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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Aggarwal L, Biswas P. Effect of Alzheimer’s Disease Causative and Protective Mutations on the Hydration Environment of Amyloid-β. J Phys Chem B 2020; 124:2311-2322. [DOI: 10.1021/acs.jpcb.9b10425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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3
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Mandal M, Das A, Mukhopadhyay C. Ubiquitin folds via a flip-twist-lock mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140299. [DOI: 10.1016/j.bbapap.2019.140299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/14/2019] [Accepted: 10/01/2019] [Indexed: 01/08/2023]
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4
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Mondal S, Bandyopadhyay S. Flexibility of the Binding Regions of a Protein-DNA Complex and the Structure and Ordering of Interfacial Water. J Chem Inf Model 2019; 59:4427-4437. [PMID: 31580657 DOI: 10.1021/acs.jcim.9b00685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Noncovalent interactions between protein and DNA are important to comprehend different biological activities in living organisms. One important issue is how the protein identifies the target DNA and the influence of the resulting protein-DNA complex on the hydration environment around it. In this study, we have carried out atomistic molecular dynamics simulations of the protein-DNA complex formed by the dimeric form of the α-helical N-terminal domain of the λ-repressor protein with its operator DNA. Local heterogeneous flexibilities of the residues of the protein and the DNA components that are involved in binding and the microscopic structure and ordering of water around those have been investigated in detail. The calculations revealed concurrent existence of highly ordered as well as disordered water molecules at the interface. It is found that a fraction of doubly coordinated water molecules exhibit high degree of ordering at the interface, while the randomly oriented ones are coordinated with three water molecules. The effect has been found to be more around the protein and DNA residues that are in contact in the complexed state. We believe that such highly ordered two-coordinated water molecules are likely to act as an adhesive to facilitate the formation of a protein-DNA complex and maintain its structural stability.
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5
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Monroe JI, Shell MS. Decoding signatures of structure, bulk thermodynamics, and solvation in three-body angle distributions of rigid water models. J Chem Phys 2019; 151:094501. [PMID: 31492058 DOI: 10.1063/1.5111545] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A tetrahedral structure resulting from hydrogen bonding is a hallmark of liquid water and plays a significant role in determining its unique thermophysical properties. This water feature has helped understand anomalous properties and physically interpret and model hydrophobic solvation thermodynamics. Tetrahedrality is well described by the geometric relationship of any central water molecule with two of its nearest neighbors in the first coordination shell, as defined by the corresponding "three-body" angle. While order parameters and even full water models have been developed using specific or average features of the three-body angle distribution, here we examine the distribution holistically, tracking its response to changes in temperature, density, and the presence of model solutes. Surprisingly, we find that the three-body distribution responds by varying primarily along a single degree of freedom, suggesting a remarkably simplified view of water structure. We characterize three-body angle distributions across temperature and density space and identify principal components of the variations with state conditions. We show that these principal components embed physical significance and trace out transitions between tetrahedral and simple-fluid-like behavior. Moreover, we find that the ways three-body angles vary within the hydration shells of model colloids of different types and sizes are nearly identical to the variations seen in bulk water across density and temperature. Importantly, through the principal directions of these variations, we find that perturbations to the hydration-water distributions well predict the thermodynamics associated with colloid solvation, in particular, the relative entropy of this process that captures indirect, solvent-mediated contributions to the hydration free energy.
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Affiliation(s)
- Jacob I Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-9010, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-9010, USA
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6
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Dallin BC, Yeon H, Ostwalt AR, Abbott NL, Van Lehn RC. Molecular Order Affects Interfacial Water Structure and Temperature-Dependent Hydrophobic Interactions between Nonpolar Self-Assembled Monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:2078-2088. [PMID: 30645942 DOI: 10.1021/acs.langmuir.8b03287] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Understanding how material properties affect hydrophobic interactions-the water-mediated interactions that drive the association of nonpolar materials-is vital to the design of materials in contact with water. Conventionally, the magnitude of the hydrophobic interactions between extended interfaces is attributed to interfacial chemical properties, such as the amount of nonpolar solvent-exposed surface area. However, recent experiments have demonstrated that the hydrophobic interactions between uniformly nonpolar self-assembled monolayers (SAMs) also depend on molecular-level SAM order. In this work, we use atomistic molecular dynamics simulations to investigate the relationship between SAM order, water structure, and hydrophobic interactions to explain these experimental observations. The SAM-SAM hydrophobic interactions calculated from the simulations increase in magnitude as SAM order increases, matching experimental observations. We explain this trend by showing that the molecular-level order of the SAM impacts the nanoscale structure of interfacial water molecules, leading to an increase in water structure near disordered SAMs. These findings are consistent with a decrease in the solvation entropy of disordered SAMs, which is confirmed by measuring the temperature dependence of hydrophobic interactions using both simulations and experiments. This study elucidates how hydrophobic interactions can be influenced by an interfacial physical property, which may guide the design of synthetic materials with fine-tuned interfacial hydrophobicity.
