arise: how did this composition influence the early peptide properties, and to what extent could they contribute to early metabolism?Recent research from our group and colleagues shows that highly acidic peptides/proteins comprising only the presumably "early" amino acids are in fact competent at secondary structure formation and even possess adaptive folding characteristics such as spontaneous refoldability and chaperone independence to achieve soluble structures. Moreover, we showed that highly acidic proteins of presumably "early" composition can still bind RNA by utilizing metal ions as cofactors to bridge carboxylate and phosphoester functional groups. And finally, ancient organic cofactors were shown to be capable of binding to sequences from amino acids considered prebiotically plausible, supporting their folding properties and providing functional groups, which would nominate them as catalytic hubs of great prebiotic relevance.These findings underscore the biochemical plausibility of an early peptide/protein world devoid of more complex amino acids yet collaborating with other catalytic species. Drawing from the mechanistic properties of protein-cofactor catalysis, it is speculated here that the early peptide/protein-cofactor ensemble could facilitate a similar range of chemical reactions, albeit with lower catalytic rates. This hypothesis invites a systematic experimental test.Nonetheless, this Account does not exclude other scenarios of prebiotic-to-biotic catalysis or prioritize any specific pathways of prebiotic syntheses. The objective is to examine peptide availability, composition, and functional potential among the various factors involved in the emergence of early life.
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Affiliation(s)
- Klára Hlouchová
- Department
of Cell Biology, Faculty of Science, Charles
University, Prague 12800, Czech Republic
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Prague 16610, Czech Republic
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3
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Poddar A, Satthiyasilan N, Wang PH, Chen C, Yi R, Chandru K, Jia TZ. Reactions Driven by Primitive Nonbiological Polyesters. Acc Chem Res 2024; 57:2048-2057. [PMID: 39013010 DOI: 10.1021/acs.accounts.4c00167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
ConspectusAll life on Earth is composed of cells, which are built from and run by biological reactions and structures. These reactions and structures are generally the result of action by cellular biomolecules, which are indispensable for the function and survival of all living organisms. Specifically, biological catalysis, namely by protein enzymes, but also by other biomolecules including nucleic acids, is an essential component of life. How the biomolecules themselves that perform biological catalysis came to exist in the first place is a major unanswered question that plagues researchers to this day, which is generally the focus of the origins of life (OoL) research field. Based on current knowledge, it is generally postulated that early Earth was full of a myriad of different chemicals, and that these chemicals reacted in specific ways that led to the emergence of biochemistry, cells, and later, life. In particular, a significant part of OoL research focuses on the synthesis, evolution, and function of biomolecules potentially present under early Earth conditions, as a way to understand their eventual transition into modern life. However, this narrative overlooks possibilities that other molecules contributed to the OoL, as while biomolecules that led to life were certainly present on early Earth, at the same time, other molecules that may not have strict, direct biological lineage were also widely and abundantly present. For example, hydroxy acids, although playing a role in metabolism or as parts of certain biological structures, are not generally considered to be as essential to modern biology as amino acids (a chemically similar monomer), and thus research in the OoL field tends to perhaps focus more on amino acids than hydroxy acids. However, their likely abundance on early Earth coupled with their ability to spontaneously condense into polymers (i.e., polyesters) make hydroxy acids, and their subsequent products, functions, and reactions, a reasonable target of investigation for prebiotic chemists. Whether "non-biological" hydroxy acids or polyesters can contribute to the emergence of life on early Earth is an inquiry that deserves attention within the OoL community, as this knowledge can also contribute to our understanding of the plausibility of extraterrestrial life that does not exactly use the biochemical set found in terrestrial organisms. While some demonstrations have been made with respect to compartment assembly, compartmentalization, and growth of primitive polyester-based systems, whether these "non-biological" polymers can contribute any catalytic function and/or drive primitive reactions is still an important step toward the development of early life. Here, we review research both from the OoL field as well as from industry and applied sciences regarding potential catalysis or reaction driven by "non-biological" polyesters in various forms: as linear polymers, as hyperbranched polyesters, and as membraneless microdroplets.
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Affiliation(s)
- Arunava Poddar
- Blue Marble Space Institute of Science, 600 First Ave, Floor 1, Seattle, Washington 98104, United States
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country, Areatza Pasealekua, 48620 Plentzia Bizkaia, Basque Country, Spain
| | - Nirmell Satthiyasilan
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia, Bandar Baru Bangi, Selangor 43600, Malaysia
| | - Po-Hsiang Wang
- Graduate Institute of Environmental Engineering, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan 32001, Taiwan (Republic of China)
- Department of Chemical and Materials Engineering, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan 32001, Taiwan (R.O.C.)
| | - Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ruiqin Yi
- State Key Laboratory of Isotope Geochemistry and Chinese Academy of Sciences Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia, Bandar Baru Bangi, Selangor 43600, Malaysia
- Polymer Research Center (PORCE), Faculty of Science and Technology, National University of Malaysia, Bandar Baru Bangi, Selangor 43600, Malaysia
| | - Tony Z Jia
- Blue Marble Space Institute of Science, 600 First Ave, Floor 1, Seattle, Washington 98104, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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Castanedo LAM, Matta CF. Prebiotic N-(2-Aminoethyl)-Glycine (AEG)-Assisted Synthesis of Proto-RNA? J Mol Evol 2024:10.1007/s00239-024-10185-w. [PMID: 39052031 DOI: 10.1007/s00239-024-10185-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 06/23/2024] [Indexed: 07/27/2024]
Abstract
Quantum mechanical calculations are used to explore the thermodynamics of possible prebiotic synthesis of the building blocks of nucleic acids. Different combinations of D-ribofuranose (Ribf) and N-(2-aminoethyl)-glycine (AEG) (trifunctional connectors (TCs)); the nature of the Ribf, its anomeric form, and its ring puckering (conformation); and the nature of the nucleobases (recognition units (RUs)) are considered. The combinatorial explosion of possible nucleosides has been drastically reduced on physicochemical grounds followed by a detailed thermodynamic evaluation of alternative synthetic pathways. The synthesis of nucleosides containing N-(2-aminoethyl)-glycine (AEG) is predicted to be thermodynamically favored suggesting a possible role of AEG as a component of an ancestral proto-RNA that may have preceded today's nucleic acids. A new pathway for the building of free nucleotides (exemplified by 5'-uridine monophosphate (UMP)) and of AEG dipeptides is proposed. This new pathway leads to a spontaneous formation of free UMP assisted by an AEG nucleoside in an aqueous environment. This appears to be a workaround to the "water problem" that prohibits the synthesis of nucleotides in water.
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Affiliation(s)
- Lázaro A M Castanedo
- Department of Chemistry, Saint Mary's University, Halifax, NS, B3H 3C3, Canada
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, NS, B3M 2J6, Canada
| | - Chérif F Matta
- Department of Chemistry, Saint Mary's University, Halifax, NS, B3H 3C3, Canada.
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, NS, B3M 2J6, Canada.
- Département de Chimie, Université Laval, Québec, QC, G1V 0A6, Canada.
- Department of Chemistry, Dalhousie University, Halifax, NS, B3H 4J3, Canada.
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5
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Wei W, Chu F, Chen G, Zhou S, Sun C, Feng H, Pan Y. Prebiotic Formation of Peptides Through Bubbling and Arc Plasma. Chemistry 2024; 30:e202401809. [PMID: 38802327 DOI: 10.1002/chem.202401809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
The abiotic synthesis of peptides, widely regarded as one of the key chemical reactions on the prebiotic Earth, is thermodynamically constrained in solution. Herein, a simulation of the lightning phenomenon on the sea surface using bubble bursting and arc plasma under ambient conditions enables dipeptide formation of six amino acids with conversion ratios ranging from 2.6 % to 25.5 %. Additionally, we observed the formation of biologically active tripeptides and investigated the stereoselectivity of the dipeptide formation reaction. By utilizing a mixture of 20 amino acids in the reaction, 102 possible dipeptides were generated. These results establish experimental constructions to mimic achievable prebiotic conditions and provide a credible pathway for endogenous biopolymer synthesis on prebiotic Earth.
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Affiliation(s)
- Wei Wei
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - Fengjian Chu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Guanru Chen
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - Shiwen Zhou
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - Cuirong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hongru Feng
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
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6
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Smokers IB, Visser BS, Slootbeek AD, Huck WTS, Spruijt E. How Droplets Can Accelerate Reactions─Coacervate Protocells as Catalytic Microcompartments. Acc Chem Res 2024; 57:1885-1895. [PMID: 38968602 PMCID: PMC11256357 DOI: 10.1021/acs.accounts.4c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/24/2024] [Accepted: 06/03/2024] [Indexed: 07/07/2024]
Abstract
ConspectusCoacervates are droplets formed by liquid-liquid phase separation (LLPS) and are often used as model protocells-primitive cell-like compartments that could have aided the emergence of life. Their continued presence as membraneless organelles in modern cells gives further credit to their relevance. The local physicochemical environment inside coacervates is distinctly different from the surrounding dilute solution and offers an interesting microenvironment for prebiotic reactions. Coacervates can selectively take up reactants and enhance their effective concentration, stabilize products, destabilize reactants and lower transition states, and can therefore play a similar role as micellar catalysts in providing rate enhancement and selectivity in reaction outcome. Rate enhancement and selectivity must have been essential for the origins of life by enabling chemical reactions to occur at appreciable rates and overcoming competition from hydrolysis.In this Accounts, we dissect the mechanisms by which coacervate protocells can accelerate reactions and provide selectivity. These mechanisms can similarly be exploited by membraneless organelles to control cellular processes. First, coacervates can affect the local concentration of reactants and accelerate reactions by copartitioning of reactants or exclusion of a product or inhibitor. Second, the local environment inside the coacervate can change the energy landscape for reactions taking place inside the droplets. The coacervate is more apolar than the surrounding solution and often rich in charged moieties, which can affect the stability of reactants, transition states and products. The crowded nature of the droplets can favor complexation of large molecules such as ribozymes. Their locally different proton and water activity can facilitate reactions involving a (de)protonation step, condensation reactions and reactions that are sensitive to hydrolysis. Not only the coacervate core, but also the surface can accelerate reactions and provides an interesting site for chemical reactions with gradients in pH, water activity and charge. The coacervate is often rich in catalytic amino acids and can localize catalysts like divalent metal ions, leading to further rate enhancement inside the droplets. Lastly, these coacervate properties can favor certain reaction pathways, and thereby give selectivity over the reaction outcome.These mechanisms are further illustrated with a case study on ribozyme reactions inside coacervates, for which there is a fine balance between concentration and reactivity that can be tuned by the coacervate composition. Furthermore, coacervates can both catalyze ribozyme reactions and provide product selectivity, demonstrating that coacervates could have functioned as enzyme-like catalytic microcompartments at the origins of life.
