1
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Singh A, Parvin P, Saha B, Das D. Non-equilibrium self-assembly for living matter-like properties. Nat Rev Chem 2024:10.1038/s41570-024-00640-z. [PMID: 39179623 DOI: 10.1038/s41570-024-00640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
The soft and wet machines of life emerged as the spatially enclosed ensemble of biomolecules with replicating capabilities integrated with metabolic reaction cycles that operate at far-from-equilibrium. A thorough step-by-step synthetic integration of these elements, namely metabolic and replicative properties all confined and operating far-from-equilibrium, can set the stage from which we can ask questions related to the construction of chemical-based evolving systems with living matter-like properties - a monumental endeavour of systems chemistry. The overarching concept of this Review maps the discoveries on this possible integration of reaction networks, self-reproduction and compartmentalization under non-equilibrium conditions. We deconvolute the events of reaction networks and transient compartmentalization and extend the discussion towards self-reproducing systems that can be sustained under non-equilibrium conditions. Although enormous challenges lie ahead in terms of molecular diversity, information transfer, adaptation and selection that are required for open-ended evolution, emerging strategies to generate minimal metabolic cycles can extend our growing understanding of the chemical emergence of the biosphere of Earth.
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Affiliation(s)
- Abhishek Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Payel Parvin
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Bapan Saha
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
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2
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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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3
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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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4
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Wang Y, Pan T, Li J, Zou L, Wei X, Zhang Q, Wei T, Xu L, Ulijn RV, Zhang C. Developing Isomeric Peptides for Mimicking the Sequence-Activity Landscapes of Enzyme Evolution. ACS APPLIED MATERIALS & INTERFACES 2024; 16:22369-22378. [PMID: 38644563 DOI: 10.1021/acsami.4c00501] [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: 04/23/2024]
Abstract
Enzymes catalyze almost all material conversion processes within living organisms, yet their natural evolution remains unobserved. Short peptides, derived from proteins and featuring active sites, have emerged as promising building blocks for constructing bioactive supramolecular materials that mimic native proteins through self-assembly. Herein, we employ histidine-containing isomeric tetrapeptides KHFF, HKFF, KFHF, HFKF, FKHF, and FHKF to craft supramolecular self-assemblies, aiming to explore the sequence-activity landscapes of enzyme evolution. Our investigations reveal the profound impact of peptide sequence variations on both assembly behavior and catalytic activity as hydrolytic simulation enzymes. During self-assembly, a delicate balance of multiple intermolecular interactions, particularly hydrogen bonding and aromatic-aromatic interactions, influences nanostructure formation, yielding various morphologies (e.g., nanofibers, nanospheres, and nanodiscs). Furthermore, the analysis of the structure-activity relationship demonstrates a strong correlation between the distribution of the His active site on the nanostructures and the formation of the catalytic microenvironment. This investigation of the sequence-structure-activity paradigm reflects how natural enzymes enhance catalytic activity by adjusting the primary structure during evolution, promoting fundamental research related to enzyme evolutionary processes.
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Affiliation(s)
- Yaling Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tiezheng Pan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Jie Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lina Zou
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xuewen Wei
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Qian Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tingting Wei
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Li Xu
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), New York, New York 10031, United States
- Department of Chemistry, Hunter College, City University of New York, New York, New York 10065, United States
| | - Chunqiu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education and College of Life Sciences, Nankai University, Tianjin 300071, China
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5
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Rout SK, Rhyner D, Greenwald J, Riek R. Characterization of self-templating catalytic amyloids. Methods Enzymol 2024; 697:51-75. [PMID: 38816135 DOI: 10.1016/bs.mie.2024.04.004] [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] [Indexed: 06/01/2024]
Abstract
Amyloid aggregates with unique periodic structures have garnered significant attention due to their association with numerous diseases, including systemic amyloidoses and the neurodegenerative diseases Parkinson's, Alzheimer's, and Creutzfeld-Jakob. However, more recent investigations have expanded our understanding of amyloids, revealing their diverse functional biological roles. Amyloids have also been proposed to have played a significant role in prebiotic molecular evolution because of their exceptional stability, spontaneous formation in a prebiotic environment, catalytic and templating abilities, and cooperative interaction with fatty acids, polysaccharides, and nucleic acids. This chapter summarizes methods and techniques associated with studying short amyloidogenic peptides, including detailed procedures for investigating cross-templating and autocatalytic templating reactions. Since the work with amyloidogenic peptides and their aggregates present unique challenges, we have attempted to address these with essential details throughout the procedures. The lessons herein may be used in any amyloid-related research to ensure more reproducible results and reduce entrance barriers for researchers new to the field.
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Affiliation(s)
- Saroj K Rout
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland; Systems Biophysics, Department of Physics, Ludwig Maximilian University Munich, Munich, Germany
| | - David Rhyner
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland
| | - Jason Greenwald
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland.
| | - Roland Riek
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland.
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6
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Kwiatkowski W, Greenwald J, Murzakhmetov L, Robinson RC, Riek R. Short Peptide Amyloids Are a Potential Sequence Pool for the Emergence of Proteins. J Mol Biol 2024; 436:168495. [PMID: 38360090 DOI: 10.1016/j.jmb.2024.168495] [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: 10/19/2023] [Revised: 01/15/2024] [Accepted: 02/10/2024] [Indexed: 02/17/2024]
Abstract
Under prebiotic conditions, peptides are capable of self-replication through a structure-based template-assisted mechanism when they form amyloids. Furthermore, peptide amyloids can spontaneously form inside fatty acid vesicles creating membrane enclosed complex structures of variable morphologies. This is possible because fatty acid vesicle membranes act as filters allowing passage of activated amino acids while some amino acids derived from the activated species become non-permeable and trapped in the vesicles. Similarly, nascent peptides derived from the condensation of the activated amino acids are also trapped in the vesicles. It is hypothesized that such preselected peptide amyloids become a sequence pool for the emergence of proteins in life and that after billions of years of cellular evolution, the sequences in the current proteome have diverged significantly from these original seed peptides. If this hypothesis is correct, it could be possible to detect the traces of these seed sequences in current proteomes. Here, we show for all possible 3, 6, 7, 8 or 9 residue sequence motifs that those motifs that are most amyloidogenic/aggregation prone are over-represented in extant proteomes compared to a sequence-randomized proteome. Furthermore, we find that there is a greater proportion of amyloidogenic sequence motifs in archaea proteomes than in the larger primate proteomes. This suggests that the evolution towards larger proteomes leads to smaller proportion of amyloidogenic sequences.
