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Kenchel J, Vázquez-Salazar A, Wells R, Brunton K, Janzen E, Schultz KM, Liu Z, Li W, Parker ET, Dworkin JP, Chen IA. Prebiotic chiral transfer from self-aminoacylating ribozymes may favor either handedness. Nat Commun 2024; 15:7980. [PMID: 39266567 PMCID: PMC11393417 DOI: 10.1038/s41467-024-52362-x] [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: 11/21/2022] [Accepted: 09/05/2024] [Indexed: 09/14/2024] Open
Abstract
Modern life is essentially homochiral, containing D-sugars in nucleic acid backbones and L-amino acids in proteins. Since coded proteins are theorized to have developed from a prebiotic RNA World, the homochirality of L-amino acids observed in all known life presumably resulted from chiral transfer from a homochiral D-RNA World. This transfer would have been mediated by aminoacyl-RNAs defining the genetic code. Previous work on aminoacyl transfer using tRNA mimics has suggested that aminoacylation using D-RNA may be inherently biased toward reactivity with L-amino acids, implying a deterministic path from a D-RNA World to L-proteins. Using a model system of self-aminoacylating D-ribozymes and epimerizable activated amino acid analogs, we test the chiral selectivity of 15 ribozymes derived from an exhaustive search of sequence space. All of the ribozymes exhibit detectable selectivity, and a substantial fraction react preferentially to produce the D-enantiomer of the product. Furthermore, chiral preference is conserved within sequence families. These results are consistent with the transfer of chiral information from RNA to proteins but do not support an intrinsic bias of D-RNA for L-amino acids. Different aminoacylation structures result in different directions of chiral selectivity, such that L-proteins need not emerge from a D-RNA World.
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Affiliation(s)
- Josh Kenchel
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, USA
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA
| | - Alberto Vázquez-Salazar
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA
| | - Reno Wells
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Krishna Brunton
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Evan Janzen
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, USA
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Kyle M Schultz
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Ziwei Liu
- Department of Earth Sciences, University of Cambridge, Cambridge, USA
- MRC - Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Weiwei Li
- Bren School of Environmental Management, University of California, Santa Barbara, CA, USA
| | - Eric T Parker
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - Jason P Dworkin
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - Irene A Chen
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, USA.
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA.
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
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2
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Syndiotactic hexamer peptide nanodots. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:483-491. [PMID: 35876872 DOI: 10.1007/s00249-022-01610-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/24/2022] [Accepted: 07/03/2022] [Indexed: 10/16/2022]
Abstract
Spatial confinement of excitons in the nano-crystalline region of semiconducting nanostructures differ significantly from the optoelectronic properties exhibited by the bulk material. We report spike-like absorption observed in the UV spectrum of a phenylalanine hexamer peptide [(Ff)3-OH] nano-assembly, which may be attributed to the spatial confinement of electrons to the dimension of quantum dots. Interdependency of the UV and PLE spectrum of the peptide confirms the existence of quantum confinement in (Ff)3-OH nano-assemblies.
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3
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Sasidharan S, Ramakrishnan V. Aromatic interactions directing peptide nano-assembly. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:119-160. [PMID: 35534106 DOI: 10.1016/bs.apcsb.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Self-assembly is a process of spontaneous organization of molecules as a result of non-covalent interactions. Organized self-assembly at the nano level is emerging as a powerful tool in the bottom-up fabrication of functional nanostructures for targeted applications. Aromatic π-π stacking plays a significant role by facilitating the persistent supramolecular association of individual subunits to the self-assembled structures of high stability. Understanding, the supramolecular chemistry of the materials interacting through aromatic interactions, is of tremendous interest in not only constructing functional materials but also in revealing the mechanism of molecular assembly in living organisms. This chapter aims to focus on understanding the potential role of π-π interactions in directing and regulating the self-assembly of peptide nanostructures. The scope of the chapter starts with an outline of the history and mechanism of the aromatic π-π interactions. It progresses through the design strategy for the assembly of peptides containing aromatic rings, the conditions affecting the aromatic stacking interactions, their resulting nanoassemblies, properties, and applications. The properties and applications of the supramolecular materials formed through the aromatic stacking interactions are highlighted to provide an increased understanding of the role of weak interactions in the design and construction of novel functional materials.