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Affiliation(s)
- Iris B.
A. Smokers
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6523 AJ Nijmegen, The Netherlands
| | - Brent S. Visser
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6523 AJ Nijmegen, The Netherlands
| | - Annemiek D. Slootbeek
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6523 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6523 AJ Nijmegen, The Netherlands
| | - Evan Spruijt
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6523 AJ Nijmegen, The Netherlands
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7
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Moreno A, Bonduelle C. New Insights on the Chemical Origin of Life: The Role of Aqueous Polymerization of N-carboxyanhydrides (NCA). Chempluschem 2024; 89:e202300492. [PMID: 38264807 DOI: 10.1002/cplu.202300492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/29/2023] [Indexed: 01/25/2024]
Abstract
At the origin, the emergence of proteins was based on crucial prebiotic stages in which simple amino acids-based building blocks spontaneously evolved from the prebiotic soup into random proto-polymers called protoproteins. Despite advances in modern peptide synthesis, these prebiotic chemical routes to protoproteins remain puzzling. We discuss in this perspective how polymer science and systems chemistry are reaching a point of convergence in which simple monomers called N-carboxyanhydrides would be able to form such protoproteins via the emergence of a protometabolic cycle involving aqueous polymerization and featuring macromolecular Darwinism behavior.
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Affiliation(s)
- Abel Moreno
- Instituto de Quimica, UNAM, Ciudad Universitaria, Coyoacan, 04510, Mexico DF
| | - Colin Bonduelle
- CNRS, Bordeaux INP, LCPO UMR5629, Univ. Bordeaux, 33600, Pessac, France
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8
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Kocher CD, Dill KA. The prebiotic emergence of biological evolution. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240431. [PMID: 39050718 PMCID: PMC11265915 DOI: 10.1098/rsos.240431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/10/2024] [Indexed: 07/27/2024]
Abstract
The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal framework for describing any origin story for evolutionary dynamics. We find that cooperative autocatalysts, i.e. autocatalysts whose per-unit reproductive rate grows as their population increases, have the special property of being able to cross a barrier that separates their initial degradation-dominated state from a growth-dominated state with evolutionary dynamics. For some model parameters, this leap to persistent propagation is likely, not rare. We apply this analysis to the Foldcat Mechanism, wherein peptides fold and help catalyse the elongation of each other. Foldcats are found to have cooperative autocatalysis and be capable of emergent evolutionary dynamics.
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Affiliation(s)
- Charles D. Kocher
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
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9
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Wang L, Lv J, Zhang Y, Yang D. Asymmetric magnesium catalysis for important chiral scaffold synthesis. Org Biomol Chem 2024; 22:4778-4800. [PMID: 38809153 DOI: 10.1039/d4ob00521j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Magnesium catalysts are widely used in catalytic asymmetric reactions, and a series of catalytic strategies have been developed in recent years. Herein, in this review, we have tried to summarize asymmetric magnesium catalysis for the synthesis of important chiral scaffolds. Several important optically active motifs that are present in classic chiral ligands or natural products synthesized by Mg(II) catalytic methods are briefly discussed. Moreover, the representative mechanisms for different magnesium catalytic strategies, including in situ generated magnesium catalysts, are also shown in relation to synthetic routes for obtaining these important chiral scaffolds.
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Affiliation(s)
- Linqing Wang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou, 730000, China.
| | - Jiaming Lv
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou, 730000, China.
| | - Yongshuo Zhang
- Scientific Research and Innovation Expert Studio of China Inspection and Certification Group Liaoning Co., Ltd, Dalian, 116039, China
| | - Dongxu Yang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou, 730000, China.
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10
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Mori T, Sumida S, Sakata K, Shirakawa S. Efficient synthetic methods for α,β-dehydroamino acids as useful and environmentally benign building blocks in biological and materials science. Org Biomol Chem 2024; 22:4625-4636. [PMID: 38804977 DOI: 10.1039/d4ob00507d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Both natural and unnatural amino acids, peptides, and proteins are widely recognized as green and sustainable organic chemicals, not only in the field of biological sciences but also in materials science. It has been discovered that artificially designed unnatural peptides and proteins exhibit advanced properties in medical and materials science. In this context, the development of precise chemical modification methods for amino acids and peptides is acknowledged as an important research project in the field of organic synthesis. While a wide variety of modification methods for amino acid residues have been developed to artificially modify peptides and proteins, the representative methods for modifying amino acid residues have traditionally relied on the nucleophilic properties of the functionalities on the residues. In this context, the development of different modification methods using an umpolung-like approach by utilizing the electrophilic nature of amino acid derivatives appears to be very attractive. One of the promising electrophilic amino acid compounds for realizing important modification methods of amino acid derivatives is α,β-dehydroamino acids, which possess an α,β-unsaturated carbonyl structure. This review article summarizes methods for the preparation of α,β-dehydroamino acids derived from natural and unnatural amino acid derivatives. The utilities of α,β-dehydroamino acid derivatives, including peptides and proteins containing dehydroalanine units, in bioconjugations are also discussed.
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Affiliation(s)
- Taiki Mori
- Institute of Integrated Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Sao Sumida
- Institute of Integrated Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Kazuki Sakata
- Spiber Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Seiji Shirakawa
- Institute of Integrated Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
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Chatterjee A, Goswami S, Kumar R, Laha J, Das D. Emergence of a short peptide based reductase via activation of the model hydride rich cofactor. Nat Commun 2024; 15:4515. [PMID: 38802430 PMCID: PMC11130128 DOI: 10.1038/s41467-024-48930-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
In extant biology, large and complex enzymes employ low molecular weight cofactors such as dihydronicotinamides as efficient hydride transfer agents and electron carriers for the regulation of critical metabolic processes. In absence of complex contemporary enzymes, these molecular cofactors are generally inefficient to facilitate any reactions on their own. Herein, we report short peptide-based amyloid nanotubes featuring exposed arrays of cationic and hydrophobic residues that can bind small molecular weak hydride transfer agents (NaBH4) to facilitate efficient reduction of ester substrates in water. In addition, the paracrystalline amyloid phases loaded with borohydrides demonstrate recyclability, substrate selectivity and controlled reduction and surpass the capabilities of standard reducing agent such as LiAlH4. The amyloid microphases and their collaboration with small molecular cofactors foreshadow the important roles that short peptide-based assemblies might have played in the emergence of protometabolism and biopolymer evolution in prebiotic earth.
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Affiliation(s)
- Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Surashree Goswami
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Raushan Kumar
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Janmejay Laha
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India.
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12
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Rezaeerod K, Heinzmann H, Torrence AV, Patel J, Forsythe JG. Qualitative Monitoring of Proto-Peptide Condensation by Differential FTIR Spectroscopy. ACS EARTH & SPACE CHEMISTRY 2024; 8:937-944. [PMID: 38774359 PMCID: PMC11103710 DOI: 10.1021/acsearthspacechem.3c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/24/2024]
Abstract
Condensation processes such as wet-dry cycling are thought to have played significant roles in the emergence of proto-peptides. Here, we describe a simple and low-cost method, differential Fourier transform infrared (FTIR) spectroscopy, for qualitative analysis of peptide condensation products in model primordial reactions. We optimize differential FTIR for depsipeptides and apply this method to investigate their polymerization in the presence of extraterrestrial dust simulants.
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Affiliation(s)
- Keon Rezaeerod
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
| | - Hanna Heinzmann
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
- Analytical
and Bioanalytical Chemistry, Aalen University, 73430 Aalen, Germany
| | - Alexis V. Torrence
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
| | - Jui Patel
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
| | - Jay G. Forsythe
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
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13
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Nitschke W, Farr O, Gaudu N, Truong C, Guyot F, Russell MJ, Duval S. The Winding Road from Origin to Emergence (of Life). Life (Basel) 2024; 14:607. [PMID: 38792628 PMCID: PMC11123232 DOI: 10.3390/life14050607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Humanity's strive to understand why and how life appeared on planet Earth dates back to prehistoric times. At the beginning of the 19th century, empirical biology started to tackle this question yielding both Charles Darwin's Theory of Evolution and the paradigm that the crucial trigger putting life on its tracks was the appearance of organic molecules. In parallel to these developments in the biological sciences, physics and physical chemistry saw the fundamental laws of thermodynamics being unraveled. Towards the end of the 19th century and during the first half of the 20th century, the tensions between thermodynamics and the "organic-molecules-paradigm" became increasingly difficult to ignore, culminating in Erwin Schrödinger's 1944 formulation of a thermodynamics-compliant vision of life and, consequently, the prerequisites for its appearance. We will first review the major milestones over the last 200 years in the biological and the physical sciences, relevant to making sense of life and its origins and then discuss the more recent reappraisal of the relative importance of metal ions vs. organic molecules in performing the essential processes of a living cell. Based on this reassessment and the modern understanding of biological free energy conversion (aka bioenergetics), we consider that scenarios wherein life emerges from an abiotic chemiosmotic process are both thermodynamics-compliant and the most parsimonious proposed so far.