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Affiliation(s)
| | | | | | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand; Research Institute for Interdisciplinary Science, Okayama University, Japan
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7
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. Role of Post-Transcriptional Regulation in Learning and Memory in Mammals. Genes (Basel) 2024; 15:337. [PMID: 38540396 PMCID: PMC10970538 DOI: 10.3390/genes15030337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 06/14/2024] Open
Abstract
After many decades, during which most molecular studies on the regulation of gene expression focused on transcriptional events, it was realized that post-transcriptional control was equally important in order to determine where and when specific proteins were to be synthesized. Translational regulation is of the most importance in the brain, where all the steps of mRNA maturation, transport to different regions of the cells and actual expression, in response to specific signals, constitute the molecular basis for neuronal plasticity and, as a consequence, for structural stabilization/modification of synapses; notably, these latter events are fundamental for the highest brain functions, such as learning and memory, and are characterized by long-term potentiation (LTP) of specific synapses. Here, we will discuss the molecular bases of these fundamental events by considering both the role of RNA-binding proteins (RBPs) and the effects of non-coding RNAs involved in controlling splicing, editing, stability and translation of mRNAs. Importantly, it has also been found that dysregulation of mRNA metabolism/localization is involved in many pathological conditions, arising either during brain development or in the adult nervous system.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (C.M.D.L.); (G.S.)
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (C.M.D.L.); (G.S.)
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
- Neurology and Multiple Sclerosis Center, Unità Operativa Complessa (UOC), Foundation Institute “G. Giglio”, 90015 Cefalù, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
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8
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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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9
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Louros N, Schymkowitz J, Rousseau F. Mechanisms and pathology of protein misfolding and aggregation. Nat Rev Mol Cell Biol 2023; 24:912-933. [PMID: 37684425 DOI: 10.1038/s41580-023-00647-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/10/2023]
Abstract
Despite advances in machine learning-based protein structure prediction, we are still far from fully understanding how proteins fold into their native conformation. The conventional notion that polypeptides fold spontaneously to their biologically active states has gradually been replaced by our understanding that cellular protein folding often requires context-dependent guidance from molecular chaperones in order to avoid misfolding. Misfolded proteins can aggregate into larger structures, such as amyloid fibrils, which perpetuate the misfolding process, creating a self-reinforcing cascade. A surge in amyloid fibril structures has deepened our comprehension of how a single polypeptide sequence can exhibit multiple amyloid conformations, known as polymorphism. The assembly of these polymorphs is not a random process but is influenced by the specific conditions and tissues in which they originate. This observation suggests that, similar to the folding of native proteins, the kinetics of pathological amyloid assembly are modulated by interactions specific to cells and tissues. Here, we review the current understanding of how intrinsic protein conformational propensities are modulated by physiological and pathological interactions in the cell to shape protein misfolding and aggregation pathology.
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Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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10
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Rout S, Cadalbert R, Schröder N, Wang J, Zehnder J, Gampp O, Wiegand T, Güntert P, Klingler D, Kreutz C, Knörlein A, Hall J, Greenwald J, Riek R. An Analysis of Nucleotide-Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA. J Am Chem Soc 2023; 145:21915-21924. [PMID: 37782045 PMCID: PMC10571083 DOI: 10.1021/jacs.3c06287] [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: 06/15/2023] [Indexed: 10/03/2023]
Abstract
Interactions between RNA and proteins are the cornerstone of many important biological processes from transcription and translation to gene regulation, yet little is known about the ancient origin of said interactions. We hypothesized that peptide amyloids played a role in the origin of life and that their repetitive structure lends itself to building interfaces with other polymers through avidity. Here, we report that short RNA with a minimum length of three nucleotides binds in a sequence-dependent manner to peptide amyloids. The 3'-5' linked RNA backbone appears to be well-suited to support these interactions, with the phosphodiester backbone and nucleobases both contributing to the affinity. Sequence-specific RNA-peptide interactions of the kind identified here may provide a path to understanding one of the great mysteries rooted in the origin of life: the origin of the genetic code.
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Affiliation(s)
- Saroj
K. Rout
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Riccardo Cadalbert
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Nina Schröder
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Julia Wang
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Johannes Zehnder
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Olivia Gampp
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Thomas Wiegand
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
- Max
Planck Institute for Chemical Energy Conversion, 45470 Mülheim/Ruhr, Germany
| | - Peter Güntert
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
- Institute
of Biophysical Chemistry, Goethe University, 60438 Frankfurt
am Main, Germany
- Department
of Chemistry, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - David Klingler
- Institute
of Organic Chemistry and Center for Molecular Biosciences Innsbruck
(CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute
of Organic Chemistry and Center for Molecular Biosciences Innsbruck
(CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Anna Knörlein
- Institute
of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jonathan Hall
- Institute
of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jason Greenwald
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Roland Riek
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
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11
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Wu H, Xu S, Du P, Liu Y, Li H, Yang H, Wang T, Wang ZG. A nucleotide-copper(II) complex possessing a monooxygenase-like catalytic function. J Mater Chem B 2023. [PMID: 37409588 DOI: 10.1039/d3tb00780d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The de novo design of artificial biocatalysts with enzyme-like active sites and catalytic functions has long been an attractive yet challenging goal. In this study, we present a nucleotide-Cu2+ complex, synthesized through a one-pot approach, capable of catalyzing ortho-hydroxylation reactions resembling those of minimalist monooxygenases. Both experimental and theoretical findings demonstrate that the catalyst, in which Cu2+ coordinates with both the nucleobase and phosphate moieties, forms a ternary-complex intermediate with H2O2 and tyramine substrates through multiple weak interactions. The subsequent electron transfer and hydrogen (or proton) transfer steps lead to the ortho-hydroxylation of tyramine, where the single copper center exhibits a similar function to natural dicopper sites. Moreover, Cu2+ bound to nucleotides or oligonucleotides exhibits thermophilic catalytic properties within the temperature range of 25 °C to 75 °C, while native enzymes are fully deactivated above 35 °C. This study may provide insights for the future design of oxidase-mimetic catalysts and serve as a guide for the design of primitive metallocentre-dependent enzymes.