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Affiliation(s)
- Sajitha Sasidharan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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4
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Dyakin VV, Uversky VN. Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality. Int J Mol Sci 2022; 23:ijms23073687. [PMID: 35409047 PMCID: PMC8998916 DOI: 10.3390/ijms23073687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
Chirality is a universal phenomenon, embracing the space–time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are determined by utilizing the energy stored, transferred, and released, via adenosine triphosphate (ATP). At the protein level, the synthesis of a homochiral polypeptide chain of L-amino acids (L-AAs) represents the first state in the evolution of the dynamic non-equilibrium state of the system. At the next step the non-equilibrium state of a protein-centric system is supported and amended by a broad set of posttranslational modifications (PTMs). The enzymatic phosphorylation, being the most abundant and ATP-driven form of PTMs, illustrates the principal significance of the energy-coupling, in maintaining and reshaping the system. However, the physiological functions of phosphorylation are under the permanent risk of being compromised by spontaneous racemization. Therefore, the major distinct steps in protein-centric aging include the biosynthesis of a polypeptide chain, protein folding assisted by the system of PTMs, and age-dependent spontaneous protein racemization and degradation. To the best of our knowledge, we are the first to pay attention to the biphasic, alternative, and stepwise changes in the conformational entropy of protein folding. The broader view on protein folding, including the impact of spontaneous racemization, will help in the goal-oriented experimental design in the field of chiral proteomics.
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Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Bldg, 35, Orangeburg, NY 10962, USA
- Correspondence:
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA;
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5
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Dyakin VV, Dyakina-Fagnano NV, Mcintire LB, Uversky VN. Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology. Int J Mol Sci 2021; 23:ijms23010285. [PMID: 35008708 PMCID: PMC8745688 DOI: 10.3390/ijms23010285] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/24/2021] [Accepted: 12/22/2021] [Indexed: 12/23/2022] Open
Abstract
In humans, age-associated degrading changes, widely observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psychological abilities, and memory. Cross-talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, genome, proteome, and lipidome instability are widely recognized as the primary causal factors in aging. We narrow attention to the roles of protein aging linked to prevalent amino acids chirality, enzymatic and spontaneous (non-enzymatic) post-translational modifications (PTMs SP), and non-equilibrium phase transitions. The homochirality of protein synthesis, resulting in the steady-state non-equilibrium condition of protein structure, makes them prone to multiple types of enzymatic and spontaneous PTMs, including racemization and isomerization. Spontaneous racemization leads to the loss of the balanced prevalent chirality. Advanced biological aging related to irreversible PTMs SP has been associated with the nontrivial interplay between somatic (molecular aging) and mental (psychological aging) health conditions. Through stress response systems (SRS), the environmental and psychological stressors contribute to the age-associated “collapse” of protein homochirality. The role of prevalent protein chirality and entropy of protein folding in biological aging is mainly overlooked. In a more generalized context, the time-dependent shift from enzymatic to the non-enzymatic transformation of biochirality might represent an important and yet underappreciated hallmark of aging. We provide the experimental arguments in support of the racemization theory of aging.
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Affiliation(s)
- Victor V. Dyakin
- The Nathan S. Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Bldg, 35, Bld. 35. Rom 201-C, Orangeburg, NY 10962, USA
- Correspondence: ; Tel.: +1-845-548-96-94; Fax: +1-845-398-5510
| | - Nuka V. Dyakina-Fagnano
- Child, Adolescent and Young Adult Psychiatry, 36 Franklin Turnpike, Waldwick, NJ 07463, USA;
| | - Laura B. Mcintire
- Department of Pathology and Cell Biology, Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA;
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA;
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6
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7
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Goyal B, Srivastava KR, Durani S. N-terminal diproline and charge group effects on the stabilization of helical conformation in alanine-based short peptides: CD studies with water and methanol as solvent. J Pept Sci 2017; 23:431-437. [PMID: 28425159 DOI: 10.1002/psc.3005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 12/25/2022]
Abstract
Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine-based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N-terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine-based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac-Pro-Pro-Ala-Lys-Ala-Lys-Ala-Lys-Ala-NH2 ) is designed to assess the effect of N-terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac-Pro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH2 ) and A3 (Ac-dPro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH2 ) with N-terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i, i + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1, A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature-dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and β-strand conformation, which is consistent with the previous studies. The results illuminate the effect of N-terminal diproline and charged side chains in dictating the preferences for extended-β, semi-extended PPII and helical conformation in alanine-based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Department of Chemistry, School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406, Punjab, India
| | - Kinshuk Raj Srivastava
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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8
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Jafarpour F, Biancalani T, Goldenfeld N. Noise-induced symmetry breaking far from equilibrium and the emergence of biological homochirality. Phys Rev E 2017; 95:032407. [PMID: 28415353 DOI: 10.1103/physreve.95.032407] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Indexed: 05/02/2023]
Abstract
The origin of homochirality, the observed single-handedness of biological amino acids and sugars, has long been attributed to autocatalysis, a frequently assumed precursor for early life self-replication. However, the stability of homochiral states in deterministic autocatalytic systems relies on cross-inhibition of the two chiral states, an unlikely scenario for early life self-replicators. Here we present a theory for a stochastic individual-level model of autocatalytic prebiotic self-replicators that are maintained out of thermal equilibrium. Without chiral inhibition, the racemic state is the global attractor of the deterministic dynamics, but intrinsic multiplicative noise stabilizes the homochiral states. Moreover, we show that this noise-induced bistability is robust with respect to diffusion of molecules of opposite chirality, and systems of diffusively coupled autocatalytic chemical reactions synchronize their final homochiral states when the self-replication is the dominant production mechanism for the chiral molecules. We conclude that nonequilibrium autocatalysis is a viable mechanism for homochirality, without imposing additional nonlinearities such as chiral inhibition.
