1
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Chung MKJ, Miller RJ, Novak B, Wang Z, Ponder JW. Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field. J Chem Inf Model 2023; 63:2769-2782. [PMID: 37075788 PMCID: PMC10878370 DOI: 10.1021/acs.jcim.3c00155] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
A grand challenge of computational biophysics is accurate prediction of interactions between molecules. Molecular dynamics (MD) simulations have recently gained much interest as a tool to directly compute rigorous intermolecular binding affinities. The choice of a fixed point-charge or polarizable multipole force field used in MD is a topic of ongoing discussion. To compare alternative methods, we participated in the SAMPL7 and SAMPL8 Gibb octaacid host-guest challenges to assess the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) polarizable multipole force field. Advantages of AMOEBA over fixed charge models include improved representation of molecular electrostatic potentials and better description of water occupying the unligated host cavity. Prospective predictions for 26 host-guest systems exhibit a mean unsigned error vs experiment of 0.848 kcal/mol across all absolute binding free energies, demonstrating excellent agreement between computational and experimental results. In addition, we explore two topics related to the inclusion of ions in MD simulations: use of a neutral co-alchemical protocol and the effect of salt concentration on binding affinity. Use of the co-alchemical method minimally affects computed energies, but salt concentration significantly perturbs our binding results. Higher salt concentration strengthens binding through classical charge screening. In particular, added Na+ ions screen negatively charged carboxylate groups near the binding cavity, thereby diminishing repulsive coulomb interactions with negatively charged guests. Overall, the AMOEBA results demonstrate the accuracy available through a force field providing a detailed energetic description of the four octaacid hosts and 13 charged organic guests. Use of the AMOEBA polarizable atomic multipole force field in conjunction with an alchemical free energy protocol can achieve chemical accuracy in application to realistic molecular systems.
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Affiliation(s)
- Moses K. J. Chung
- Medical Scientist Training Program, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Physics, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Ryan J. Miller
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Borna Novak
- Medical Scientist Training Program, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Zhi Wang
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Jay W. Ponder
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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2
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El Samrout O, Berlier G, Lambert JF, Martra G. Polypeptide Chain Growth Mechanisms and Secondary Structure Formation in Glycine Gas-Phase Deposition on Silica Surfaces. J Phys Chem B 2023; 127:673-684. [PMID: 36637235 PMCID: PMC9884078 DOI: 10.1021/acs.jpcb.2c07382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Peptide formation by amino acids condensation represents a crucial reaction in the quest of the origins of life as well as in synthetic chemistry. However, it is still poorly understood in terms of efficiency and reaction mechanism. In the present work, peptide formation has been investigated through thermal condensation of gas-phase glycine in fluctuating silica environments as a model of prebiotic environments. In-situ IR spectroscopy measurements under a controlled atmosphere reveal that a humidity fluctuating system subjected to both temperature and water activity variations results in the formation of more abundant peptides compared to a dehydrated system subjected only to temperature fluctuations cycles. A model is proposed in which hydration steps result in the hydrolysis and redistribution of the oligomers formed during previous deposition in dry conditions. This results in the formation of self-assembled aggregates with well-defined secondary structures (especially β-sheets). Upon further monomers feeding, structural elements are conserved in newly growing chains, with indications of templated polymerization. The structural dynamics of peptides were also evaluated. Rigid self-assembled structures with a high resistance to further wetting/drying cycles and inaccessibility to isotopic exchange were present in the humidity fluctuating system compared to more flexible structures in the dehydrated system. The resistance and growth of self-assembled structures were also investigated for an extended duration of Gly deposition using isotope labeling.