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Affiliation(s)
- Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Shichao Xu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Peidong Du
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Hui Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Haijun Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ting Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
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12
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Effect of the Addition of the Fifth Amino Acid to [GADV]-Protein on the Three-Dimensional Structure. LIFE (BASEL, SWITZERLAND) 2023; 13:life13010246. [PMID: 36676195 PMCID: PMC9863117 DOI: 10.3390/life13010246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023]
Abstract
The [GADV]-protein, consisting only of glycine (G), alanine (A), aspartic acid (D), and valine (V), is frequently studied as a candidate for a primitive protein that existed at the beginning of life on Earth. The number of proteogenic amino acids increased during evolution, and glutamic acid may have been added as the fifth amino acid. In this study, we used molecular dynamics simulations to estimate the conformation of random peptides when glutamate is added to G, A, D, and V ([GADVE]), when leucine is added ([GADVL]), and when the frequency of alanine is doubled ([GADVA]). The results showed that the secondary structure contents of the [GADVE]-peptide and [GADVL]-peptide were higher than that of the [GADVA]-peptide. Although the [GADVL]-peptide had a higher secondary structure formation ability than the [GADVE]-peptide, it was less water soluble, suggesting that it may not be a primitive protein. The [GA(D/E)V]-peptide with G:A:D:V:E = 2:2:1:2:1 according to the occurrence ratio in the codon table also increased the secondary structure contents compared to the [GADV]-peptide, indicating that the addition of glutamic acid increased the structure formation ability of the primitive protein candidates.
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13
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Self-assembled nanomaterials as vaccines for COVID-19 and future pandemics. Nanomedicine (Lond) 2023. [DOI: 10.1016/b978-0-12-818627-5.00006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
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14
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. RNA-Binding Proteins as Epigenetic Regulators of Brain Functions and Their Involvement in Neurodegeneration. Int J Mol Sci 2022; 23:ijms232314622. [PMID: 36498959 PMCID: PMC9739182 DOI: 10.3390/ijms232314622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
A central aspect of nervous system development and function is the post-transcriptional regulation of mRNA fate, which implies time- and site-dependent translation, in response to cues originating from cell-to-cell crosstalk. Such events are fundamental for the establishment of brain cell asymmetry, as well as of long-lasting modifications of synapses (long-term potentiation: LTP), responsible for learning, memory, and higher cognitive functions. Post-transcriptional regulation is in turn dependent on RNA-binding proteins that, by recognizing and binding brief RNA sequences, base modifications, or secondary/tertiary structures, are able to control maturation, localization, stability, and translation of the transcripts. Notably, most RBPs contain intrinsically disordered regions (IDRs) that are thought to be involved in the formation of membrane-less structures, probably due to liquid-liquid phase separation (LLPS). Such structures are evidenced as a variety of granules that contain proteins and different classes of RNAs. The other side of the peculiar properties of IDRs is, however, that, under altered cellular conditions, they are also prone to form aggregates, as observed in neurodegeneration. Interestingly, RBPs, as part of both normal and aggregated complexes, are also able to enter extracellular vesicles (EVs), and in doing so, they can also reach cells other than those that produced them.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
- Correspondence: ; Tel.: +39-091-238-97 (ext. 415/446)
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15
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Roy S, Chatterjee A, Bal S, Das D. Cross β Amyloid Nanotubes Demonstrate Promiscuous Catalysis in a Chemical Reaction Network via Co‐option. Angew Chem Int Ed Engl 2022; 61:e202210972. [DOI: 10.1002/anie.202210972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Soumili Roy
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Ayan Chatterjee
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Subhajit Bal
- 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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16
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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17
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Abstract
Amyloids are protein aggregates bearing a highly ordered cross β structural motif, which may be functional but are mostly pathogenic. Their formation, deposition in tissues and consequent organ dysfunction is the central event in amyloidogenic diseases. Such protein aggregation may be brought about by conformational changes, and much attention has been directed toward factors like metal binding, post-translational modifications, mutations of protein etc., which eventually affect the reactivity and cytotoxicity of the associated proteins. Over the past decade, a global effort from different groups working on these misfolded/unfolded proteins/peptides has revealed that the amino acid residues in the second coordination sphere of the active sites of amyloidogenic proteins/peptides cause changes in H-bonding pattern or protein-protein interactions, which dramatically alter the structure and reactivity of these proteins/peptides. These second sphere effects not only determine the binding of transition metals and cofactors, which define the pathology of some of these diseases, but also change the mechanism of redox reactions catalyzed by these proteins/peptides and form the basis of oxidative damage associated with these amyloidogenic diseases. The present review seeks to discuss such second sphere modifications and their ramifications in the etiopathology of some representative amyloidogenic diseases like Alzheimer's disease (AD), type 2 diabetes mellitus (T2Dm), Parkinson's disease (PD), Huntington's disease (HD), and prion diseases.
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Affiliation(s)
- Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Arnab Kumar Nath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Ishita Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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18
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Tiwari OS, Ganesh KN, Gazit E. Effect of Stereochemistry and Hydrophobicity on the Self‐assembly of Phe‐Phe‐Nucleoside Conjugates. MACROMOL CHEM PHYS 2022. [DOI: 10.1002/macp.202200011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Om Shanker Tiwari
- Shmunis School of Biomedicine and Cancer Research Tel Aviv University Ramat Aviv Tel Aviv 6997801 Israel
- Department of Chemistry Indian Institute of Science Education and Research (IISER) Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Krishna N. Ganesh
- Department of Chemistry Indian Institute of Science Education and Research (IISER) Pune Dr. Homi Bhabha Road Pune 411008 India
- Department of Chemistry Indian Institute of Science Education and Research (IISER) Tirupati Karkambadi Road Tirupati 517507 India
| | - Ehud Gazit
- Shmunis School of Biomedicine and Cancer Research Tel Aviv University Ramat Aviv Tel Aviv 6997801 Israel
- Department of Materials Science and Engineering Tel Aviv University, Ramat Aviv Tel Aviv 6997801 Israel
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19
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Chatterjee A, Reja A, Pal S, Das D. Systems chemistry of peptide-assemblies for biochemical transformations. Chem Soc Rev 2022; 51:3047-3070. [PMID: 35316323 DOI: 10.1039/d1cs01178b] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.