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Affiliation(s)
- Bradley C Dallin
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 United States
| | - Hongseung Yeon
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 United States
| | - Alexis R Ostwalt
- Department of Chemical and Biological Engineering , Montana State University , 306 Cobleigh Hall , Bozeman , Montana 59715 United States
| | - Nicholas L Abbott
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 United States
- Department of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall , Ithaca , New York 14853 , United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 United States
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7
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Mohanta D, Jana M. Effects of ethanol on the secondary structure specific hydration properties of Chymotrypsin Inhibitor 2 in its folded and unfolded forms. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1496246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Dayanidhi Mohanta
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
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8
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Khatua P, Bandyopadhyay S. Understanding the microscopic origin behind heterogeneous properties of water confined in and around A β17-42 protofilaments. J Chem Phys 2018; 149:065101. [PMID: 30111136 DOI: 10.1063/1.5040672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aggregation of amyloid beta (Aβ) peptides in the brain is responsible for one of the most devastating neurodegenerative diseases, namely, Alzheimer's disease. In this study, we have carried out atomistic molecular dynamics simulations to explore the effects of non-uniform structural distortions of Aβ17-42 pre-fibrillar aggregates of different sizes on the microscopic structure and ordering of water molecules confined within their amphiphilic nanocores. The calculations revealed non-uniform peptide-water interactions resulting in simultaneous existence of both highly ordered and disordered water molecules within the spatially heterogeneous confined environment of the protofilament cores. It is found that the high degree of ordering originates from a sizable fraction of doubly coordinated core water molecules, while the randomly oriented ones are those that are coordinated with three neighbors in their first coordination shells. Furthermore, it is quantitatively demonstrated that relative fractions of these two types of water molecules are correlated with the protofilament core topology and the degree of confinement within that. It is proposed that the ordered core waters are likely to stabilize the Aβ protofilaments by screening the residue charges and favoring water-mediated salt bridge formations, while the randomly oriented ones can drive further growth of the protofilaments by being displaced easily during the docking of additional peptides. In that way, both types of core water molecules can play equally important roles in controlling the growth and stability of the Aβ-aggregates.
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Affiliation(s)
- 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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9
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Dahanayake JN, Mitchell-Koch KR. Entropy connects water structure and dynamics in protein hydration layer. Phys Chem Chem Phys 2018; 20:14765-14777. [PMID: 29780979 PMCID: PMC6005386 DOI: 10.1039/c8cp01674g] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The enzyme Candida Antarctica lipase B (CALB) serves here as a model for understanding connections among hydration layer dynamics, solvation shell structure, and protein surface structure. The structure and dynamics of water molecules in the hydration layer were characterized for regions of the CALB surface, divided around each α-helix, β-sheet, and loop structure. Heterogeneous hydration dynamics were observed around the surface of the enzyme, in line with spectroscopic observations of other proteins. Regional differences in the structure of the biomolecular hydration layer were found to be concomitant with variations in dynamics. In particular, it was seen that regions of higher density exhibit faster water dynamics. This is analogous to the behavior of bulk water, where dynamics (diffusion coefficients) are connected to water structure (density and tetrahedrality) by excess (or pair) entropy, detailed in the Rosenfeld scaling relationship. Additionally, effects of protein surface topology and hydrophobicity on water structure and dynamics were evaluated using multiregression analysis, showing that topology has a somewhat larger effect on hydration layer structure-dynamics. Concave and hydrophobic protein surfaces favor a less dense and more tetrahedral solvation layer, akin to a more ice-like structure, with slower dynamics. Results show that pairwise entropies of local hydration layers, calculated from regional radial distribution functions, scale logarithmically with local hydration dynamics. Thus, the Rosenfeld relationship describes the heterogeneous structure-dynamics of the hydration layer around the enzyme CALB. These findings raise the question of whether this may be a general principle for understanding the structure-dynamics of biomolecular solvation.