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Affiliation(s)
- Wolfgang Nitschke
- BIP (UMR 7281), CNRS, Aix-Marseille-University, 13009 Marseille, France; (O.F.); (N.G.); (C.T.); (S.D.)
| | - Orion Farr
- BIP (UMR 7281), CNRS, Aix-Marseille-University, 13009 Marseille, France; (O.F.); (N.G.); (C.T.); (S.D.)
- CINaM, CNRS, Aix-Marseille-University, 13009 Marseille, France
| | - Nil Gaudu
- BIP (UMR 7281), CNRS, Aix-Marseille-University, 13009 Marseille, France; (O.F.); (N.G.); (C.T.); (S.D.)
| | - Chloé Truong
- BIP (UMR 7281), CNRS, Aix-Marseille-University, 13009 Marseille, France; (O.F.); (N.G.); (C.T.); (S.D.)
| | - François Guyot
- IMPMC (UMR 7590), CNRS, Sorbonne University, 75005 Paris, France;
| | - Michael J. Russell
- Dipartimento di Chimica, Università degli Studi di Torino, 10124 Torino, Italy;
| | - Simon Duval
- BIP (UMR 7281), CNRS, Aix-Marseille-University, 13009 Marseille, France; (O.F.); (N.G.); (C.T.); (S.D.)
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14
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Samrout OE, Berlier G, Lambert JF. Amino Acid Polymerization on Silica Surfaces. Chempluschem 2024; 89:e202300642. [PMID: 38226922 DOI: 10.1002/cplu.202300642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.
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Affiliation(s)
- Ola El Samrout
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Gloria Berlier
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, LRS, Sorbonne Université Place Jussieu, 75005, Paris, France
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15
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Zhang L, Ying J. Amino acid analogues provide multiple plausible pathways to prebiotic peptides. J R Soc Interface 2024; 21:20240014. [PMID: 38715323 PMCID: PMC11077012 DOI: 10.1098/rsif.2024.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Prebiotic peptide synthesis has consistently been a prominent topic within the field of the origin of life. While research predominantly centres on the 20 classical amino acids, the synthesis process encounters significant thermodynamic barriers. Consequently, amino acid analogues are being explored as potential building blocks for prebiotic peptide synthesis. This review delves into the pathway of polypeptide formation, identifying specific amino acid analogues that might have existed on early Earth, potentially participating in peptide synthesis and chemical evolution. Moreover, considering the complexity and variability of the environment on early Earth, we propose the plausibility of coevolution between amino acids and their analogues.
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Affiliation(s)
- Li Zhang
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, People's Republic of China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, People's Republic of China
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16
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Cohen ZR, Todd ZR, Maibaum L, Catling DC, Black RA. Stabilization of Prebiotic Vesicles by Peptides Depends on Sequence and Chirality: A Mechanism for Selection of Protocell-Associated Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8971-8980. [PMID: 38629792 DOI: 10.1021/acs.langmuir.4c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Cells require oligonucleotides and polypeptides with specific, homochiral sequences to perform essential functions, but it is unclear how such oligomers were selected from random sequences at the origin of life. Cells were probably preceded by simple compartments such as fatty acid vesicles, and oligomers that increased the stability, growth, or division of vesicles could have thereby increased in frequency. We therefore tested whether prebiotic peptides alter the stability or growth of vesicles composed of a prebiotic fatty acid. We find that three of 15 dipeptides tested reduce salt-induced flocculation of vesicles. All three contain leucine, and increasing their length increases the efficacy. Also, leucine-leucine but not alanine-alanine increases the size of vesicles grown by multiple additions of micelles. In a molecular simulation, leucine-leucine docks to the membrane, with the side chains inserted into the hydrophobic core of the bilayer, while alanine-alanine fails to dock. Finally, the heterochiral forms of leucine-leucine, at a high concentration, rapidly shrink the vesicles and make them leakier and less stable to high pH than the homochiral forms do. Thus, prebiotic peptide-membrane interactions influence the flocculation, growth, size, leakiness, and pH stability of prebiotic vesicles, with differential effects due to sequence, length, and chirality. These differences could lead to a population of vesicles enriched for peptides with beneficial sequence and chirality, beginning selection for the functional oligomers that underpin life.
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Affiliation(s)
- Zachary R Cohen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Zoe R Todd
- Department of Earth and Space Science, University of Washington, Seattle, Washington 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - David C Catling
- Department of Earth and Space Science, University of Washington, Seattle, Washington 98195, United States
| | - Roy A Black
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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17
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Vijayakanth T, Dasgupta S, Ganatra P, Rencus-Lazar S, Desai AV, Nandi S, Jain R, Bera S, Nguyen AI, Gazit E, Misra R. Peptide hydrogen-bonded organic frameworks. Chem Soc Rev 2024; 53:3640-3655. [PMID: 38450536 DOI: 10.1039/d3cs00648d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Hydrogen-bonded porous frameworks (HPFs) are versatile porous crystalline frameworks with diverse applications. However, designing chiral assemblies or biocompatible materials poses significant challenges. Peptide-based hydrogen-bonded porous frameworks (P-HPFs) are an exciting alternative to conventional HPFs due to their intrinsic chirality, tunability, biocompatibility, and structural diversity. Flexible, ultra-short peptide-based P-HPFs (composed of 3 or fewer amino acids) exhibit adaptable porous topologies that can accommodate a variety of guest molecules and capture hazardous greenhouse gases. Longer, folded peptides present challenges and opportunities in designing P-HPFs. This review highlights recent developments in P-HPFs using ultra-short peptides, folded peptides, and foldamers, showcasing their utility for gas storage, chiral recognition, chiral separation, and medical applications. It also addresses design challenges and future directions in the field.
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Affiliation(s)
- Thangavel Vijayakanth
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-6997801, Israel.
| | - Sneha Dasgupta
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, S.A.S. Nagar (Mohali) 160062, India.
| | - Pragati Ganatra
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA.
| | - Sigal Rencus-Lazar
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-6997801, Israel.
| | - Aamod V Desai
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Shyamapada Nandi
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, 600127, Chennai, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, S.A.S. Nagar (Mohali) 160062, India.
| | - Santu Bera
- Department of Chemistry, Ashoka University, Sonipat, Haryana 131029, India
| | - Andy I Nguyen
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA.
| | - Ehud Gazit
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-6997801, Israel.
- Sagol School of Neuroscience, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Rajkumar Misra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, S.A.S. Nagar (Mohali) 160062, India.
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18
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Krasnokutski SA, Jäger C, Henning T, Geffroy C, Remaury QB, Poinot P. Formation of extraterrestrial peptides and their derivatives. SCIENCE ADVANCES 2024; 10:eadj7179. [PMID: 38630826 PMCID: PMC11023503 DOI: 10.1126/sciadv.adj7179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
The formation of protein precursors, due to the condensation of atomic carbon under the low-temperature conditions of the molecular phases of the interstellar medium, opens alternative pathways for the origin of life. We perform peptide synthesis under conditions prevailing in space and provide a comprehensive analytic characterization of its products. The application of 13C allowed us to confirm the suggested pathway of peptide formation that proceeds due to the polymerization of aminoketene molecules that are formed in the C + CO + NH3 reaction. Here, we address the question of how the efficiency of peptide production is modified by the presence of water molecules. We demonstrate that although water slightly reduces the efficiency of polymerization of aminoketene, it does not prevent the formation of peptides.
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Affiliation(s)
- Serge A. Krasnokutski
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena, Helmholtzweg 3, D-07743 Jena, Germany
| | - Cornelia Jäger
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena, Helmholtzweg 3, D-07743 Jena, Germany
| | | | - Claude Geffroy
- Institut de Chimie des Milieux et Materiaux de Poitiers, University of Poitiers, UMR CNRS 7285, France
| | - Quentin B. Remaury
- Institut de Chimie des Milieux et Materiaux de Poitiers, University of Poitiers, UMR CNRS 7285, France
| | - Pauline Poinot
- Institut de Chimie des Milieux et Materiaux de Poitiers, University of Poitiers, UMR CNRS 7285, France
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19
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Ranganath VA, Maity I. Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises. Angew Chem Int Ed Engl 2024; 63:e202318134. [PMID: 38226567 DOI: 10.1002/anie.202318134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.
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Affiliation(s)
- Vinay Ambekar Ranganath
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
| | - Indrajit Maity
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
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20
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Mustieles-del-Ser P, Ruano-Gallego D, Parro V. Immunoanalytical Detection of Conserved Peptides: Refining the Universe of Biomarker Targets in Planetary Exploration. Anal Chem 2024; 96:4764-4773. [PMID: 38484023 PMCID: PMC10975014 DOI: 10.1021/acs.analchem.3c04165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 02/19/2024] [Indexed: 03/27/2024]
Abstract
Ancient peptides are remnants of early biochemistry that continue to play pivotal roles in current proteins. They are simple molecules yet complex enough to exhibit independent functions, being products of an evolved biochemistry at the interface of life and nonlife. Their adsorption to minerals may contribute to their stabilization and preservation over time. To investigate the feasibility of conserved peptide sequences and structures as target biomarkers for the search for life on Mars or other planetary bodies, we conducted a bioinformatics selection of well-conserved ancient peptides and produced polyclonal antibodies for their detection using fluorescence microarray immunoassays. Additionally, we explored how adsorbing peptides to Mars-representative minerals to form organomineral complexes could affect their immunological detection. The results demonstrated that the selected peptides exhibited autonomous folding, with some of them regaining their structure, even after denaturation. Furthermore, their cognate antibodies detected their conformational features regardless of amino acid sequences, thereby broadening the spectrum of target peptide sequences. While certain antibodies displayed unspecific binding to bare minerals, we validated that peptide-mineral complexes can be detected using sandwich immunoassays, as confirmed through desorption and competitive assays. Consequently, we conclude that the diversity of peptide sequences and structures suitable for use as target biomarkers in astrobiology can be constrained to a few well conserved sets, and they can be detected even if they are adsorbed in organomineral complexes.