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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.
| | - Antara Reja
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Sumit Pal
- 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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20
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Makam P, Yamijala SSRKC, Bhadram VS, Shimon LJW, Wong BM, Gazit E. Single amino acid bionanozyme for environmental remediation. Nat Commun 2022; 13:1505. [PMID: 35314678 PMCID: PMC8938493 DOI: 10.1038/s41467-022-28942-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractEnzymes are extremely complex catalytic structures with immense biological and technological importance. Nevertheless, their widespread environmental implementation faces several challenges, including high production costs, low operational stability, and intricate recovery and reusability. Therefore, the de novo design of minimalistic biomolecular nanomaterials that can efficiently mimic the biocatalytic function (bionanozymes) and overcome the limitations of natural enzymes is a critical goal in biomolecular engineering. Here, we report an exceptionally simple yet highly active and robust single amino acid bionanozyme that can catalyze the rapid oxidation of environmentally toxic phenolic contaminates and serves as an ultrasensitive tool to detect biologically important neurotransmitters similar to the laccase enzyme. While inspired by the laccase catalytic site, the substantially simpler copper-coordinated bionanozyme is ∼5400 times more cost-effective, four orders more efficient, and 36 times more sensitive compared to the natural protein. Furthermore, the designed mimic is stable under extreme conditions (pH, ionic strength, temperature, storage time), markedly reusable for several cycles, and displays broad substrate specificity. These findings hold great promise in developing efficient bionanozymes for analytical chemistry, environmental protection, and biotechnology.
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21
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Fried SD, Fujishima K, Makarov M, Cherepashuk I, Hlouchova K. Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids. J R Soc Interface 2022; 19:20210641. [PMID: 35135297 PMCID: PMC8833103 DOI: 10.1098/rsif.2021.0641] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.
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Affiliation(s)
- Stephen D. Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21212, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
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22
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Dong Y, Zhang S, Zhao L. Unraveling the Structural Development of
Peptide‐Coordinated Iron‐Sulfur
Clusters: Prebiotic Evolution and Biosynthetic Strategies. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yijun Dong
- School of Life Sciences, Tsinghua University Beijing 100084 China
| | - Siqi Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
| | - Liang Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
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23
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Rout SK, Rhyner D, Riek R, Greenwald J. Prebiotically Plausible Autocatalytic Peptide Amyloids. Chemistry 2022; 28:e202103841. [PMID: 34812556 PMCID: PMC9299922 DOI: 10.1002/chem.202103841] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Indexed: 12/19/2022]
Abstract
The prebiotic emergence of molecules capable both of self-replication and of storing information was a defining event at the dawn of life. Still, no plausible prebiotic self-replication of biologically relevant molecules has been demonstrated. Building upon the known templating nature of amyloids, we present two systems in which the products of a peptide-bond-forming reaction act as self-replicators to enhance the yield and stereoselectivity of their formation. This first report of an amino acid condensation that can undergo autocatalysis further supports the potential role of amyloids in prebiotic molecular evolution as an environment-responsive and information-coding system capable of self-replication.
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Affiliation(s)
- Saroj K. Rout
- Laboratory of Physical ChemistrySwiss Federal Institute of TechnologyETH HönggerbergVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - David Rhyner
- Laboratory of Physical ChemistrySwiss Federal Institute of TechnologyETH HönggerbergVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Roland Riek
- Laboratory of Physical ChemistrySwiss Federal Institute of TechnologyETH HönggerbergVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Jason Greenwald
- Laboratory of Physical ChemistrySwiss Federal Institute of TechnologyETH HönggerbergVladimir-Prelog-Weg 28093ZürichSwitzerland
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24
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Pal S, Reja A, Bal S, Tikader B, Das D. Emergence of a Promiscuous Peroxidase Under Non-Equilibrium Conditions. Angew Chem Int Ed Engl 2022; 61:e202111857. [PMID: 34767668 DOI: 10.1002/anie.202111857] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Indexed: 11/07/2022]
Abstract
Herein, we report the substrate induced generation of a transient catalytic microenvironment from a single amino acid functionalized fatty acid in presence of a cofactor hemin. The catalytic state accessed under non-equilibrium conditions showed acceleration of peroxidase activity resulting in degradation of the substrate and subsequently led to disassembly. Equilibrated systems could not access the three-dimensional microphases and showed substantially lower catalytic activity. Further, the assembled state showed latent catalytic function (promiscuity) to hydrolyze a precursor to yield the same substrate. Consequently, the assembly demonstrated protometabolism by exploiting the peroxidase-hydrolase cascade to augment the lifetime and the mechanical properties of the catalytic state.