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Affiliation(s)
- Farshid Jafarpour
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, Indiana 47907, USA
| | - Tommaso Biancalani
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nigel Goldenfeld
- Department of Physics, University of Illinois at Urbana-Champaign, Loomis Laboratory of Physics, 1110 West Green Street, Urbana, Illinois 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
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9
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Srivastava KR, Goyal B, Kumar A, Durani S. Scrutiny of electrostatic-driven conformational ordering of polypeptide chains in DMSO: a study with a model oligopeptide. RSC Adv 2017. [DOI: 10.1039/c7ra02137b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The molecular mechanism of DMSO-induced stabilisation of β-sheets is attributed to the combination of polar electrostatic interactions among side chains, and backbone desolvation through bulky side chains which promotes backbone hydrogen bonding.
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Affiliation(s)
| | - Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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10
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Goyal B, Kumar A, Srivastava KR, Durani S. Scrutiny of chain-length and N-terminal effects in α-helix folding: a molecular dynamics study on polyalanine peptides. J Biomol Struct Dyn 2016; 35:1923-1935. [DOI: 10.1080/07391102.2016.1199972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Chemistry, School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Kinshuk Raj Srivastava
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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11
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Goyal B, Kumar A, Srivastava KR, Durani S. Computational scrutiny of the effect of N-terminal proline and residue stereochemistry in the nucleation of α-helix fold. RSC Adv 2016. [DOI: 10.1039/c6ra10934a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
N-Terminal l- to d-residue mutation nucleate helical fold in Ac–DAla–LAla3–NHMe (Ib, m2), Ac–DPro–LAla3–NHMe (IIb, m1), and Ac–DPro–LPro–LAla2–NHMe (IIIb, m2) peptides.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | | | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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12
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Goyal B, Srivastava KR, Kumar A, Patwari GN, Durani S. Probing the role of electrostatics of polypeptide main-chain in protein folding by perturbing N-terminal residue stereochemistry: DFT study with oligoalanine models. RSC Adv 2016. [DOI: 10.1039/c6ra22870d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Energetics of folding (ΔHE→F, in kcal mol−1) from the extended (E) structure to the folded (F) structure for Ia and Ib critically depend on the geometrical relationship between the backbone peptide units of the polypeptide structure.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | | | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - G. Naresh Patwari
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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13
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Gupta P, Durani S. Algorithm to design inhibitors using stereochemically mixed l,d polypeptides: Validation against HIV protease. Int J Biol Macromol 2015; 81:410-7. [PMID: 26279121 DOI: 10.1016/j.ijbiomac.2015.08.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 08/11/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
Polypeptides have potential to be designed as drugs or inhibitors against the desired targets. In polypeptides, every chiral α-amino acid has enantiomeric structural possibility to become l or d amino acids and can be used as design monomer. Among the various possibilities, use of stereochemistry as a design tool has potential to determine both functional specificity and metabolic stability of the designed polypeptides. The polypeptides with mixed l,d amino acids are a class of peptidomimitics, an attractive drug like molecules and also less susceptible to proteolytic activities. Therefore in this study, a three step algorithm is proposed to design the polypeptides against desired drug targets. For this, all possible configurational isomers of mixed l,d polyleucine (Ac-Leu8-NHMe) structure were randomly modeled with simulated annealing molecular dynamics and the resultant library of discrete folds were scored against HIV protease as a model target. The best scored folds of mixed l,d structures were inverse optimized for sequences in situ and the resultant sequences as inhibitors were validated for conformational integrity using molecular dynamics. This study presents and validates an algorithm to design polypeptides of mixed l,d structures as drugs/inhibitors by inverse fitting them as molecular ligands against desired target.