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Affiliation(s)
- Pedro Mustieles-del-Ser
- Centro
de Astrobiología (CAB) INTA-CSIC, Torrejón de Ardoz 28850, Spain
- Departments
of Physics and Mathematics, and Automatics, Universidad de Alcalá (UAH), Alcalá de Henares 28805, Spain
| | | | - Víctor Parro
- Centro
de Astrobiología (CAB) INTA-CSIC, Torrejón de Ardoz 28850, Spain
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21
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Maguire OR, Smokers IBA, Oosterom BG, Zheliezniak A, Huck WTS. A Prebiotic Precursor to Life's Phosphate Transfer System with an ATP Analog and Histidyl Peptide Organocatalysts. J Am Chem Soc 2024; 146:7839-7849. [PMID: 38448161 PMCID: PMC10958518 DOI: 10.1021/jacs.4c01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/08/2024]
Abstract
Biochemistry is dependent upon enzyme catalysts accelerating key reactions. At the origin of life, prebiotic chemistry must have incorporated catalytic reactions. While this would have yielded much needed amplification of certain reaction products, it would come at the possible cost of rapidly depleting the high energy molecules that acted as chemical fuels. Biochemistry solves this problem by combining kinetically stable and thermodynamically activated molecules (e.g., ATP) with enzyme catalysts. Here, we demonstrate a prebiotic phosphate transfer system involving an ATP analog (imidazole phosphate) and histidyl peptides, which function as organocatalytic enzyme analogs. We demonstrate that histidyl peptides catalyze phosphorylations via a phosphorylated histidyl intermediate. We integrate these histidyl-catalyzed phosphorylations into a complete prebiotic scenario whereby inorganic phosphate is incorporated into organic compounds though physicochemical wet-dry cycles. Our work demonstrates a plausible system for the catalyzed production of phosphorylated compounds on the early Earth and how organocatalytic peptides, as enzyme precursors, could have played an important role in this.
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Affiliation(s)
- Oliver R. Maguire
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Iris B. A. Smokers
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Bob G. Oosterom
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Alla Zheliezniak
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
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22
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Rodriguez LE, Altair T, Hermis NY, Jia TZ, Roche TP, Steller LH, Weber JM. Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth. ASTROBIOLOGY 2024; 24:S76-S106. [PMID: 38498817 DOI: 10.1089/ast.2021.0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.
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Affiliation(s)
- Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA. (Current)
| | - Thiago Altair
- Institute of Chemistry of São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Department of Chemistry, College of the Atlantic, Bar Harbor, Maine, USA. (Current)
| | - Ninos Y Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Physics and Space Sciences, University of Granada, Granada Spain. (Current)
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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23
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Li N, Pan C, Lu G, Pan H, Han Y, Wang K, Jin P, Liu Q, Jiang J. Hydrophobic Trinuclear Copper Cluster-Containing Organic Framework for Synergetic Electrocatalytic Synthesis of Amino Acids. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311023. [PMID: 38050947 DOI: 10.1002/adma.202311023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/22/2023] [Indexed: 12/07/2023]
Abstract
Electrocatalytic synthesis of amino acids provides a promising green and efficient pathway to manufacture the basic substances of life. Herein, reaction of 2,5-perfluroalkyl-terepthalohydrazide and tris(4-µ2 -O-carboxaldehyde-pyrazolato-N, N')-tricopper affords a crystalline trinuclear copper cluster-containing organic framework, named F-Cu3 -OF. Incorporation of abundant hydrophobic perfluroalkyl groups inside the channels of F-Cu3 -OF is revealed to successfully suppress the hydrogen evolution reaction via preventing H+ cation with large polarity from the framework of F-Cu3 -OF and in turn increasing the adsorption of other substrates with relatively small polarity like NO3 - and keto acids on the active sites. The copper atoms with short distance in the trinuclear copper clusters of F-Cu3 -OF enable simultaneous activization of NO3 - and keto acids, facilitating the following synergistic and efficient C─N coupling on the basis of in situ spectroscopic investigations together with theoretical calculation. Combination of these effects leads to efficient electroproduction of various amino acids including glycine, alanine, leucine, valine, and phenylalanine from NO3 - and keto acids with a Faraday efficiency of 42%-71% and a yield of 187-957 µmol cm-2 h-1 , representing the thus far best performance. This work shall be helpful for developing economical, eco-friendly, and high-efficiency strategy for the production of amino acids and other life substances.
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Affiliation(s)
- Ning Li
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Chenliang Pan
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Guang Lu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Houhe Pan
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yuesheng Han
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Kang Wang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Peng Jin
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Qingyun Liu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Jianzhuang Jiang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
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24
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Qiu L, Cooks RG. Oxazolone mediated peptide chain extension and homochirality in aqueous microdroplets. Proc Natl Acad Sci U S A 2024; 121:e2309360120. [PMID: 38165938 PMCID: PMC10786291 DOI: 10.1073/pnas.2309360120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/20/2023] [Indexed: 01/04/2024] Open
Abstract
Peptide formation from amino acids is thermodynamically unfavorable but a recent study provided evidence that the reaction occurs at the air/solution interfaces of aqueous microdroplets. Here, we show that i) the suggested amino acid complex in microdroplets undergoes dehydration to form oxazolone; ii) addition of water to oxazolone forms the dipeptide; and iii) reaction of oxazolone with other amino acids forms tripeptides. Furthermore, the chirality of the reacting amino acids is preserved in the oxazolone product, and strong chiral selectivity is observed when converting the oxazolone to tripeptide. This last fact ensures that optically impure amino acids will undergo chain extension to generate pure homochiral peptides. Peptide formation in bulk by wet-dry cycling shares a common pathway with the microdroplet reaction, both involving the oxazolone intermediate.
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Affiliation(s)
- Lingqi Qiu
- Department of Chemistry, Purdue University, West Lafayette, IN47907
| | - R. Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN47907
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25
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Cao S, Ivanov T, Heuer J, Ferguson CTJ, Landfester K, Caire da Silva L. Dipeptide coacervates as artificial membraneless organelles for bioorthogonal catalysis. Nat Commun 2024; 15:39. [PMID: 38169470 PMCID: PMC10761997 DOI: 10.1038/s41467-023-44278-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Artificial organelles can manipulate cellular functions and introduce non-biological processes into cells. Coacervate droplets have emerged as a close analog of membraneless cellular organelles. Their biomimetic properties, such as molecular crowding and selective partitioning, make them promising components for designing cell-like materials. However, their use as artificial organelles has been limited by their complex molecular structure, limited control over internal microenvironment properties, and inherent colloidal instability. Here we report the design of dipeptide coacervates that exhibit enhanced stability, biocompatibility, and a hydrophobic microenvironment. The hydrophobic character facilitates the encapsulation of hydrophobic species, including transition metal-based catalysts, enhancing their efficiency in aqueous environments. Dipeptide coacervates carrying a metal-based catalyst are incorporated as active artificial organelles in cells and trigger an internal non-biological chemical reaction. The development of coacervates with a hydrophobic microenvironment opens an alternative avenue in the field of biomimetic materials with applications in catalysis and synthetic biology.
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Affiliation(s)
- Shoupeng Cao
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Tsvetomir Ivanov
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Julian Heuer
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Calum T J Ferguson
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Lucas Caire da Silva
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany.
- Department of Chemistry, McGill University, Montreal, H3A 0B8, Canada.
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26
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Singh A, Goswami S, Singh P, Das D. Exploitation of Catalytic Dyads by Short Peptide-Based Nanotubes for Enantioselective Covalent Catalysis. Angew Chem Int Ed Engl 2023; 62:e202315716. [PMID: 37922218 DOI: 10.1002/anie.202315716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/05/2023]
Abstract
Extant enzymes with precisely arranged multiple residues in their three-dimensional binding pockets are capable of exhibiting remarkable stereoselectivity towards a racemic mixture of substrates. However, how early protein folds that possibly featured short peptide fragments facilitated enantioselective catalytic transformations important for the emergence of homochirality still remains an intriguing open question. Herein, enantioselective hydrolysis was shown by short peptide-based nanotubes that could exploit multiple solvent-exposed residues to create chiral binding grooves to covalently interact and subsequently hydrolyse one enantiomer preferentially from a racemic pool. Single or double-site chiral mutations led to opposite but diminished and even complete loss of enantioselectivities, suggesting the critical roles of the binding enthalpies from the precise localization of the active site residues, despite the short sequence lengths. This work underpins the enantioselective catalytic prowess of short peptide-based folds and argues their possible role in the emergence of homochiral chemical inventory.
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Affiliation(s)
- Abhishek Singh
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Surashree Goswami
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Priyanshu Singh
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
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27
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Kedia H, Pan D, Slotine JJ, England JL. Drive-specific selection in multistable mechanical networks. J Chem Phys 2023; 159:214106. [PMID: 38047510 DOI: 10.1063/5.0171993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/05/2023] [Indexed: 12/05/2023] Open
Abstract
Systems with many stable configurations abound in nature, both in living and inanimate matter, encoding a rich variety of behaviors. In equilibrium, a multistable system is more likely to be found in configurations with lower energy, but the presence of an external drive can alter the relative stability of different configurations in unexpected ways. Living systems are examples par excellence of metastable nonequilibrium attractors whose structure and stability are highly dependent on the specific form and pattern of the energy flow sustaining them. Taking this distinctively lifelike behavior as inspiration, we sought to investigate the more general physical phenomenon of drive-specific selection in nonequilibrium dynamics. To do so, we numerically studied driven disordered mechanical networks of bistable springs possessing a vast number of stable configurations arising from the two stable rest lengths of each spring, thereby capturing the essential physical properties of a broad class of multistable systems. We found that there exists a range of forcing amplitudes for which the attractor states of driven disordered multistable mechanical networks are fine-tuned with respect to the pattern of external forcing to have low energy absorption from it. Additionally, we found that these drive-specific attractor states are further stabilized by precise matching between the multidimensional shape of their orbit and that of the potential energy well they inhabit. Lastly, we showed evidence of drive-specific selection in an experimental system and proposed a general method to estimate the range of drive amplitudes for drive-specific selection.