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10
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Aggarwal L, Biswas P. Hydration Water Distribution around Intrinsically Disordered Proteins. J Phys Chem B 2018; 122:4206-4218. [DOI: 10.1021/acs.jpcb.7b11091] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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11
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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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12
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Shrivastav G, Agarwal M, Chakravarty C, Kashyap HK. Thermodynamic regimes over which homologous alkane fluids can be treated as simple liquids. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.01.085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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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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Gavrilov Y, Leuchter JD, Levy Y. On the coupling between the dynamics of protein and water. Phys Chem Chem Phys 2017; 19:8243-8257. [DOI: 10.1039/c6cp07669f] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The solvation entropy of flexible protein regions is higher than that of rigid regions and contributes differently to the overall thermodynamic stability.
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Affiliation(s)
- Yulian Gavrilov
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Jessica D. Leuchter
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yaakov Levy
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
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15
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Stanzione F, Jayaraman A. Hybrid Atomistic and Coarse-Grained Molecular Dynamics Simulations of Polyethylene Glycol (PEG) in Explicit Water. J Phys Chem B 2016; 120:4160-73. [DOI: 10.1021/acs.jpcb.6b02327] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesca Stanzione
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
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16
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Khatua P, Jose JC, Sengupta N, Bandyopadhyay S. Conformational features of the Aβ42 peptide monomer and its interaction with the surrounding solvent. Phys Chem Chem Phys 2016; 18:30144-30159. [DOI: 10.1039/c6cp04925g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Heterogeneous conformational flexibility of the Aβ monomers has been found to be correlated with the corresponding non-uniform entropy gains.
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Affiliation(s)
- Prabir Khatua
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | - Jaya C. Jose
- Physical Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Neelanjana Sengupta
- Department of Biological Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur-741246
- 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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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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18
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Huggins DJ. Estimating Translational and Orientational Entropies Using the k-Nearest Neighbors Algorithm. J Chem Theory Comput 2015; 10:3617-25. [PMID: 26588506 DOI: 10.1021/ct500415g] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inhomogeneous fluid solvation theory (IFST) and free energy perturbation (FEP) calculations were performed for a set of 20 solutes to compute the hydration free energies. We identify the weakness of histogram methods in computing the IFST hydration entropy by showing that previously employed histogram methods overestimate the translational and orientational entropies and thus underestimate their contribution to the free energy by a significant amount. Conversely, we demonstrate the accuracy of the k-nearest neighbors (KNN) algorithm in computing these translational and orientational entropies. Implementing the KNN algorithm within the IFST framework produces a powerful method that can be used to calculate free-energy changes for large perturbations. We introduce a new KNN approach to compute the total solute-water entropy with six degrees of freedom, as well as the translational and orientational contributions. However, results suggest that both the solute-water and water-water entropy terms are significant and must be included. When they are combined, the IFST and FEP hydration free energies are highly correlated, with an R(2) of 0.999 and a mean unsigned difference of 0.9 kcal/mol. IFST predictions are also highly correlated with experimental hydration free energies, with an R(2) of 0.997 and a mean unsigned error of 1.2 kcal/mol. In summary, the KNN algorithm is shown to yield accurate estimates of the combined translational-orientational entropy and the novel approach of combining distance metrics that is developed here could be extended to provide a powerful method for entropy estimation in numerous contexts.