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Affiliation(s)
- Sumit Pal
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Antara Reja
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Subhajit Bal
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Baishakhi Tikader
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, 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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25
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Pal S, Reja A, Bal S, Tikader B, Das D. Emergence of a Promiscuous Peroxidase Under Non‐Equilibrium Conditions**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sumit Pal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Subhajit Bal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Baishakhi Tikader
- Department of Chemistry Indian Institute of Technology Bombay Powai Mumbai 400076 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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26
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Mahato C, Menon S, Singh A, Afrose SP, Mondal J, Das D. Short Peptide-based Cross-β Amyloids Exploit Dual Residues for Phosphoesterase like Activity. Chem Sci 2022; 13:9225-9231. [PMID: 36092997 PMCID: PMC9384705 DOI: 10.1039/d2sc03205h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/17/2022] [Indexed: 11/21/2022] Open
Abstract
Herein, we report that short peptides are capable of exploiting their anti-parallel registry to access cross-β stacks to expose more than one catalytic residue, exhibiting the traits of advanced binding pockets of enzymes. Binding pockets decorated with more than one catalytic residue facilitate substrate binding and process kinetically unfavourable chemical transformations. The solvent-exposed guanidinium and imidazole moieties on the cross-β microphases synergistically bind to polarise and hydrolyse diverse kinetically stable model substrates of nucleases and phosphatase. Mutation of either histidine or arginine results in a drastic decline in the rate of hydrolysis. These results not only support the argument of short amyloid peptides as the earliest protein folds but also suggest their interactions with nucleic acid congeners, foreshadowing the mutualistic biopolymer relationships that fueled the chemical emergence of life. Amyloid based short peptide assemblies use antiparallel registry to expose multiple catalytic residues to bind and cleave kinetically stable phosphoester bonds of nucleic acid congeners, foreshadowing interactions of protein folds with nucleic acids.![]()
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Affiliation(s)
- Chiranjit Mahato
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Sneha Menon
- Tata Institute of Fundamental Research Hyderabad Telangana 500046 India
| | - 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
| | - Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research Hyderabad Telangana 500046 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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Pal S, Goswami S, Das D. Cross β amyloid assemblies as complex catalytic machinery. Chem Commun (Camb) 2021; 57:7597-7609. [PMID: 34278403 DOI: 10.1039/d1cc02880d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
How modern enzymes evolved as complex catalytic machineries to facilitate diverse chemical transformations is an open question for the emerging field of systems chemistry. Inspired by Nature's ingenuity in creating complex catalytic structures for exotic functions, short peptide-based cross β amyloid sequences have been shown to access intricate binding surfaces demonstrating the traits of extant enzymes and proteins. Based on their catalytic proficiencies reported recently, these amyloid assemblies have been argued as the earliest protein folds. Herein, we map out the recent progress made by our laboratory and other research groups that demonstrate the catalytic diversity of cross β amyloid assemblies. The important role of morphology and specific mutations in peptide sequences has been underpinned in this review. We have divided the feature article into different sections where examples from biology have been covered demonstrating the mechanism of extant biocatalysts and compared with recent works on cross β amyloid folds showing covalent catalysis, aldolase, hydrolase, peroxidase-like activities and complex cascade catalysis. Beyond equilibrium, we have extended our discussion towards transient catalytic amyloid phases mimicking the energy driven cytoskeleton polymerization. Finally, a future outlook has been provided on the way ahead for short peptide-based systems chemistry approaches that can lead to the development of robust catalytic networks with improved enzyme-like proficiencies and higher complexities. The discussed examples along with the rationale behind selecting specific amino acids sequence will benefit readers to design systems for achieving catalytic reactivity similar to natural complex enzymes.
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Affiliation(s)
- Sumit Pal
- 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.
| | - 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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28
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation*. Angew Chem Int Ed Engl 2021; 60:12727-12731. [PMID: 33769680 DOI: 10.1002/anie.202100806] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/11/2021] [Indexed: 12/15/2022]
Abstract
The presence of amino acids on the prebiotic Earth, either stemming from endogenous chemical routes or delivered by meteorites, is consensually accepted. Prebiotically plausible pathways to peptides from inactivated amino acids are still unclear as most oligomerization approaches rely on thermodynamically disfavored reactions in solution. Now, a combination of prebiotically plausible minerals and mechanochemical activation enables the oligomerization of glycine at ambient temperature in the absence of water. Raising the reaction temperature increases the degree of oligomerization concomitantly with the formation of a commonly unwanted cyclic glycine dimer (DKP). However, DKP is a productive intermediate in the mechanochemical oligomerization of glycine. The findings of this research show that mechanochemical peptide bond formation is a dynamic process that provides alternative routes towards oligopeptides and establishes new synthetic approaches for prebiotic chemistry.
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Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Nikola Cindro
- Department of Organic Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - José G Hernández
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
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29
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Nikola Cindro
- Department of Organic Chemistry Faculty of Science University of Zagreb Horvatovac 102a 10000 Zagreb Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - José G. Hernández
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
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30
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Kwiatkowski W, Bomba R, Afanasyev P, Boehringer D, Riek R, Greenwald J. Präbiotische Peptid‐Synthese und spontane Amyloid‐Bildung im Inneren eines protozellulären Kompartiments. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Witek Kwiatkowski
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
| | - Radoslaw Bomba
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
| | - Pavel Afanasyev
- Wissenschaftliches Zentrum für optische und Elektronenmikroskopie Eidgenössische Technische Hochschule, ETH-Hönggerberg Otto-Stern-Weg 3 CH-8093 Zürich Schweiz
| | - Daniel Boehringer
- Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule, ETH-Hönggerberg Otto-Stern-Weg 5 CH-8093 Zürich Schweiz
| | - Roland Riek
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
| | - Jason Greenwald
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
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31
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Liu Q, Wan K, Shang Y, Wang ZG, Zhang Y, Dai L, Wang C, Wang H, Shi X, Liu D, Ding B. Cofactor-free oxidase-mimetic nanomaterials from self-assembled histidine-rich peptides. NATURE MATERIALS 2021; 20:395-402. [PMID: 33257794 DOI: 10.1038/s41563-020-00856-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/14/2020] [Indexed: 05/21/2023]
Abstract
Natural oxidases mainly rely on cofactors and well-arranged amino acid residues for catalysing electron-transfer reactions but suffer from non-recovery of their activity upon externally induced protein unfolding. However, it remains unknown whether residues at the active site can catalyse similar reactions in the absence of the cofactor. Here, we describe a series of self-assembling, histidine-rich peptides, as short as a dipeptide, with catalytic function similar to that of haem-dependent peroxidases. The histidine residues of the peptide chains form periodic arrays that are able to catalyse H2O2 reduction reactions efficiently through the formation of reactive ternary complex intermediates. The supramolecular catalyst exhibiting the highest activity could be switched between inactive and active states without loss of activity for ten cycles of heating/cooling or acidification/neutralization treatments, demonstrating the reversible assembly/disassembly of the active residues. These findings may aid the design of advanced biomimetic catalytic materials and provide a model for primitive cofactor-free enzymes.
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Affiliation(s)
- Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Kaiwei Wan
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Laboratory of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing, China.
| | - Yiyang Zhang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, China
| | - Luru Dai
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Chen Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China.
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China.
- University of the Chinese Academy of Sciences, Beijing, People's Republic of China.
