1
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Panigrahy S, Sahu R, Reddy SK, Nayar D. Structure, energetics and dynamics in crowded amino acid solutions: a molecular dynamics study. Phys Chem Chem Phys 2023; 25:5430-5442. [PMID: 36744506 DOI: 10.1039/d2cp04238j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A comprehensive understanding of crowding effects on biomolecular processes necessitates investigating the bulk thermodynamic and kinetic properties of the solutions with an accurate molecular representation of the crowded milieu. Recent studies have reparameterized the non-bonded dispersion interaction of solutes to precisely model intermolecular interactions, which would circumvent artificial aggregation as shown by the original force-fields. However, the performance of this reparameterization is yet to be assessed for concentrated crowded solutions in terms of investigating the hydration shell structure, energetics and dynamics. In this study, we perform molecular dynamics simulations of crowded aqueous solutions of five zwitterionic neutral amino acids (Gly, Ala, Thr, Pro, and Ser), mimicking the molecular crowding environment, using a modified AMBER ff99SB-ILDN force-field. We systematically examine and show that the reproducibility of the osmotic coefficients, density, viscosity and self-diffusivity of amino acids improves using the modified force-field in crowded concentrations. The modified force-field also improves the structuring of the solute solvation shells, solute interaction energy and convergence of tails of radial distribution functions, indicating reduction in the artificial aggregation. Our results also indicate that the hydrogen bonding network of water weakens and water molecules anomalously diffuse at small time scales in the crowded solutions. These results underscore the significance of examining the solution properties and anomalous hydration behaviour of water in crowded solutions, which have implications in shaping the structure and dynamics of biomolecules. The findings also illustrate the improvement in predicting bulk solution properties using the modified force-field, thereby providing an approach towards accurate modeling of crowded molecular solutions.
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Affiliation(s)
- Sibasankar Panigrahy
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
| | - Rahul Sahu
- Center for Computational and Data Sciences, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Sandeep K Reddy
- Center for Computational and Data Sciences, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Divya Nayar
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
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2
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Shahfar H, Forder JK, Roberts CJ. Toward a Suite of Coarse-Grained Models for Molecular Simulation of Monoclonal Antibodies and Therapeutic Proteins. J Phys Chem B 2021; 125:3574-3588. [PMID: 33821645 DOI: 10.1021/acs.jpcb.1c01903] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of coarse-grained models for molecular simulation of proteins are considered, with emphasis on the application of predicting protein-protein self-interactions for monoclonal antibodies (MAbs). As an illustrative example and for quantitative comparison, the models are used to predict osmotic virial coefficients over a broad range of attractive and repulsive self-interactions and solution conditions for a series of MAbs where the second osmotic virial coefficient has been experimentally determined in prior work. The models are compared based on how well they can predict experimental behavior, their computational burdens, and scalability. An intermediate-resolution model is also introduced that can capture specific electrostatic interactions with improved efficiency and similar or improved accuracy when compared to the previously published models. Guidance is included for the selection of coarse-grained models more generally for capturing a balance of electrostatic, steric, and short-ranged nonelectrostatic interactions for proteins from low to high concentrations.
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Affiliation(s)
- Hassan Shahfar
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - James K Forder
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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3
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Bogunia M, Makowski M. Influence of Ionic Strength on Hydrophobic Interactions in Water: Dependence on Solute Size and Shape. J Phys Chem B 2020; 124:10326-10336. [PMID: 33147018 PMCID: PMC7681779 DOI: 10.1021/acs.jpcb.0c06399] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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Hydrophobicity is a phenomenon of
great importance in biology,
chemistry, and biochemistry. It is defined as the interaction between
nonpolar molecules or groups in water and their low solubility. Hydrophobic
interactions affect many processes in water, for example, complexation,
surfactant aggregation, and coagulation. These interactions play a
pivotal role in the formation and stability of proteins or biological
membranes. In the present study, we assessed the effect of ionic strength,
solute size, and shape on hydrophobic interactions between pairs of
nonpolar particles. Pairs of methane, neopentane, adamantane, fullerene,
ethane, propane, butane, hexane, octane, and decane were simulated
by molecular dynamics in AMBER 16.0 force field. As a solvent, TIP3P
and TIP4PEW water models were used. Potential of mean force (PMF)
plots of these dimers were determined at four values of ionic strength,
0, 0.04, 0.08, and 0.40 mol/dm3, to observe its impact
on hydrophobic interactions. The characteristic shape of PMFs with
three extrema (contact minimum, solvent-separated minimum, and desolvation
maximum) was observed for most of the compounds for hydrophobic interactions.