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Affiliation(s)
- David J Huggins
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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19
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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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20
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Duboué-Dijon E, Laage D. Characterization of the Local Structure in Liquid Water by Various Order Parameters. J Phys Chem B 2015; 119:8406-18. [PMID: 26054933 PMCID: PMC4516314 DOI: 10.1021/acs.jpcb.5b02936] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A wide
range of geometric order parameters have been suggested
to characterize the local structure of liquid water and its tetrahedral
arrangement, but their respective merits have remained elusive. Here,
we consider a series of popular order parameters and analyze molecular
dynamics simulations of water, in the bulk and in the hydration shell
of a hydrophobic solute, at 298 and 260 K. We show that these parameters
are weakly correlated and probe different distortions, for example
the angular versus radial disorders. We first combine these complementary
descriptions to analyze the structural rearrangements leading to the
density maximum in liquid water. Our results reveal no sign of a heterogeneous
mixture and show that the density maximum arises from the depletion
in interstitial water molecules upon cooling. In the hydration shell
of the hydrophobic moiety of propanol, the order parameters suggest
that the water local structure is similar to that in the bulk, with
only a very weak depletion in ordered configurations, thus confirming
the absence of any iceberg-type structure. Finally, we show that the
main structural fluctuations that affect water reorientation dynamics
in the bulk are angular distortions, which we explain by the jump
hydrogen-bond exchange mechanism.
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Affiliation(s)
- Elise Duboué-Dijon
- École Normale Supérieure-PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
| | - Damien Laage
- École Normale Supérieure-PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
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21
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Fogarty AC, Potestio R, Kremer K. Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties. J Chem Phys 2015; 142:195101. [DOI: 10.1063/1.4921347] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aoife C. Fogarty
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Raffaello Potestio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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22
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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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23
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Sinha SK, Jana M, Chakraborty K, Bandyopadhyay S. In silico studies of the properties of water hydrating a small protein. J Chem Phys 2014; 141:22D502. [DOI: 10.1063/1.4895533] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Chatterjee P, Bagchi S, Sengupta N. The non-uniform early structural response of globular proteins to cold denaturing conditions: a case study with Yfh1. J Chem Phys 2014; 141:205103. [PMID: 25429964 DOI: 10.1063/1.4901897] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The mechanism of cold denaturation in proteins is often incompletely understood due to limitations in accessing the denatured states at extremely low temperatures. Using atomistic molecular dynamics simulations, we have compared early (nanosecond timescale) structural and solvation properties of yeast frataxin (Yfh1) at its temperature of maximum stability, 292 K (Ts), and the experimentally observed temperature of complete unfolding, 268 K (Tc). Within the simulated timescales, discernible "global" level structural loss at Tc is correlated with a distinct increase in surface hydration. However, the hydration and the unfolding events do not occur uniformly over the entire protein surface, but are sensitive to local structural propensity and hydrophobicity. Calculated infrared absorption spectra in the amide-I region of the whole protein show a distinct red shift at Tc in comparison to Ts. Domain specific calculations of IR spectra indicate that the red shift primarily arises from the beta strands. This is commensurate with a marked increase in solvent accessible surface area per residue for the beta-sheets at Tc. Detailed analyses of structure and dynamics of hydration water around the hydrophobic residues of the beta-sheets show a more bulk water like behavior at Tc due to preferential disruption of the hydrophobic effects around these domains. Our results indicate that in this protein, the surface exposed beta-sheet domains are more susceptible to cold denaturing conditions, in qualitative agreement with solution NMR experimental results.
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Affiliation(s)
- Prathit Chatterjee
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Sayan Bagchi
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Neelanjana Sengupta
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
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25
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Chakraborty K, Mantha S, Bandyopadhyay S. Molecular dynamics simulation of a single-stranded DNA with heterogeneous distribution of nucleobases in aqueous medium. J Chem Phys 2014; 139:075103. [PMID: 23968115 DOI: 10.1063/1.4818537] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The DNA metabolic processes often involve single-stranded DNA (ss-DNA) molecules as important intermediates. In the absence of base complementarity, ss-DNAs are more flexible and interact strongly with water in aqueous media. Ss-DNA-water interactions are expected to control the conformational flexibility of the DNA strand, which in turn should influence the properties of the surrounding water molecules. We have performed room temperature molecular dynamics simulation of an aqueous solution containing the ss-DNA dodecamer, 5'-CGCGAATTCGCG-3'. The conformational flexibility of the DNA strand and the microscopic structure and ordering of water molecules around it have been explored. The simulation reveals transformation of the initial base-stacked form of the ss-DNA to a fluctuating collapsed coil-like conformation with the formation of a few non-sequentially stacked base pairs. A preliminary analysis shows further collapse of the DNA conformation in presence of additional salt (NaCl) due to screening of negative charges along the backbone by excess cations. Additionally, higher packing of water molecules within a short distance from the DNA strand is found to be associated with realignment of water molecules by breaking their regular tetrahedral ordering.