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Affiliation(s)
- Pooja Gupta
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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14
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Hyland LL, Twomey JD, Vogel S, Hsieh AH, Yu YB. Enhancing biocompatibility of D-oligopeptide hydrogels by negative charges. Biomacromolecules 2013; 14:406-12. [PMID: 23256640 DOI: 10.1021/bm301598g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Oligopeptide hydrogels are emerging as useful matrices for cell culture with commercial products on the market, but L-oligopeptides are labile to proteases. An obvious solution is to create D-oligopeptide hydrogels, which lack enzymatic recognition. However, D-oligopeptide matrices do not support cell growth as well as L-oligopeptide matrices. In addition to chiral interactions, many cellular activities are strongly governed by charge-charge interactions. In this work, the effects of chirality and charge on human mesenchymal stem cell (hMSC) behavior were studied using hydrogels assembled from oppositely charged oligopeptides. It was found that negative charges significantly improved hMSC viability and proliferation in D-oligopeptide gels but had little effect on their interactions with L-oligopeptide gels. This result points to the possibility of using charge and other factors to engineer biomaterials whose chirality is distinct from that of natural biomaterials, but whose performance is close to that of natural biomaterials.
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Affiliation(s)
- Laura L Hyland
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, United States
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15
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Taraban MB, Feng Y, Hammouda B, Hyland LL, Yu YB. Chirality-Mediated Mechanical and Structural Properties of Oligopeptide Hydrogels. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2012; 24:2299-2310. [PMID: 23641124 PMCID: PMC3639503 DOI: 10.1021/cm300422q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The origin and the effects of homochirality in the biological world continuously stimulate numerous hypotheses and much debate. This work attempts to look at the biohomochirality issue from a different angle-the mechanical properties of the bulk biomaterial and their relation to nanoscale structures. Using a pair of oppositely charged peptides that co-assemble into hydrogels, we systematically investigated the effect of chirality on the mechanical properties of these hydrogels through different combinations of syndiotactic and isotactic peptides. It was found that homochirality confers mechanical advantage, resulting in higher elastic modulus and strain yield value. Yet, heterochirality confer kinetic advantage, resulting in faster gelation. Structurally, both homochiral and heterochiral hydrogels are made of fibers interconnected by lappet-like webs, but the homochiral peptide fibers are thicker and denser. The result highlights the possible role of biohomochirality in the evolution and/or natural selection of biomaterials.
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Affiliation(s)
- Marc B Taraban
- Fischell Department of Bioengineering, University of Maryland, College Park, USA
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16
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Srivastava KR, Kumar A, Goyal B, Durani S. Stereochemistry and Solvent Role in Protein Folding: Nuclear Magnetic Resonance and Molecular Dynamics Studies of Poly-l and Alternating-l,d Homopolypeptides in Dimethyl Sulfoxide. J Phys Chem B 2011; 115:6700-8. [DOI: 10.1021/jp200743w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
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17
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Kumar A, Ramakrishnan V. Creating novel protein scripts beyond natural alphabets. SYSTEMS AND SYNTHETIC BIOLOGY 2011; 4:247-56. [PMID: 22132051 DOI: 10.1007/s11693-011-9068-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 02/03/2011] [Indexed: 11/29/2022]
Abstract
Natural proteins are concatenated amino acids with definite handedness or chirality, with their spatial orientation being preferentially left handed or L-chiral. This paper discusses the biophysics of stereo-chemical perturbation to proteins using D-(α) amino acid and its utility as an additional design alphabet while scripting novel protein structures.
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18
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Patel K, Goyal B, Kumar A, Kishore N, Durani S. Cured of “Stickiness”, Poly-l β-Hairpin is Promoted with ll-to-dd Mutation as a Protein and a Hydrolase Mimic. J Phys Chem B 2010; 114:16887-93. [DOI: 10.1021/jp1062572] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Kirti Patel
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
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