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Affiliation(s)
- Hridesh Kedia
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Deng Pan
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jean-Jacques Slotine
- Nonlinear Systems Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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28
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Dai K, Pol MD, Saile L, Sharma A, Liu B, Thomann R, Trefs JL, Qiu D, Moser S, Wiesler S, Balzer BN, Hugel T, Jessen HJ, Pappas CG. Spontaneous and Selective Peptide Elongation in Water Driven by Aminoacyl Phosphate Esters and Phase Changes. J Am Chem Soc 2023; 145:26086-26094. [PMID: 37992133 DOI: 10.1021/jacs.3c07918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Nature chose phosphates to activate amino acids, where reactive intermediates and complex machinery drive the construction of polyamides. Outside of biology, the pathways and mechanisms that allow spontaneous and selective peptide elongation in aqueous abiotic systems remain unclear. Herein we work to uncover those pathways by following the systems chemistry of aminoacyl phosphate esters, synthetic counterparts of aminoacyl adenylates. The phosphate esters act as solubility tags, making hydrophobic amino acids and their oligomers soluble in water and enabling selective elongation and different pathways to emerge. Thus, oligomers up to dodecamers were synthesized in one flask and on the minute time scale, where consecutive additions activated autonomous phase changes. Depending on the pathway, the resulting phases initially carry nonpolar peptides and amphiphilic oligomers containing phosphate esters. During elongation and phosphate release, shorter oligomers dominate in solution, while the aggregated phase favors the presence of longer oligomers due to their self-assembly propensity. Furthermore we demonstrated that the solution phases can be isolated and act as a new environment for continuous elongation, by adding various phosphate esters. These findings suggest that the systems chemistry of aminoacyl phosphate esters can activate a selection mechanism for peptide bond formation by merging aqueous synthesis and self-assembly.
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Affiliation(s)
- Kun Dai
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Mahesh D Pol
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Lenard Saile
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Arti Sharma
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bin Liu
- College of Materials and Chemical Engineering, China Three Gorges University, Yichang, Hubei 443002, China
| | - Ralf Thomann
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Strasse 21, 79104 Freiburg, Germany
| | - Johanna L Trefs
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Sandra Moser
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Stefan Wiesler
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Bizan N Balzer
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Strasse 21, 79104 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Thorsten Hugel
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Henning J Jessen
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Charalampos G Pappas
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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29
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Edri R, Fisher S, Menor-Salvan C, Williams LD, Frenkel-Pinter M. Assembly-driven protection from hydrolysis as key selective force during chemical evolution. FEBS Lett 2023; 597:2879-2896. [PMID: 37884438 DOI: 10.1002/1873-3468.14766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
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.
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Affiliation(s)
- Rotem Edri
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Sarah Fisher
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Cesar Menor-Salvan
- Department of Biología de Sistemas, Universidad de Alcalá, Madrid, Spain
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Moran Frenkel-Pinter
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
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30
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Catalanotto C, Barbato C, Cogoni C, Benelli D. The RNA-Binding Function of Ribosomal Proteins and Ribosome Biogenesis Factors in Human Health and Disease. Biomedicines 2023; 11:2969. [PMID: 38001969 PMCID: PMC10669870 DOI: 10.3390/biomedicines11112969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The ribosome is a macromolecular complex composed of RNA and proteins that interact through an integrated and interconnected network to preserve its ancient core activities. In this review, we emphasize the pivotal role played by RNA-binding proteins as a driving force in the evolution of the current form of the ribosome, underscoring their importance in ensuring accurate protein synthesis. This category of proteins includes both ribosomal proteins and ribosome biogenesis factors. Impairment of their RNA-binding activity can also lead to ribosomopathies, which is a group of disorders characterized by defects in ribosome biogenesis that are detrimental to protein synthesis and cellular homeostasis. A comprehensive understanding of these intricate processes is essential for elucidating the mechanisms underlying the resulting diseases and advancing potential therapeutic interventions.
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Affiliation(s)
- Caterina Catalanotto
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
| | - Christian Barbato
- National Research Council (CNR), Department of Sense Organs DOS, Institute of Biochemistry and Cell Biology (IBBC), Sapienza University of Rome, 00185 Rome, Italy;
| | - Carlo Cogoni
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
| | - Dario Benelli
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
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31
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Harold SE, Warf SL, Shields GC. Prebiotic dimer and trimer peptide formation in gas-phase atmospheric nanoclusters of water. Phys Chem Chem Phys 2023; 25:28517-28532. [PMID: 37847315 DOI: 10.1039/d3cp02915h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Insight into the origin of prebiotic molecules is key to our understanding of how living systems evolved into the complex network of biological processes on Earth. By modelling diglycine and triglycine peptide formation in the prebiotic atmosphere, we provide a plausible pathway for peptide growth. By examining different transition states (TSs), we conclude that the formation of diglycine and triglycine in atmospheric nanoclusters of water in the prebiotic atmosphere kinetically favors peptide growth by an N-to-C synthesis of glycines through a trans conformation. Addition of water stabilizes the TS structures and lowers the Gibbs free activation energies. At temperatures that model the prebiotic atmosphere, the free energies of activation with a six water nanocluster as part of the TS are predicted to be 16 kcal mol-1 relative to the prereactive complex. Examination of the trans vs. cis six water transition states reveals that a homodromic water network that maximizes the acceptor/donor nature of the six waters is responsible for enhanced kinetic favorability of the trans N-to-C pathway. Compared to the non-hydrated trans TS, the trans six-water TS accelerates the reaction of diglycine and glycine to form triglycine by 13 orders of magnitude at 217 K. Nature uses the trans N-to-C pathway to synthesize proteins in the ribosome, and we note the similarities in hydrogen bond stabilization between the transition state for peptide synthesis in the ribosome and the transition states formed in nanoclusters of water in the same pathway. These results support the hypothesis that small oligomers formed in the prebiotic atmosphere and rained onto earth's surface.
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Affiliation(s)
- Shannon E Harold
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
| | - Skyler L Warf
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
| | - George C Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
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32
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Farnsworth KD. How biological codes break causal chains to enable autonomy for organisms. Biosystems 2023; 232:105013. [PMID: 37657747 DOI: 10.1016/j.biosystems.2023.105013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/03/2023]
Abstract
Autonomy, meaning freedom from exogenous control, requires independence of both constitution and cybernetic regulation. Here, the necessity of biological codes to achieve both is explained, assuming that Aristotelian efficient cause is 'formal cause empowered by physical force'. Constitutive independence requires closure to efficient causation (in the Rosen sense); cybernetic independence requires transformation of cause-effect into signal-response relations at the organism boundary; the combination of both kinds of independence enables adaptation and evolution. Codes and cyphers translate information from one form of physical embodiment (domain) to another. Because information can only contribute as formal cause to efficient cause within the domain of its embodiment, translation can extend or restrict the range over which information is effective. Closure to efficient causation requires internalised information to be isolated from the cycle of efficient causes that it informs: e.g. Von Neumann self-replicator requires a (template) source of information that is causally isolated from the physical replication system. Life operationalises this isolation with the genetic code translating from the (isolated) domain of codons to that of protein interactions. Separately, cybernetic freedom is achieved at the cell boundary because transducers, which embody molecular coding, translate exogenous information into a domain where it no longer has the power of efficient cause. Information, not efficient cause, passes through the boundary to serve as stimulus for an internally generated response. Coding further extends freedom by enabling historically accumulated information to be selectively transformed into efficient cause under internal control, leaving it otherwise stored inactive. Code-based translation thus enables selective causal isolation, controlling the flow from cause to effect. Genetic code, cell-signalling codes and, in eukaryotes, the histone code, signal sequence based protein sorting and other code-dependent processes all regulate and separate causal chains. The existence of life can be seen as an expression of the power of molecular codes to selectively isolate and thereby organise causal relations among molecular interactions to form an organism.
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Affiliation(s)
- Keith D Farnsworth
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT95DL, UK.
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33
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Boigenzahn H, González LD, Thompson JC, Zavala VM, Yin J. Kinetic Modeling and Parameter Estimation of a Prebiotic Peptide Reaction Network. J Mol Evol 2023; 91:730-744. [PMID: 37796316 DOI: 10.1007/s00239-023-10132-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/23/2023] [Indexed: 10/06/2023]
Abstract
Although our understanding of how life emerged on Earth from simple organic precursors is speculative, early precursors likely included amino acids. The polymerization of amino acids into peptides and interactions between peptides are of interest because peptides and proteins participate in complex interaction networks in extant biology. However, peptide reaction networks can be challenging to study because of the potential for multiple species and systems-level interactions between species. We developed and employed a computational network model to describe reactions between amino acids to form di-, tri-, and tetra-peptides. Our experiments were initiated with two of the simplest amino acids, glycine and alanine, mediated by trimetaphosphate-activation and drying to promote peptide bond formation. The parameter estimates for bond formation and hydrolysis reactions in the system were found to be poorly constrained due to a network property known as sloppiness. In a sloppy model, the behavior mostly depends on only a subset of parameter combinations, but there is no straightforward way to determine which parameters should be included or excluded. Despite our inability to determine the exact values of specific kinetic parameters, we could make reasonably accurate predictions of model behavior. In short, our modeling has highlighted challenges and opportunities toward understanding the behaviors of complex prebiotic chemical experiments.