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32
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An Individual Amino Acid as a Possible Prebiotic Catalyst. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202100005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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33
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Kwiatkowski W, Bomba R, Afanasyev P, Boehringer D, Riek R, Greenwald J. Prebiotic Peptide Synthesis and Spontaneous Amyloid Formation Inside a Proto-Cellular Compartment. Angew Chem Int Ed Engl 2021; 60:5561-5568. [PMID: 33325627 DOI: 10.1002/anie.202015352] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Indexed: 12/12/2022]
Abstract
Cellular life requires a high degree of molecular complexity and self-organization, some of which must have originated in a prebiotic context. Here, we demonstrate how both of these features can emerge in a plausibly prebiotic system. We found that chemical gradients in simple mixtures of activated amino acids and fatty acids can lead to the formation of amyloid-like peptide fibrils that are localized inside of a proto-cellular compartment. In this process, the fatty acid or lipid vesicles act both as a filter, allowing the selective passage of activated amino acids, and as a barrier, blocking the diffusion of the amyloidogenic peptides that form spontaneously inside the vesicles. This synergy between two distinct building blocks of life induces a significant increase in molecular complexity and spatial order thereby providing a route for the early molecular evolution that could give rise to a living cell.
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Affiliation(s)
- Witek Kwiatkowski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Radoslaw Bomba
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Pavel Afanasyev
- Scientific Center for Optical and Electron Microscopy, Swiss Federal Institute of Technology, ETH-Hönggerberg, Otto-Stern-Weg 3, CH-8093, Zürich, Switzerland
| | - Daniel Boehringer
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, ETH-Hönggerberg, Otto-Stern-Weg 5, CH-8093, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
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34
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Abstract
Self-assembly of proteins and peptides into the amyloid fold is a widespread phenomenon in the natural world. The structural hallmark of self-assembly into amyloid fibrillar assemblies is the cross-beta motif, which conveys distinct morphological and mechanical properties. The amyloid fibril formation has contrasting results depending on the organism, in the sense that it can bestow an organism with the advantages of mechanical strength and improved functionality or, on the contrary, could give rise to pathological states. In this chapter we review the existing information on amyloid-like peptide aggregates, which could either be derived from protein sequences, but also could be rationally or de novo designed in order to self-assemble into amyloid fibrils under physiological conditions. Moreover, the development of self-assembled fibrillar biomaterials that are tailored for the desired properties towards applications in biomedical or environmental areas is extensively analyzed. We also review computational studies predicting the amyloid propensity of the natural amino acid sequences and the structure of amyloids, as well as designing novel functional amyloid materials.
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Affiliation(s)
- C. Kokotidou
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
| | - P. Tamamis
- Texas A&M University, Artie McFerrin Department of Chemical Engineering College Station Texas 77843-3122 USA
| | - A. Mitraki
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
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35
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Abstract
Thresholds are widespread in origin of life scenarios, from the emergence of chirality, to the appearance of vesicles, of autocatalysis, all the way up to Darwinian evolution. Here, we analyze the “error threshold,” which poses a condition for sustaining polymer replication, and generalize the threshold approach to other properties of prebiotic systems. Thresholds provide theoretical predictions, prescribe experimental tests, and integrate interdisciplinary knowledge. The coupling between systems and their environment determines how thresholds can be crossed, leading to different categories of prebiotic transitions. Articulating multiple thresholds reveals evolutionary properties in prebiotic scenarios. Overall, thresholds indicate how to assess, revise, and compare origin of life scenarios.
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Affiliation(s)
- Cyrille Jeancolas
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, 75005 Paris, France.,Laboratoire d'Anthropologie Sociale, Collège de France, 52 rue du Cardinal Lemoine, 75005 Paris, France
| | - Christophe Malaterre
- Département de Philosophie and Centre de Recherche Interuniversitaire sur la Science et la Technologie (CIRST), Université du Québec à Montréal (UQAM), 455 boulevard René-Lévesque Est, Montréal, QC H3C 3P8, Canada
| | - Philippe Nghe
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, 75005 Paris, France
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36
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Protoenzymes: The Case of Hyperbranched Polymer-Scaffolded ZnS Nanocrystals. Life (Basel) 2020; 10:life10080150. [PMID: 32823487 PMCID: PMC7460482 DOI: 10.3390/life10080150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/03/2020] [Accepted: 07/04/2020] [Indexed: 12/15/2022] Open
Abstract
Enzymes are biological catalysts that are comprised of small-molecule, metal, or cluster catalysts augmented by biopolymeric scaffolds. It is conceivable that early in chemical evolution, ancestral enzymes opted for simpler, easier to assemble scaffolds. Herein, we describe such possible protoenzymes: hyperbranched polymer-scaffolded metal-sulfide nanocrystals. Hyperbranched polyethyleneimine (HyPEI) and glycerol citrate polymer-supported ZnS nanocrystals (NCs) are formed in a simple process. Transmission electron microscopy (TEM) analyses of HyPEI-supported NCs reveal spherical particles with an average size of 10 nm that undergo only a modest aggregation over a 14-day incubation. The polymer-supported ZnS NCs are shown to possess a high photocatalytic activity in an eosin B photodegradation assay, making them an attractive model for the study of the origin of life under the “Zn world” theory dominated by a photocatalytic proto-metabolic redox reaction network. The catalyst, however, could be easily adapted to apply broadly to different protoenzymatic systems.
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37
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Engelberg Y, Landau M. The Human LL-37(17-29) antimicrobial peptide reveals a functional supramolecular structure. Nat Commun 2020; 11:3894. [PMID: 32753597 PMCID: PMC7403366 DOI: 10.1038/s41467-020-17736-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 07/10/2020] [Indexed: 11/09/2022] Open
Abstract
Here, we demonstrate the self-assembly of the antimicrobial human LL-37 active core (residues 17–29) into a protein fibril of densely packed helices. The surface of the fibril encompasses alternating hydrophobic and positively charged zigzagged belts, which likely underlie interactions with and subsequent disruption of negatively charged lipid bilayers, such as bacterial membranes. LL-3717–29 correspondingly forms wide, ribbon-like, thermostable fibrils in solution, which co-localize with bacterial cells. Structure-guided mutagenesis analyses supports the role of self-assembly in antibacterial activity. LL-3717–29 resembles, in sequence and in the ability to form amphipathic helical fibrils, the bacterial cytotoxic PSMα3 peptide that assembles into cross-α amyloid fibrils. This argues helical, self-assembling, basic building blocks across kingdoms of life and points to potential structural mimicry mechanisms. The findings expose a protein fibril which performs a biological activity, and offer a scaffold for functional and durable biomaterials for a wide range of medical and technological applications. The human antibacterial and immunomodulatory peptide LL-37 is a hCAP-18 protein cleavage product that self-assembles. Here, the authors present the human and gorilla LL-37 (17–29) crystal structures, revealing a self-assembly of amphipathic helices into a densely packed and elongated hexameric structure with a central pore and mutagenesis experiments support the role of self-assembly for antibacterial activity.