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Affiliation(s)
- Ola El Samrout
- Department
of Chemistry and NIS Centre, University
of Torino, Via P. Giuria 7, 10125Torino, Italy,Laboratoire
de Réactivité de Surface, LRS (UMR 7197 CNRS), Sorbonne Université, Place Jussieu, 75005Paris, France
| | - Gloria Berlier
- Department
of Chemistry and NIS Centre, University
of Torino, Via P. Giuria 7, 10125Torino, Italy,
| | - Jean-François Lambert
- Laboratoire
de Réactivité de Surface, LRS (UMR 7197 CNRS), Sorbonne Université, Place Jussieu, 75005Paris, France,
| | - Gianmario Martra
- Department
of Chemistry and NIS Centre, University
of Torino, Via P. Giuria 7, 10125Torino, Italy
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3
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Barani Pour S, Jahanbin Sardroodi J, Rastkar Ebrahimzadeh A, Sadegh Avestan M. Using Molecular Dynamics Simulations to Understand the Effect of Fatty Acids Chain Length on Structural and Dynamic Properties of Deep Eutectic Solvents Based on Choline Chloride and Fatty Acids. ChemistrySelect 2022. [DOI: 10.1002/slct.202202591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Samaneh Barani Pour
- Molecular Science and Engineering Research Group (MSERG) Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Science and Engineering Research Group (MSERG) Department of Chemistry Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
| | - Alireza Rastkar Ebrahimzadeh
- Molecular Science and Engineering Research Group (MSERG Department of Physics Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
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4
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Donets S, Guskova O, Sommer JU. Searching for Aquamelt Behavior among Silklike Biomimetics during Fibrillation under Flow. J Phys Chem B 2021; 125:3238-3250. [PMID: 33750140 DOI: 10.1021/acs.jpcb.1c00647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this paper, we elucidate a generic mechanism behind strain-induced phase transition in aqueous solutions of silk-inspired biomimetics by atomistic molecular dynamics simulations. We show the results of modeling of homopeptides polyglycine Gly30 and polyalanine Ala30 and a heteropeptide (Gly-Ala-Gly-Ala-Gly-Ser)5, i.e., the simplest and yet relevant sequences that could mimic the behavior of natural silk under stress conditions. First, we analyze hydrophobicities of the sequences by calculating the Gibbs free energy of hydration and inspecting the interchain hydrogen bonding and hydration by water. Second, the force-extension profiles are scanned and compared with the results for poly(ethylene oxide), the synthetic polymer for which the aquamelt behavior has been proved recently. Additionally, the conformational transitions of oligopeptides from coiled to extended states are characterized by a generalized order parameter and by the dependence of the solvent-accessible surface area of the chains on applied stretching. Fibrillation itself is surveyed using both the two-dimensional interchain pair correlation function and the SAXS/WAXS patterns for the aggregates formed under stress. These are compared with experimental data found in the literature on fibril structure of silk composite materials doped with oligoalanine peptides. Our results show that tensile stress introduced into aqueous oligopeptide solutions facilitates interchain interactions. The oligopeptides display both a greater resistance to extension as compared to poly(ethylene oxide) and a reduced ability for hydrogen bonding of the stretched chains between oligomers and with water. Fiber formation is proved for all simulated objects, but the most structured one is made of a heteropeptide (Gly-Ala-Gly-Ala-Gly-Ser)5: For this sequence, we obtain the highest degree of the secondary structure motifs in the fiber. We conclude that this is the most promising candidate among considered sequences to find the aquamelt behavior in further experimental studies.