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Affiliation(s)
- Hayley Boigenzahn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA
| | - Leonardo D González
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Jaron C Thompson
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Victor M Zavala
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA.
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34
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Liu X, Cheng X, Sun Y, Nie J, Cheng M, Li W, Zhao J. Peptide/glycyrrhizic acid supramolecular polymer: An emerging medical adhesive for dural sealing and repairing. Biomaterials 2023; 301:122239. [PMID: 37451001 DOI: 10.1016/j.biomaterials.2023.122239] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/24/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Medical adhesives have emerged as potential materials for sealing, hemostasis and wound repairing in modern clinical surgery. However, most of existing medical adhesives are still far away from the clinical requirements for simultaneously meeting desirable tissue adhesion, safety, biodegradability, anti-swelling property, and convenient operability. Here, we present an entirely new kind of peptide-based underwater adhesives, which are constructed via cross-linked supramolecular copolymerization between cationic short peptides and glycyrrhizic acid (GA) in an aqueous solution. We revealed the unique molecular mechanism of the peptide/GA supramolecular polymers and underlined the importance of arginine residues in the enhancement of the bulk cohesion of the peptide/GA adhesive. We thus concluded a design guideline that the peptide sequence has to be encoded with multiple arginine termini and hydrophobic residues. The resulting adhesives exhibited effective tissue adhesion, robust cohesion, low cell cytotoxicity, acceptable hemocompatibility, inappreciable inflammation response, appropriate biodegradability, and excellent anti-swelling property. More attractively, the dried peptide/GA powder was able to rapidly self-gel into adhesives by absorbing water, suggesting conveniently clinical operability. Animal experiments showed that the peptide/GA supramolecular polymers could be utilized as reliable medical adhesives for dural sealing and repairing.
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Affiliation(s)
- Xiaohuan Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun, 130012, China
| | - Xueliang Cheng
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, China
| | - Yingchuan Sun
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, China
| | - Junlian Nie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun, 130012, China
| | - Meng Cheng
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, China
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun, 130012, China.
| | - Jianwu Zhao
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, China.
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35
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Wang SM, Wang YF, Huang L, Zheng LS, Nian H, Zheng YT, Yao H, Jiang W, Wang X, Yang LP. Chiral recognition of neutral guests by chiral naphthotubes with a bis-thiourea endo-functionalized cavity. Nat Commun 2023; 14:5645. [PMID: 37704639 PMCID: PMC10499783 DOI: 10.1038/s41467-023-41390-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023] Open
Abstract
Developing chiral receptors with an endo-functionalized cavity for chiral recognition is of great significance in the field of molecular recognition. This study presents two pairs of chiral naphthotubes containing a bis-thiourea endo-functionalized cavity. Each chiral naphthotube has two homochiral centers which were fixed adjacent to the thiourea groups, causing the skeleton and thiourea groups to twist enantiomerically through chiral transfer. These chiral naphthotubes are highly effective at enantiomerically recognizing various neutral chiral molecules with an enantioselectivity up to 17.0. Furthermore, the mechanism of the chiral recognition has been revealed to be originated from differences in multiple non-covalent interactions. Various factors, such as the shape of cavities, substituents of guests, flexibility of host and binding modes are demonstrated to contribute to creating differences in the non-covalent interactions. Additionally, the driving force behind enantioselectivity is mainly attributed to enthalpic differences, and enthalpy -entropy compensation has also been observed to influence enantioselectivity.
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Affiliation(s)
- Song-Meng Wang
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Yan-Fang Wang
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Liping Huang
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Li-Shuo Zheng
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Hao Nian
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Yu-Tao Zheng
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Huan Yao
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Wei Jiang
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China.
| | - Xiaoping Wang
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China.
| | - Liu-Pan Yang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
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36
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Hong YK, Nakamoto M, Matsusaki M. Engineering metabolic cycle-inspired hydrogels with enzyme-fueled programmable transient volume changes. J Mater Chem B 2023; 11:8136-8141. [PMID: 37565488 DOI: 10.1039/d3tb00638g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
An enzyme-fueled transient volume phase transition (TVPT) of hydrogels under out-of-equilibrium conditions is reported. The approach takes inspiration from the metabolic cycle, comprising nutrient intake and anabolism/catabolism followed by waste excretion. The incorporation of methacrylic acid and acrylated trypsin in a polymeric hydrogel allowed the TVPT of the gel to be fueled by lysozyme. With the intake of lysozyme as fuel, the construction/destruction of electrostatic cross-linkages induced transient shrinkage/swelling of the gel accompanied by the depletion of lysozyme activity. The system's transient response could be flexibly programmed by adjusting not only the fuel concentration but the chemical composition of materials. The lysozyme-fueled TVPT of the gel could be exploited to transient changes in the mechanical properties of the gel. Our work opens a route toward a new class of stimuli-responsive hydrogels for biomedical applications.
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Affiliation(s)
- Young Kyoung Hong
- School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masahiko Nakamoto
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Michiya Matsusaki
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.
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Vijayakanth T, Shankar S, Finkelstein-Zuta G, Rencus-Lazar S, Gilead S, Gazit E. Perspectives on recent advancements in energy harvesting, sensing and bio-medical applications of piezoelectric gels. Chem Soc Rev 2023; 52:6191-6220. [PMID: 37585216 PMCID: PMC10464879 DOI: 10.1039/d3cs00202k] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Indexed: 08/17/2023]
Abstract
The development of next-generation bioelectronics, as well as the powering of consumer and medical devices, require power sources that are soft, flexible, extensible, and even biocompatible. Traditional energy storage devices (typically, batteries and supercapacitors) are rigid, unrecyclable, offer short-lifetime, contain hazardous chemicals and possess poor biocompatibility, hindering their utilization in wearable electronics. Therefore, there is a genuine unmet need for a new generation of innovative energy-harvesting materials that are soft, flexible, bio-compatible, and bio-degradable. Piezoelectric gels or PiezoGels are a smart crystalline form of gels with polar ordered structures that belongs to the broader family of piezoelectric material, which generate electricity in response to mechanical stress or deformation. Given that PiezoGels are structurally similar to hydrogels, they offer several advantages including intrinsic chirality, crystallinity, degree of ordered structures, mechanical flexibility, biocompatibility, and biodegradability, emphasizing their potential applications ranging from power generation to bio-medical applications. Herein, we describe recent examples of new functional PiezoGel materials employed for energy harvesting, sensing, and wound dressing applications. First, this review focuses on the principles of piezoelectric generators (PEGs) and the advantages of using hydrogels as PiezoGels in energy and biomedical applications. Next, we provide a detailed discussion on the preparation, functionalization, and fabrication of PiezoGel-PEGs (P-PEGs) for the applications of energy harvesting, sensing and wound healing/dressing. Finally, this review concludes with a discussion of the current challenges and future directions of P-PEGs.
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Affiliation(s)
- Thangavel Vijayakanth
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-6997801, Israel
| | - Sudha Shankar
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-6997801, Israel
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv-6997801, Israel
| | - Gal Finkelstein-Zuta
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-6997801, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv-6997801, Israel.
| | - Sigal Rencus-Lazar
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-6997801, Israel
| | - Sharon Gilead
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-6997801, Israel
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv-6997801, Israel
| | - Ehud Gazit
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-6997801, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv-6997801, Israel.
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38
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Kubota R, Hiroi T, Ikuta Y, Liu Y, Hamachi I. Visualizing Formation and Dynamics of a Three-Dimensional Sponge-like Network of a Coacervate in Real Time. J Am Chem Soc 2023; 145:18316-18328. [PMID: 37562059 DOI: 10.1021/jacs.3c03793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Coacervates, which are formed by liquid-liquid phase separation, have been extensively explored as models for synthetic cells and membraneless organelles, so their in-depth structural analysis is crucial. However, both the inner structure dynamics and formation mechanism of coacervates remain elusive. Herein, we demonstrate real-time confocal observation of a three-dimensional sponge-like network in a dipeptide-based coacervate. In situ generation of the dipeptide allowed us to capture the emergence of the sponge-like network via unprecedented membrane folding of vesicle-shaped intermediates. We also visualized dynamic fluctuation of the network, including reversible engagement/disengagement of cross-links and a stochastic network kissing event. Photoinduced transient formation of a multiphase coacervate was achieved with a thermally responsive phase transition. Our findings expand the fundamental understanding of synthetic coacervates and provide opportunities to manipulate their physicochemical properties by engineering the inner network for potential applications in development of artificial cells and life-like material fabrication.
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Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Taro Hiroi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuriki Ikuta
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuchong Liu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Nishikyo-ku, Katsura 615-8530, Japan
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39
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Fox AC, Boettger JD, Berger EL, Burton AS. The Role of the CuCl Active Complex in the Stereoselectivity of the Salt-Induced Peptide Formation Reaction: Insights from Density Functional Theory Calculations. Life (Basel) 2023; 13:1796. [PMID: 37763200 PMCID: PMC10532638 DOI: 10.3390/life13091796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
The salt-induced peptide formation (SIPF) reaction is a prebiotically plausible mechanism for the spontaneous polymerization of amino acids into peptides on early Earth. Experimental investigations of the SIPF reaction have found that in certain conditions, the l enantiomer is more reactive than the d enantiomer, indicating its potential role in the rise of biohomochirality. Previous work hypothesized that the distortion of the CuCl active complex toward a tetrahedral-like structure increases the central chirality on the Cu ion, which amplifies the inherent parity-violating energy differences between l- and d-amino acid enantiomers, leading to stereoselectivity. Computational evaluations of this theory have been limited to the protonated-neutral l + l forms of the CuCl active complex. Here, density functional theory methods were used to compare the energies and geometries of the homochiral (l + l and d + d) and heterochiral (l + d) CuCl-amino acid complexes for both the positive-neutral and neutral-neutral forms for alanine, valine, and proline. Significant energy differences were not observed between different chiral active complexes (i.e., d + d, l + l vs. l + d), and the distortions of active complexes between stereoselective systems and non-selective systems were not consistent, indicating that the geometry of the active complex is not the primary driver of the observed stereoselectivity of the SIPF reaction.