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Affiliation(s)
- Yizhaq Engelberg
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. .,Centre for Structural Systems Biology (CSSB), and European Molecular Biology Laboratory (EMBL), 22607, Hamburg, Germany.
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38
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Gupta S, Singh I, Sharma AK, Kumar P. Ultrashort Peptide Self-Assembly: Front-Runners to Transport Drug and Gene Cargos. Front Bioeng Biotechnol 2020; 8:504. [PMID: 32548101 PMCID: PMC7273840 DOI: 10.3389/fbioe.2020.00504] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/29/2020] [Indexed: 12/18/2022] Open
Abstract
The translational therapies to promote interaction between cell and signal come with stringent eligibility criteria. The chemically defined, hierarchically organized, and simpler yet blessed with robust intermolecular association, the peptides, are privileged to make the cut-off for sensing the cell-signal for biologics delivery and tissue engineering. The signature service and insoluble network formation of the peptide self-assemblies as hydrogels have drawn a spell of research activity among the scientists all around the globe in the past decades. The therapeutic peptide market players are anticipating promising growth opportunities due to the ample technological advancements in this field. The presence of the other organic moieties, enzyme substrates and well-established protecting groups like Fmoc and Boc etc., bring the best of both worlds. Since the large sequences of peptides severely limit the purification and their isolation, this article reviews the account of last 5 years' efforts on novel approaches for formulation and development of single molecule amino acids, ultra-short peptide self-assemblies (di- and tri- peptides only) and their derivatives as drug/gene carriers and tissue-engineering systems.
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Affiliation(s)
- Seema Gupta
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Indu Singh
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Ashwani K. Sharma
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Pradeep Kumar
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
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39
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Jaworek MW, Ruggiero A, Graziano G, Winter R, Vitagliano L. On the extraordinary pressure stability of the Thermotoga maritima arginine binding protein and its folded fragments - a high-pressure FTIR spectroscopy study. Phys Chem Chem Phys 2020; 22:11244-11248. [PMID: 32400824 DOI: 10.1039/d0cp01618g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The arginine binding protein from T. maritima (ArgBP) exhibits several distinctive biophysical and structural properties. Here we show that ArgBP is also endowed with a ramarkable pressure stability as it undergoes minor structural changes only, even at 10 kbar. A similar stability is also observed for its folded fragments (truncated monomer and individual domains). A survey of literature data on the pressure stability of proteins highlights the uncommon behavior of ArgBP.
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Affiliation(s)
- Michel W Jaworek
- Faculty of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn Str. 4a, D-44227 Dortmund, Germany.
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40
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Zozulia O, Korendovych IV. Semi-Rationally Designed Short Peptides Self-Assemble and Bind Hemin to Promote Cyclopropanation. Angew Chem Int Ed Engl 2020; 59:8108-8112. [PMID: 32128962 PMCID: PMC7274867 DOI: 10.1002/anie.201916712] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Indexed: 11/11/2022]
Abstract
The self-assembly of short peptides gives rise to versatile nanoassemblies capable of promoting efficient catalysis. We have semi-rationally designed a series of seven-residue peptides that form hemin-binding catalytic amyloids to facilitate enantioselective cyclopropanation with efficiencies that rival those of engineered hemin proteins. These results demonstrate that: 1) Catalytic amyloids can bind complex metallocofactors to promote practically important multisubstrate transformations. 2) Even essentially flat surfaces of amyloid assemblies can impart a substantial degree of enantioselectivity without the need for extensive optimization. 3) The ease of peptide preparation allows for straightforward incorporation of unnatural amino acids and the preparation of peptides made from d-amino acids with complete reversal of enantioselectivity.
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Affiliation(s)
- Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
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41
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Zozulia O, Korendovych IV. Semi‐Rationally Designed Short Peptides Self‐Assemble and Bind Hemin to Promote Cyclopropanation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916712] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Oleksii Zozulia
- Department of ChemistrySyracuse University 111 College Place Syracuse NY 13244 USA
| | - Ivan V. Korendovych
- Department of ChemistrySyracuse University 111 College Place Syracuse NY 13244 USA
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42
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Kleinsmann AJ, Nachtsheim BJ. A minimalistic hydrolase based on co-assembled cyclic dipeptides. Org Biomol Chem 2020; 18:102-107. [PMID: 31799587 DOI: 10.1039/c9ob02198a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The self-assembly of small peptides into larger aggregates is an important process for the fundamental understanding of abiogenesis. In this article we demonstrate that blends of cyclic dipeptides (2,5-diketopiperazines - DKPs) bearing either histidine or cysteine in combination with a lipophilic amino acid form highly stable aggregates in aqueous solution with esterase-like activity. We demonstrate that the catalytic activity is based on an intermolecular cooperative behavior between histidine and cysteine. A high control of the molecular arrangement of the peptide assemblies was gained by C-H-π interactions between Phe and Leu or Val sidechains, resulting in a significant increase in catalytic activity. These interactions were strongly supported by Hartree-Fock calculations and finally confirmed via1H-NMR HRMAS NOE spectroscopy.