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Affiliation(s)
- Sergii Donets
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany
| | - Olga Guskova
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany.,Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, 01062 Dresden, Germany
| | - Jens-Uwe Sommer
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany.,Institute of Theoretical Physics, Technische Universität Dresden, Zellescher Weg 17, 01069 Dresden, Germany
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5
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Chen X, Salim T, Zhang Z, Yu X, Volkova I, Nijhuis CA. Large Increase in the Dielectric Constant and Partial Loss of Coherence Increases Tunneling Rates across Molecular Wires. ACS APPLIED MATERIALS & INTERFACES 2020; 12:45111-45121. [PMID: 32897683 DOI: 10.1021/acsami.0c11106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although the dielectric behavior of monolayers is important in a large range of applications, its role in charge transport studies involving molecular junctions is largely ignored. This paper describes a large increase in the relative static dielectric constant (εr) by simply increasing the thickness of well-organized monolayers of oligoglycine and oligo(ethylene glycol) from 7 up to 14. The resulting large capacitance of 3.5-5.1 μF/cm2 is thickness-independent, which is highly attractive for field-effect transistor applications. This increase of εr results in a linear increase of the thermal activation energy by a factor of 6, which suggests that the mechanism of charge transport gradually changes from coherent to (partially) incoherent tunneling. The comparisons of oligoglycine (which readily forms hydrogen bonds with neighboring molecules) and methyl terminated oligo(ethylene glycol) (which lacks hydrogen bond donors) monolayers, kinetic isotope effects, and relative humidity-dependent measurements all indicate the importance of strong hydrogen bonds involving ionic species and strongly bonded water in the unusual dielectric behavior and the incoherent tunneling mechanism. This partial loss of coherence of the charge carriers can explain the unusually small tunneling decay coefficients across long molecular wires, and the length-dependent increase of εr of monolayers opens up interesting new applications.
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Affiliation(s)
- Xiaoping Chen
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Teddy Salim
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Ziyu Zhang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Xiaojiang Yu
- Singapore Synchrotron Light Source, National University of Singapore, 5 Research Link, Singapore 117603, Singapore
| | - Ira Volkova
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Christian A Nijhuis
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre for Advanced 2D Materials and Graphene Research Centre, National University of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
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6
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Célerse F, Lagardère L, Derat E, Piquemal JP. Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems. J Chem Theory Comput 2019; 15:3694-3709. [DOI: 10.1021/acs.jctc.9b00199] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frédéric Célerse
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Institut Parisien de Chimie Moléculaire, UMR 8232 CNRS, Sorbonne Université, 75005 Paris, France
| | - Louis Lagardère
- Institut des Sciences du Calcul et des Données, Sorbonne Université, 75005 Paris, France
- Institut Parisien de Chimie Physique et Théorique, FR 2622 CNRS, Sorbonne Université, 75005 Paris, France
- Laboratoire de Chimie théorique, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
| | - Etienne Derat
- Institut Parisien de Chimie Moléculaire, UMR 8232 CNRS, Sorbonne Université, 75005 Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
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7
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Laury ML, Wang Z, Gordon AS, Ponder JW. Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field. J Comput Aided Mol Des 2018; 32:1087-1095. [PMID: 30324303 DOI: 10.1007/s10822-018-0147-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 08/09/2018] [Indexed: 01/17/2023]
Abstract
As part of the SAMPL6 host-guest blind challenge, the AMOEBA force field was applied to calculate the absolute binding free energy for a cucurbit[8]uril host complexed with 14 diverse guests, ranging from small, rigid structures to drug molecules. The AMOEBA results from the initial submission prompted an investigation into aspects of the methodology and parameterization employed. Lessons learned from the blind challenge include: a double annihilation scheme (electrostatics and van der Waals) is needed to obtain proper sampling of guest conformations, annihilation of key torsion parameters of the guest are recommended for flexible guests, and a more thorough analysis of torsion parameters is warranted. When put in to practice with the AMOEBA model, the lessons learned improved the MUE from 2.63 to 1.20 kcal/mol and the RMSE from 3.62 to 1.68 kcal/mol, respectively. Overall, the AMOEBA protocol for determining absolute binding free energies benefitted from participation in the SAMPL6 host-guest blind challenge and the results suggest the implementation of the methodology in future host-guest calculations.