Ionic strength affected hydrophobic interactions. We observed a tendency
to deepen contact minima with an increase in ionic strength value
in the case of spherical and spheroidal molecules. Additionally, two-dimensional
distribution functions describing water density and average number
of hydrogen bonds between water molecules were calculated in both
water models for adamantane and hexane. It was observed that the density
of water did not significantly change with the increase in ionic strength,
but the average number of hydrogen bonds changed. The latter tendency
strongly depends on the water model used for simulations.
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Affiliation(s)
- Małgorzata Bogunia
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Mariusz Makowski
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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4
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Průša J, Cifra M. Dependence of amino-acid dielectric relaxation on solute-water interaction: Molecular dynamics study. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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5
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Katyal N, Deep S. A computational approach to get insights into multiple faces of additives in modulation of protein aggregation pathways. Phys Chem Chem Phys 2019; 21:24269-24285. [PMID: 31670327 DOI: 10.1039/c9cp03763b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An enormous population worldwide is presently confronted with debilitating neurodegenerative diseases. The etiology of the disease is connected to protein aggregation and the events involved therein. Thus, a complete understanding of an inhibitor at different stages in the process is imperative for the formulation of a drug molecule. This review presents a detailed summary of the current status of different cosolvents. It further develops how the complex aggregation pathway can be simplified into three steps common to all proteins and the way computer simulations can be exploited to gain insights into the ways by which known inhibitors can affect all these stages. Computation of theoretical parameters in this regard and their correlation with experimental techniques is accentuated. In addition to providing an outline of the scope of different additives, this review showcases the way by which the problem of analyzing an effect of an additive can be addressed effectively via MD simulations.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, Delhi, India.
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6
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Anandakrishnan R, Izadi S, Onufriev AV. Why Computed Protein Folding Landscapes Are Sensitive to the Water Model. J Chem Theory Comput 2018; 15:625-636. [DOI: 10.1021/acs.jctc.8b00485] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ramu Anandakrishnan
- Department of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia 24060, United States
| | - Saeed Izadi
- Early Stage Pharmaceutical Development, Genentech Inc., South San Francisco, California 94080, United States
| | - Alexey V. Onufriev
- Department of Computer Science and Physics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
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7
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Ferreira AF, Comune M, Rai A, Ferreira L, Simões PN. Atomistic-Level Investigation of a LL37-Conjugated Gold Nanoparticle By Well-Tempered Metadynamics. J Phys Chem B 2018; 122:8359-8366. [PMID: 30106592 DOI: 10.1021/acs.jpcb.8b05717] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
LL37 is a cathelicidin-derived antimicrobial peptide (AMP) with a broad spectrum of antimicrobial activity and wound-healing potential. The enhancement of these characteristics was recently demonstrated for a cysteine (CYS)-modified cathelicidin-derived LL37-SH conjugated with gold nanoparticles (AuNPs). Considering the potential of this peptide, we hereby report a computational study in which well-tempered metadynamics was applied to unveil the interaction of LL37-SH and LL37 with a AuNP with atomistic detail. A structural analysis combined with the free energy surface (FES) characterization allowed the assessment of the role of CYS residue during the formation of the conjugate, as well as to understand how the AuNP improves the antimicrobial activity of the peptide. It was found that CYS promotes a lower conformational entropy (before and after adsorption onto the AuNP) and a faster adsorption process when compared to the LL37 without CYS. The FES for LL37-SH is characterized by one global minimum, while for LL37 a potential metastable state was found. The presence of the AuNP leads to an elongation of the peptides along with the adsorption, which translates into the increase of the solvent-accessible surface area. This elongation combined with the greater availability of positively charged residues upon adsorption rationalizes the observed enhancement of the activity of the LL37-SH/AuNP conjugate.