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Affiliation(s)
- Alexander J Kleinsmann
- Institut für Organische Chemie Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
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43
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Chatterjee A, Afrose SP, Ahmed S, Venugopal A, Das D. Cross-β amyloid nanotubes for hydrolase-peroxidase cascade reactions. Chem Commun (Camb) 2020; 56:7869-7872. [PMID: 32154814 DOI: 10.1039/d0cc00279h] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Herein, we report the catalytic potential of short peptide based cross-β amyloid nanotubes with surface exposed histidine capable of binding hemin and showing facile cascade reactions, playing the dual roles of hydrolases and peroxidases, two of the most important classes of enzymes in extant biology. The activity of these simple systems exceeded those of modern and larger proteins like cytochrome C and hemoglobin. Further, evidence suggested that these self-assembled nanotubes foreshadow the process of intermediate channeling, a feature seen in the case of advanced enzymes.
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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.
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44
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Reja A, Afrose SP, Das D. Aldolase Cascade Facilitated by Self‐Assembled Nanotubes from Short Peptide Amphiphiles. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
| | - Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
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45
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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46
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Sarkhel B, Chatterjee A, Das D. Covalent Catalysis by Cross β Amyloid Nanotubes. J Am Chem Soc 2020; 142:4098-4103. [PMID: 32083482 DOI: 10.1021/jacs.9b13517] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The binding pockets of extant enzymes feature precise positioning of amino acid residues that facilitate multiple complex transformations exploiting covalent and non-covalent interactions. Reversible covalent anchoring is extensively used as an efficient tool by Nature for activating modern enzymes such as esterases and dehydratases and also for proteins like opsins for the complex process of visual phototransduction. Here we construct paracrystalline amyloid surfaces through the self-propagation of short peptides which offer binding pockets exposed with arrays of imidazoles and lysines. As covalent catalysis is utilized by modern-day enzymes, these homogeneous amyloid nanotubes exploit Schiff imine formation via the exposed lysines to efficiently hydrolyze both activated and inactivated esters. Controls where lysines were mutated with charged residues accessed similar morphologies but did not augment the rate. The designed amyloid microphases thus foreshadow the generation of binding pockets of advanced proteins and have the potential to contribute to the development of functional materials.
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Affiliation(s)
- Baishakhi Sarkhel
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Ayan Chatterjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
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Reja A, Afrose SP, Das D. Aldolase Cascade Facilitated by Self-Assembled Nanotubes from Short Peptide Amphiphiles. Angew Chem Int Ed Engl 2020; 59:4329-4334. [PMID: 31920004 DOI: 10.1002/anie.201914633] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Indexed: 12/25/2022]
Abstract
Early evolution benefited from a complex network of reactions involving multiple C-C bond forming and breaking events that were critical for primitive metabolism. Nature gradually chose highly evolved and complex enzymes such as lyases to efficiently facilitate C-C bond formation and cleavage with remarkable substrate selectivity. Reported here is a lipidated short peptide which accesses a homogenous nanotubular morphology to efficiently catalyze C-C bond cleavage and formation. This system shows morphology-dependent catalytic rates, suggesting the formation of a binding pocket and registered enhancements in the presence of the hydrogen-bond donor tyrosine, which is exploited by extant aldolases. These assemblies showed excellent substrate selectivity and templated the formation of a specific adduct from a pool of possible adducts. The ability to catalyze metabolically relevant cascade transformations suggests the importance of such systems in early evolution.
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Affiliation(s)
- Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Syed Pavel Afrose
- 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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48
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Adsorption of Rose Bengal on a self-assembled fibrillar network affords a thermally switchable oxygenation photocatalyst and a thermochromic soft material. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2019.112142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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49
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Bomba R, Rout SK, Bütikofer M, Kwiatkowski W, Riek R, Greenwald J. Carbonyl Sulfide as a Prebiotic Activation Agent for Stereo- and Sequence-Selective, Amyloid-Templated Peptide Elongation. ORIGINS LIFE EVOL B 2019; 49:213-224. [PMID: 31845164 DOI: 10.1007/s11084-019-09586-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/26/2019] [Indexed: 01/28/2023]
Abstract
Prebiotic chemical replication is a commonly assumed precursor to and prerequisite for life and as such is the one of the goals of our research. We have previously reported on the role that short peptide amyloids could have played in a template-based chemical elongation. Here we take a step closer to the goal by reproducing amyloid-templated peptide elongation with carbonyl sulfide (COS) in place of the less-prebiotically relevant carbonyldiimidazole (CDI) used in the earlier study. Our investigation shows that the sequence-selectivity and stereoselectivity of the amyloid-templated reaction is similar for both activation chemistries. Notably, the amyloid protects the peptides from some of the side-reactions that take place with the COS-activation.
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Affiliation(s)
- Radoslaw Bomba
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Saroj K Rout
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Matthias Bütikofer
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Witek Kwiatkowski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland.
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland.
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Makam P, Yamijala SSRKC, Tao K, Shimon LJW, Eisenberg DS, Sawaya MR, Wong BM, Gazit E. Non-proteinaceous hydrolase comprised of a phenylalanine metallo-supramolecular amyloid-like structure. Nat Catal 2019; 2:977-985. [PMID: 31742246 PMCID: PMC6861134 DOI: 10.1038/s41929-019-0348-x] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Enzymatic activity is crucial for various technological applications, yet the complex structures and limited stability of enzymes often hinder their use. Hence, de novo design of robust biocatalysts that are much simpler than their natural counterparts and possess enhanced catalytic activity has long been a goal in biotechnology. Here, we present evidence for the ability of a single amino acid to self-assemble into a potent and stable catalytic structural entity. Spontaneously, phenylalanine (F) molecules coordinate with zinc ions to form a robust, layered, supramolecular amyloid-like ordered architecture (F-Zn(ii)) and exhibit remarkable carbonic anhydrase-like catalytic activity. Notably, amongst the reported artificial biomolecular hydrolases, F-Zn(ii) displays the lowest molecular mass and highest catalytic efficiency, in addition to reusability, thermal stability, substrate specificity, stereoselectivity and rapid catalytic CO2 hydration ability. Thus, this report provides a rational path towards future de novo design of minimalistic biocatalysts for biotechnological and industrial applications.
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Affiliation(s)
- Pandeeswar Makam
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Linda J. W. Shimon
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - David S. Eisenberg
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael R. Sawaya
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
| | - Bryan M. Wong
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
- Department of Physics and Astronomy, and Materials Science and Engineering Program, University of California, Riverside, CA, USA
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
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