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Affiliation(s)
- Marie L Laury
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Zhi Wang
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Aaron S Gordon
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
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8
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Sunkari YK, Pulukuri KK, Kandiyal PS, Vaishnav J, Ampapathi RS, Chakraborty TK. Conformation Analysis of GalNAc-Appended Sugar Amino Acid Foldamers as Glycopeptide Mimics. Chembiochem 2018; 19:1507-1513. [PMID: 29727041 DOI: 10.1002/cbic.201800087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Indexed: 11/08/2022]
Abstract
Sugar amino acid (SAA)-based foldamers with well-defined secondary structures were appended with N-acetylgalactosamine (GalNAc) sugars to access sequence-defined, multidentate glycoconjugates with full control over number, spacing and position. Conformation analysis of these glycopeptides by extensive NMR spectroscopic studies revealed that the appended GalNAc units had a profound influence on the native conformational behaviour of the SAA foldamers. Whereas the 2,5-cis glycoconjugate showed a helical structure in water, comprising of two consecutive 16-membered hydrogen bonds, its 2,5-trans congener displayed an unprecedented 16/10-mixed turn structure not seen before in any glycopeptide foldamer.
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Affiliation(s)
- Yashoda Krishna Sunkari
- Centre for Nuclear Magnetic Resonance, SAIF, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Kiran Kumar Pulukuri
- Centre for Nuclear Magnetic Resonance, SAIF, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Pancham Singh Kandiyal
- Centre for Nuclear Magnetic Resonance, SAIF, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Jayanti Vaishnav
- Centre for Nuclear Magnetic Resonance, SAIF, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Ravi Sankar Ampapathi
- Centre for Nuclear Magnetic Resonance, SAIF, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Tushar Kanti Chakraborty
- Centre for Nuclear Magnetic Resonance, SAIF, CSIR-Central Drug Research Institute, Lucknow, 226031, India.,Department of Organic Chemistry, Indian Institute of Science, Bengaluru, 560012, India
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9
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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10
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Warkentin E, Weidenweber S, Schühle K, Demmer U, Heider J, Ermler U. A rare polyglycine type II-like helix motif in naturally occurring proteins. Proteins 2017; 85:2017-2023. [DOI: 10.1002/prot.25355] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/03/2017] [Accepted: 07/17/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Eberhard Warkentin
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3; Frankfurt am Main 60438 Germany
| | - Sina Weidenweber
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3; Frankfurt am Main 60438 Germany
| | - Karola Schühle
- Laboratorium für Mikrobiologie; Fachbereich Biologie and SYNMIKRO, Philipps-Universität; Marburg 35032 Germany
| | - Ulrike Demmer
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3; Frankfurt am Main 60438 Germany
| | - Johann Heider
- Laboratorium für Mikrobiologie; Fachbereich Biologie and SYNMIKRO, Philipps-Universität; Marburg 35032 Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3; Frankfurt am Main 60438 Germany
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11
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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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12
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Goyal B, Srivastava KR, Durani S. Examination of the Effect of N-terminal Diproline and Charged Side Chains on the Stabilization of Helical Conformation in Alanine-based Short Peptides: A Molecular Dynamics Study. ChemistrySelect 2016. [DOI: 10.1002/slct.201601381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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, 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 USA 48105
| | - Susheel Durani
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
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13
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Kuster DJ, Liu C, Fang Z, Ponder JW, Marshall GR. High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics. PLoS One 2015; 10:e0123146. [PMID: 25894612 PMCID: PMC4403875 DOI: 10.1371/journal.pone.0123146] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/24/2015] [Indexed: 11/25/2022] Open
Abstract
Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.
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Affiliation(s)
- Daniel J. Kuster
- Department of Biomedical Engineering, Washington University, St. Louis, MO, United States of America
| | - Chengyu Liu
- Department of Chemistry, Washington University, St. Louis, MO, United States of America
| | - Zheng Fang
- Department of Biomedical Engineering, Washington University, St. Louis, MO, United States of America
| | - Jay W. Ponder
- Department of Chemistry, Washington University, St. Louis, MO, United States of America
| | - Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, MO, United States of America
- * E-mail:
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