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Affiliation(s)
- André F Ferreira
- CIEPQPF, Department of Chemical Engineering , University of Coimbra , 3030-790 Coimbra , Portugal
| | - Michela Comune
- CNC-Center for Neurosciences and Cell Biology , University of Coimbra , 3004-517 Coimbra , Portugal.,Biocant , Biotechnology Innovation Center , 3060-197 Cantanhede , Portugal
| | - Akhilesh Rai
- CNC-Center for Neurosciences and Cell Biology , University of Coimbra , 3004-517 Coimbra , Portugal.,Biocant , Biotechnology Innovation Center , 3060-197 Cantanhede , Portugal
| | - Lino Ferreira
- CNC-Center for Neurosciences and Cell Biology , University of Coimbra , 3004-517 Coimbra , Portugal.,Biocant , Biotechnology Innovation Center , 3060-197 Cantanhede , Portugal
| | - Pedro N Simões
- CIEPQPF, Department of Chemical Engineering , University of Coimbra , 3030-790 Coimbra , Portugal
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8
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Jeszenői N, Schilli G, Bálint M, Horváth I, Hetényi C. Analysis of the influence of simulation parameters on biomolecule-linked water networks. J Mol Graph Model 2018; 82:117-128. [DOI: 10.1016/j.jmgm.2018.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/27/2018] [Accepted: 04/21/2018] [Indexed: 12/11/2022]
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9
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Tomobe K, Yamamoto E, Kojić D, Sato Y, Yasui M, Yasuoka K. Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds. SCIENCE ADVANCES 2017; 3:e1701400. [PMID: 29282448 PMCID: PMC5741398 DOI: 10.1126/sciadv.1701400] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 11/17/2017] [Indexed: 05/29/2023]
Abstract
Water molecules at interfaces of materials exhibit enigmatic properties. A variety of spectroscopic studies have observed a high-frequency motion in these water molecules, represented by a blueshift, at both hydrophobic and hydrophilic interfaces. However, the molecular mechanism behind this blueshift has remained unclear. Using Raman spectroscopy and ab initio molecular dynamics simulations, we reveal the molecular mechanism of the blueshift of water molecules around six monosaccharide isomers. In the first hydration shell, we found weak hydrogen-bonded water molecules that cannot have a stable tetrahedral water network. In the water molecules, the vibrational state of the OH bond oriented toward the bulk solvent strongly contributes to the observed blueshift. Our work suggests that the blueshift in various solutions originates from the vibrational motions of these observed water molecules.
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Affiliation(s)
- Katsufumi Tomobe
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Eiji Yamamoto
- Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Dušan Kojić
- Department of Pharmacology, School of Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
- Keio Advanced Research Institute for Water Biology and Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
| | - Yohei Sato
- Keio Advanced Research Institute for Water Biology and Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
- Department of System Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Masato Yasui
- Department of Pharmacology, School of Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
- Keio Advanced Research Institute for Water Biology and Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
- Keio University Global Research Institute, Keio University, Mita, Minato-ku 108-8345, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- Keio Advanced Research Institute for Water Biology and Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
- Keio University Global Research Institute, Keio University, Mita, Minato-ku 108-8345, Japan
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10
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Sieradzan AK, Lipska AG, Lubecka EA. Shielding effect in protein folding. J Mol Graph Model 2017; 79:118-132. [PMID: 29161634 DOI: 10.1016/j.jmgm.2017.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 01/01/2023]
Abstract
One of the most important interactions responsible for protein folding and stability are hydrogen bonds between peptide groups. There is a constant competition between the water molecules and peptide groups in a hydrogen bond formation. Also side-chains take part in this process by reducing hydration of peptide group (shielding effect) that promotes the protein folding. In this paper, a new approach to take into account a shielding effect is presented. A modification of the energy function is derived and incorporated into the UNited RESidue (UNRES) force field. Canonical Molecular Dynamics and Replica Exchange Molecular Dynamics with UNRES force field is applied to study the influence of this effect on protein structure, folding kinetics and free energy landscapes. The results of test calculations suggest that even small contribution of this effect into energy function changes force field behavior as well as speeds up the folding process significantly.
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Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Agnieszka G Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Emilia A Lubecka
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; Institute of Informatics, University of Gdańsk, Wita Stwosza 57, 80-308 Gdańsk, Poland
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11
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12
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Taraphder S, Halder P, Paul TK, Khatua S. Unfolding intermediates of the mutant His-107-Tyr of human carbonic anhydrase II. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Gupta M, Khatua P, Chakravarty C, Bandyopadhyay S. The sensitivity of folding free energy landscapes of trpzips to mutations in the hydrophobic core. Phys Chem Chem Phys 2017; 19:22813-22825. [DOI: 10.1039/c7cp03825a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The sensitivity of the stability of folded states and free energy landscapes to the differences in the hydrophobic content of the core residues has been studied for the set of 16-residue trpzips, namely, Trpzip4, Trpzip5 and Trpzip6.