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Affiliation(s)
- Allison C. Fox
- NASA Postdoctoral Program, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Jason D. Boettger
- Department of Earth, Environmental and Resource Sciences, University of Texas at El Paso, El Paso, TX 79968, USA;
| | - Eve L. Berger
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Aaron S. Burton
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA
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40
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Tagami S. Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life. Biophys Physicobiol 2023; 20:e200026. [PMID: 38496239 PMCID: PMC10941967 DOI: 10.2142/biophysico.bppb-v20.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/29/2023] [Indexed: 03/19/2024] Open
Abstract
Is it a miracle that life exists on the Earth, or is it a common phenomenon in the universe? If extraterrestrial organisms exist, what are they like? To answer these questions, we must understand what kinds of molecules could evolve into life, or in other words, what properties are generally required to perform biological functions and store genetic information. This review summarizes recent findings on simple ancestral proteins, outlines the basic knowledge in textbooks, and discusses the generally required properties for biological molecules from structural biology viewpoints (e.g., restriction of shapes, and types of intra- and intermolecular interactions), leading to the conclusion that proteins and nucleic acids are at least one of the simplest (and perhaps very common) forms of catalytic and genetic biopolymers in the universe. This review article is an extended version of the Japanese article, On the Origin of Life: Coevolution between RNA and Peptide, published in SEIBUTSU BUTSURI Vol. 61, p. 232-235 (2021).
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Affiliation(s)
- Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
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41
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Sadihov-Hanoch H, Bandela AK, Chotera-Ouda A, Ben David O, Cohen-Luria R, Lynn DG, Ashkenasy G. Dynamic exchange controls the assembly structure of nucleic-acid-peptide chimeras. SOFT MATTER 2023; 19:3940-3945. [PMID: 37211859 DOI: 10.1039/d2sm01528e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Recent attempts to develop the next generation of functional biomaterials focus on systems chemistry approaches exploiting dynamic networks of hybrid molecules. This task is often found challenging, but we herein present ways for profiting from the multiple interaction interfaces forming Nucleic-acid-Peptide assemblies and tuning their formation. We demonstrate that the formation of well-defined structures by double-stranded DNA-peptide conjugates (dsCon) is restricted to a specific range of environmental conditions and that precise DNA hybridization, satisfying the interaction interfaces, is a crucial factor in this process. We further reveal the impact of external stimuli, such as competing free DNA elements or salt additives, which initiate dynamic interconversions, resulting in hybrid structures exhibiting spherical and fibrillar domains or a mixture of spherical and fibrillar particles. This extensive analysis of the co-assembly systems chemistry offers new insights into prebiotic hybrid assemblies that may now facilitate the design of new functional materials. We discuss the implications of these findings for the emergence of function in synthetic materials and during early chemical evolution.
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Affiliation(s)
- Hava Sadihov-Hanoch
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Anil Kumar Bandela
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Agata Chotera-Ouda
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Oshrat Ben David
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - David G Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, USA
| | - Gonen Ashkenasy
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
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42
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Wolfram M, Tiwari MK, Hassenkam T, Li M, Bjerrum MJ, Meldal M. Cascade autohydrolysis of Alzheimer's Aβ peptides. Chem Sci 2023; 14:4986-4996. [PMID: 37206405 PMCID: PMC10189894 DOI: 10.1039/d2sc06668h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/03/2023] [Indexed: 05/21/2023] Open
Abstract
Protein/peptide self-assembly into amyloid structures associates with major neurodegenerative disorders such as Alzheimer's disease (AD). Soluble assemblies (oligomers) of the Aβ peptide and their aggregates are perceived as neurotoxic species in AD. While screening for synthetic cleavage agents that could break down such aberrant assemblies through hydrolysis, we observed that the assemblies of Aβ oligopeptides, containing the nucleation sequence Aβ14-24 (H14QKLVFFAEDV24), could act as cleavage agents by themselves. Autohydrolysis showed a common fragment fingerprint among various mutated Aβ14-24 oligopeptides, Aβ12-25-Gly and Aβ1-28, and full-length Aβ1-40/42, under physiologically relevant conditions. Primary endoproteolytic autocleavage at the Gln15-Lys16, Lys16-Leu17 and Phe19-Phe20 positions was followed by subsequent exopeptidase self-processing of the fragments. Control experiments with homologous d-amino acid enantiomers Aβ12-25-Gly and Aβ16-25-Gly showed the same autocleavage pattern under similar reaction conditions. The autohydrolytic cascade reaction (ACR) was resilient to a broad range of conditions (20-37 °C, 10-150 μM peptide concentration at pH 7.0-7.8). Evidently, assemblies of the primary autocleavage fragments acted as structural/compositional templates (autocatalysts) for self-propagating autohydrolytic processing at the Aβ16-21 nucleation site, showing the potential for cross-catalytic seeding of the ACR in larger Aβ isoforms (Aβ1-28 and Aβ1-40/42). This result may shed new light on Aβ behaviour in solution and might be useful in the development of intervention strategies to decompose or inhibit neurotoxic Aβ assemblies in AD.
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Affiliation(s)
- Martin Wolfram
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
| | - Manish K Tiwari
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
| | - Tue Hassenkam
- Globe Institute, Section for Geobiology, Copenhagen University Øster Voldgade 5-7 1350 Copenhagen K Denmark
| | - Ming Li
- Technical University of Denmark, The Danish Hydrocarbon Research and Technology Centre Elektrovej, 2800 Kongens Lyngby Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
| | - Morten Meldal
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
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43
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Kobayashi K, Ise JI, Aoki R, Kinoshita M, Naito K, Udo T, Kunwar B, Takahashi JI, Shibata H, Mita H, Fukuda H, Oguri Y, Kawamura K, Kebukawa Y, Airapetian VS. Formation of Amino Acids and Carboxylic Acids in Weakly Reducing Planetary Atmospheres by Solar Energetic Particles from the Young Sun. Life (Basel) 2023; 13:life13051103. [PMID: 37240748 DOI: 10.3390/life13051103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Life most likely started during the Hadean Eon; however, the environmental conditions which contributed to the complexity of its chemistry are poorly known. A better understanding of various environmental conditions, including global (heliospheric) and local (atmospheric, surface, and oceanic), along with the internal dynamic conditions of the early Earth, are required to understand the onset of abiogenesis. Herein, we examine the contributions of galactic cosmic rays (GCRs) and solar energetic particles (SEPs) associated with superflares from the young Sun to the formation of amino acids and carboxylic acids in weakly reduced gas mixtures representing the early Earth's atmosphere. We also compare the products with those introduced by lightning events and solar ultraviolet light (UV). In a series of laboratory experiments, we detected and characterized the formation of amino acids and carboxylic acids via proton irradiation of a mixture of carbon dioxide, methane, nitrogen, and water in various mixing ratios. These experiments show the detection of amino acids after acid hydrolysis when 0.5% (v/v) of initial methane was introduced to the gas mixture. In the set of experiments with spark discharges (simulation of lightning flashes) performed for the same gas mixture, we found that at least 15% methane was required to detect the formation of amino acids, and no amino acids were detected in experiments via UV irradiation, even when 50% methane was used. Carboxylic acids were formed in non-reducing gas mixtures (0% methane) by proton irradiation and spark discharges. Hence, we suggest that GCRs and SEP events from the young Sun represent the most effective energy sources for the prebiotic formation of biologically important organic compounds from weakly reducing atmospheres. Since the energy flux of space weather, which generated frequent SEPs from the young Sun in the first 600 million years after the birth of the solar system, was expected to be much greater than that of GCRs, we conclude that SEP-driven energetic protons are the most promising energy sources for the prebiotic production of bioorganic compounds in the atmosphere of the Hadean Earth.
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Affiliation(s)
- Kensei Kobayashi
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Jun-Ichi Ise
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Ryohei Aoki
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Miei Kinoshita
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Koki Naito
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Takumi Udo
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Bhagawati Kunwar
- Chubu Institute of Advanced Studies, Chubu University, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | - Jun-Ichi Takahashi
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Hiromi Shibata
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki 567-0047, Japan
| | - Hajime Mita
- Department of Life, Environment and Applied Chemistry, Faculty of Engineering, Fukuoka Institute of Technology, Fukuoka 811-0295, Japan
| | - Hitoshi Fukuda
- Open Facility Center, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Yoshiyuki Oguri
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Kimitaka Kawamura
- Chubu Institute of Advanced Studies, Chubu University, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | - Yoko Kebukawa
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Vladimir S Airapetian
- NASA Goddard Space Flight Center/Sellers Exoplanetary Environments Collaboration, Greenbelt, MD 20771, USA
- Department of Physics, American University, Washington, DC 20016, USA
- Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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44
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Kassem S, McPhee SA, Berisha N, Ulijn RV. Emergence of Cooperative Glucose-Binding Networks in Adaptive Peptide Systems. J Am Chem Soc 2023; 145:9800-9807. [PMID: 37075194 DOI: 10.1021/jacs.3c01620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Minimalistic peptide-based systems that bind sugars in water are challenging to design due to the weakness of interactions and required cooperative contributions from specific amino-acid side chains. Here, we used a bottom-up approach to create peptide-based adaptive glucose-binding networks by mixing glucose with selected sets of input dipeptides (up to 4) in the presence of an amidase to enable in situ reversible peptide elongation, forming mixtures of up to 16 dynamically interacting tetrapeptides. The choice of input dipeptides was based on amino-acid abundance in glucose-binding sites found in the protein data bank, with side chains that can support hydrogen bonding and CH-π interactions. Tetrapeptide sequence amplification patterns, determined through LC-MS analysis, served as a readout for collective interactions and led to the identification of optimized binding networks. Systematic variation of dipeptide input revealed the emergence of two networks of non-covalent hydrogen bonding and CH-π interactions that can co-exist, are cooperative and context-dependent. A cooperative binding mode was determined by studying the binding of the most amplified tetrapeptide (AWAD) with glucose in isolation. Overall, these results demonstrate that the bottom-up design of complex systems can recreate emergent behaviors driven by covalent and non-covalent self-organization that are not observed in reductionist designs and lead to the identification of system-level cooperative binding motifs.
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Affiliation(s)
- Salma Kassem
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Scott A McPhee
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Naxhije Berisha
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
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45
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Kang X, Ye H, Liu S, Tu X, Zhu J, Sun H, Yi L. Insights into self-degradation of cysteine esters and amides under physiological conditions yield new cleavable chemistry. Chem Commun (Camb) 2023; 59:4233-4236. [PMID: 36942527 DOI: 10.1039/d3cc00684k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
An unprecedented H2S release from cysteine esters and amides (CysO/NHR) under physiological conditions was discovered and the plausible mechanism was proposed. Alkylation of the amino moiety of cysteine esters enables the H2S release to be tuned and further provides support to the mechanistic insights. This discovery not only provides new insights into several fundamental science issues including non-enzymatic H2S-produced pathways, but also inspires new tunable cleavable motifs for sustained release of arylthiols and even for prodrug design.
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Affiliation(s)
- Xueying Kang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Haishun Ye
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Shanshan Liu
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Xiaoqiang Tu
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Jiqin Zhu
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Hongyan Sun
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 TatChee Avenue, Kowloon, Hong Kong, China
| | - Long Yi
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
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46
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Hou Y, Xu X, Kong X. K +-Selectivity Due to Coordination with a D4d-Symmetric Homochiral Proline Octamer Verified by Mass Spectrometry and Infrared Photodissociation Spectroscopy. J Phys Chem Lett 2023; 14:2660-2664. [PMID: 36892259 DOI: 10.1021/acs.jpclett.2c03838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Both phenomena of homochirality and sodium-potassium ion selectivity in cells have been regarded as important issues in the process of the origin of life. However, whether K+/Na+ selectivity was involved in homochirogenesis has never been considered. Herein, we report that a homochiral proline octamer shows high K+-selectivity. Coordination of K+ results in formation of a stable, noncovalent, D4d-symmetric complex, as demonstrated by mass spectrometry, infrared photodissociation spectroscopy, and calculations. A cooperative relationship between an eight-coordinated metal cation and a homochirality-restricted topological hydrogen-bonded proline network is the key for the K+/Na+ selectivity. As the complex comprises merely the basic chiral amino acid, it provides a possible linkage between K+/Na+ selectivity and the origin of chirality on the prebiotic Earth.
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Affiliation(s)
- Yameng Hou
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xingshi Xu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xianglei Kong
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
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47
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Gutierrez-Rus LI, Gamiz-Arco G, Gavira JA, Gaucher EA, Risso VA, Sanchez-Ruiz JM. Protection of catalytic cofactors by polypeptides as a driver for the emergence of primordial enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532612. [PMID: 36993774 PMCID: PMC10055001 DOI: 10.1101/2023.03.14.532612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Enzymes catalyze the chemical reactions of life. For nearly half of known enzymes, catalysis requires the binding of small molecules known as cofactors. Polypeptide-cofactor complexes likely formed at a primordial stage and became starting points for the evolution of many efficient enzymes. Yet, evolution has no foresight so the driver for the primordial complex formation is unknown. Here, we use a resurrected ancestral TIM-barrel protein to identify one potential driver. Heme binding at a flexible region of the ancestral structure yields a peroxidation catalyst with enhanced efficiency when compared to free heme. This enhancement, however, does not arise from protein-mediated promotion of catalysis. Rather, it reflects protection of bound heme from common degradation processes and a resulting longer life time and higher effective concentration for the catalyst. Protection of catalytic cofactors by polypeptides emerges as a general mechanism to enhance catalysis and may have plausibly benefited primordial polypeptide-cofactor associations.
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48
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Distinguishing Biotic vs. Abiotic Origins of ‘Bio’signatures: Clues from Messy Prebiotic Chemistry for Detection of Life in the Universe. Life (Basel) 2023; 13:life13030766. [PMID: 36983921 PMCID: PMC10058490 DOI: 10.3390/life13030766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/04/2023] [Accepted: 03/11/2023] [Indexed: 03/16/2023] Open
Abstract
It is not a stretch to say that the search for extraterrestrial life is possibly the biggest of the cosmic endeavors that humankind has embarked upon. With the continued discovery of several Earth-like exoplanets, the hope of detecting potential biosignatures is multiplying amongst researchers in the astrobiology community. However, to be able to discern these signatures as being truly of biological origin, we also need to consider their probable abiotic origin. The field of prebiotic chemistry, which is aimed at understanding enzyme-free chemical syntheses of biologically relevant molecules, could particularly aid in this regard. Specifically, certain peculiar characteristics of prebiotically pertinent messy chemical reactions, including diverse and racemic product yields and lower synthesis efficiencies, can be utilized in analyzing whether a perceived ‘signature of life’ could possibly have chemical origins. The knowledge gathered from understanding the transition from chemistry to biology during the origin of life could be used for creating a library of abiotically synthesized biologically relevant organic molecules. This can then be employed in designing, standardizing, and testing mission-specific instruments/analysis systems, while also enabling the effective targeting of exoplanets with potentially ‘ongoing’ molecular evolutionary processes for robust detection of life in future explorative endeavors.
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Makarov M, Sanchez Rocha AC, Krystufek R, Cherepashuk I, Dzmitruk V, Charnavets T, Faustino AM, Lebl M, Fujishima K, Fried SD, Hlouchova K. Early Selection of the Amino Acid Alphabet Was Adaptively Shaped by Biophysical Constraints of Foldability. J Am Chem Soc 2023; 145:5320-5329. [PMID: 36826345 PMCID: PMC10017022 DOI: 10.1021/jacs.2c12987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Whereas modern proteins rely on a quasi-universal repertoire of 20 canonical amino acids (AAs), numerous lines of evidence suggest that ancient proteins relied on a limited alphabet of 10 "early" AAs and that the 10 "late" AAs were products of biosynthetic pathways. However, many nonproteinogenic AAs were also prebiotically available, which begs two fundamental questions: Why do we have the current modern amino acid alphabet and would proteins be able to fold into globular structures as well if different amino acids comprised the genetic code? Here, we experimentally evaluate the solubility and secondary structure propensities of several prebiotically relevant amino acids in the context of synthetic combinatorial 25-mer peptide libraries. The most prebiotically abundant linear aliphatic and basic residues were incorporated along with or in place of other early amino acids to explore these alternative sequence spaces. The results show that foldability was likely a critical factor in the selection of the canonical alphabet. Unbranched aliphatic amino acids were purged from the proteinogenic alphabet despite their high prebiotic abundance because they generate polypeptides that are oversolubilized and have low packing efficiency. Surprisingly, we find that the inclusion of a short-chain basic amino acid also decreases polypeptides' secondary structure potential, for which we suggest a biophysical model. Our results support the view that, despite lacking basic residues, the early canonical alphabet was remarkably adaptive at supporting protein folding and explain why basic residues were only incorporated at a later stage of protein evolution.
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Affiliation(s)
- Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12843, Czech Republic
| | - Alma C Sanchez Rocha
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12843, Czech Republic
| | - Robin Krystufek
- Department of Physical Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12843, Czech Republic
| | - Volha Dzmitruk
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec 25250, Czech Republic
| | - Tatsiana Charnavets
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec 25250, Czech Republic
| | - Anneliese M Faustino
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Michal Lebl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12843, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
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50
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Singh H, Pragya P, Mittal A, Haridas V. Pseudopeptosomes: non-lipidated vesicular assemblies from bispidine-appended pseudopeptides. Org Biomol Chem 2023; 21:3557-3566. [PMID: 36883655 DOI: 10.1039/d3ob00201b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
We report a novel molecular topology-based approach for creating reproducible vesicular assemblies in different solvent environments (including aqueous) using specifically designed pseudopeptides. Deviating from the classical "polar head group and hydrophobic tail" model of amphiphiles, we showed (reversible) self-assembly of synthesized pseudopeptides into vesicles. Naming these new type/class of vesicles "pseudopetosomes", we characterized them by high-resolution microscopy (scanning electron, transmission electron, atomic force, epifluorescence and confocal) along with dynamic light scattering. While accounting for hydropathy index of the constituent amino acids (side chains) of pseudopeptides, we probed molecular interactions, resulting in assembly of pseudopeptosomes by spectroscopy (fourier-transform infrared and fluorescence). Molecular characterization by X-ray crystallography and circular dichroism revealed "tryptophan (Trp)-Zip" arrangements and/or hydrogen-bonded one-dimensional assembly depending on specific pseudopeptides and solvent environments. Our data indicated that pseudopeptosomes are formed in solutions by self-assembly of bispidine pseudopeptides (of Trp, leucine and alanine amino-acid constituents) into sheets that transform into vesicular structures. Thus, we showed that assembly of pseudopeptosomes utilizes the full spectrum of all four weak interactions essential in biological systems. Our findings have direct implications in chemical and synthetic biology, but may also provide a new avenue of investigations on origins of life via pseudopeptosome-like assemblies. We also showed that these designer peptides can act as carriers for cellular transport.
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Affiliation(s)
- Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
| | - Pragya Pragya
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Aditya Mittal
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India. .,Supercomputing Facility for Bioinformatics, and Computational Biology (SCFBio), IIT Delhi, Hauz Khas, New Delhi 110016, India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
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