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Affiliation(s)
- Madhulika Gupta
- Department of Chemistry
- Indian Institute of Technology-Delhi
- New Delhi 110016
- India
| | - Prabir Khatua
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
| | | | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
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14
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Gupta M, Chakravarty C, Bandyopadhyay S. Sensitivity of Protein Glass Transition to the Choice of Water Model. J Chem Theory Comput 2016; 12:5643-5655. [DOI: 10.1021/acs.jctc.6b00825] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Madhulika Gupta
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Charusita Chakravarty
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department
of Chemistry, Indian Institute of Technology-Kharagpur, Kharagpur 721302, India
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15
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Jeszenői N, Bálint M, Horváth I, van der Spoel D, Hetényi C. Exploration of Interfacial Hydration Networks of Target–Ligand Complexes. J Chem Inf Model 2016; 56:148-58. [DOI: 10.1021/acs.jcim.5b00638] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Norbert Jeszenői
- Department
of Genetics, Eötvös Loránd University, Pázmány
Péter sétány 1/C, 1117 Budapest, Hungary
- MTA
NAP-B Molecular Neuroendocrinology Group, Institute of Physiology,
Szentágothai Research Center, Center for Neuroscience, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Mónika Bálint
- Department
of Biochemistry, Eötvös Loránd University, Pázmány
Péter sétány 1/C, 1117 Budapest, Hungary
| | - István Horváth
- Chemistry
Doctoral School, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - David van der Spoel
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, University of Uppsala, Box 596, SE-75124 Uppsala, Sweden
| | - Csaba Hetényi
- MTA-ELTE
Molecular Biophysics Research Group, Hungarian Academy of Sciences, Pázmány sétány 1/C, 1117 Budapest, Hungary
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16
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Gupta M, Nayar D, Chakravarty C, Bandyopadhyay S. Comparison of hydration behavior and conformational preferences of the Trp-cage mini-protein in different rigid-body water models. Phys Chem Chem Phys 2016; 18:32796-32813. [DOI: 10.1039/c6cp04634g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trp-cage unfolds at different temperatures in different water models revealing the sensitivity of conformational order metrics to the choice of water models.
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Affiliation(s)
- Madhulika Gupta
- Department of Chemistry
- Indian Institute of Technology-Delhi
- New Delhi 110016
- India
| | - Divya Nayar
- Department of Chemistry
- Indian Institute of Technology-Delhi
- New Delhi 110016
- India
| | | | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
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17
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Abstract
Protein aggregation and loss of protein's biological functionality are manifestations of protein instability. Cosolvents, in particular trehalose, are widely accepted antidotes against such destabilization. Although numerous theories have been promulgated in the literature with regard to its mechanism of stabilization, the present scenario is still elusive in view of the discrepancies existing in them. To this end, we have revisited the conundrum and attempted to rationalize the mechanism by conducting thorough investigation of the effect of trehalose on the native, partially unfolded and denatured states of protein "Lysozyme" by means of molecular dynamic (MD) simulations under different temperature and concentration regimes. Two-dimensional contour plots along with principal component analysis suggest that trehalose molecules offer on-pathway stabilization unaltering the principal direction of protein's motion, although it slows down protein dynamics so that the protein gets trapped in the homogeneous ensemble of conformations closer to the native state. Free energy landscape reveals higher population of native compared to intermediate and denatured states. Delphi results and calculation of the preferential interaction parameter demonstrate that this relative stabilization of the native state can be ascribed to be the consequence of favourable interactions of trehalose with side chains of certain loci on the protein surface encompassing polar flexible residues. Stability of protein results from the observed difference in binding affinity of trehalose for native and denatured states of protein. Our findings are at variance with the common conception of relative destabilization of the denatured state. Rather, we provide evidence for relative stabilization of the native state. This stabilization is due to interplay of protein-trehalose, water-trehalose, water-water, protein-water and trehalose-trehalose interactions.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, 110016, India.
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18
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Nayar D, Chakravarty C. Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models. J Phys Chem B 2015; 119:11106-20. [PMID: 26132437 DOI: 10.1021/acs.jpcb.5b02937] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.
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Affiliation(s)
- Divya Nayar
- Department of Chemistry, Indian Institute of Technology-Delhi , New Delhi 110016, India
| | - Charusita Chakravarty
- Department of Chemistry, Indian Institute of Technology-Delhi , New Delhi 110016, India
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19
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Rani P, Biswas P. Local Structure and Dynamics of Hydration Water in Intrinsically Disordered Proteins. J Phys Chem B 2015; 119:10858-67. [DOI: 10.1021/jp511961c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Pooja Rani
- Department of Chemistry, University of Delhi, Delhi - 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi - 110007, India
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