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Affiliation(s)
- Kaushik Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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26
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Prasad S, Chakravarty C. Onset of simple liquid behaviour in modified water models. J Chem Phys 2014; 140:164501. [DOI: 10.1063/1.4870823] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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28
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Huggins DJ. Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation. J Comput Chem 2014; 35:377-85. [PMID: 24311273 PMCID: PMC4238811 DOI: 10.1002/jcc.23504] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/08/2013] [Accepted: 11/14/2013] [Indexed: 01/17/2023]
Abstract
Distance metrics facilitate a number of methods for statistical analysis. For statistical mechanical applications, it is useful to be able to compute the distance between two different orientations of a molecule. However, a number of distance metrics for rotation have been employed, and in this study, we consider different distance metrics and their utility in entropy estimation using the k-nearest neighbors (KNN) algorithm. This approach shows a number of advantages over entropy estimation using a histogram method, and the different approaches are assessed using uniform randomly generated data, biased randomly generated data, and data from a molecular dynamics (MD) simulation of bulk water. The results identify quaternion metrics as superior to a metric based on the Euler angles. However, it is demonstrated that samples from MD simulation must be independent for effective use of the KNN algorithm and this finding impacts any application to time series data.
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Affiliation(s)
- David J Huggins
- Theory of Condensed Matter Group, University of Cambridge, Cavendish Laboratory19 J J Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- Cambridge Molecular Therapeutics Programme, University of Cambridge, Hutchison/MRC Research CentreHills Road, Cambridge, CB2 0XZ, United Kingdom
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, UK CB2 1EW, United Kingdom
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29
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Nayar D, Chakravarty C. Sensitivity of local hydration behaviour and conformational preferences of peptides to choice of water model. Phys Chem Chem Phys 2014; 16:10199-213. [DOI: 10.1039/c3cp55147d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Secondary structural preferences of the beta-hairpin of the 2GB1 protein in the folded and unfolded ensembles are shown to be sensitive to the choice of water model.
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Affiliation(s)
- Divya Nayar
- Department of Chemistry
- Indian Institute of Technology-Delhi
- New Delhi: 110016, India
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30
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Pal S, Bandyopadhyay S. Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms. J Chem Phys 2013; 139:235101. [DOI: 10.1063/1.4844255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Desmond JL, Rodger PM, Walsh TR. Testing the inter-operability of the CHARMM and SPC/Fw force fields for conformational sampling. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.824574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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Nayar D, Chakravarty C. Water and water-like liquids: relationships between structure, entropy and mobility. Phys Chem Chem Phys 2013; 15:14162-77. [PMID: 23892732 DOI: 10.1039/c3cp51114f] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Liquids with very diverse underlying interactions share the thermodynamic and transport anomalies of water, including metalloids, ionic melts and mesoscopic fluids. The generic feature that characterises such water-like liquids is a density-driven shift in the nature of local order in the condensed phases. The key semiquantitative relationships between structural order, thermodynamics and transport that are necessary in order to map out the consequences of this common qualitative feature for liquid-state properties and phase transformations of such systems are reviewed here. The application of these ideas to understand and model tetrahedral liquids, especially water, is discussed and possible extensions to other complex fluids are considered.
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Affiliation(s)
- Divya Nayar
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi, 110016, India
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33
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Jana M, Bandyopadhyay S. Molecular Dynamics Study of β-Cyclodextrin–Phenylalanine (1:1) Inclusion Complex in Aqueous Medium. J Phys Chem B 2013; 117:9280-7. [DOI: 10.1021/jp404348u] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Madhurima Jana
- Molecular Simulation Laboratory,
Department of Chemistry, National Institute of Technology, Rourkela-769008, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory,
Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
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34
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Pal S, Bandyopadhyay S. Effects of protein conformational motions in the native form and non-uniform distribution of electrostatic interaction sites on interfacial water. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.04.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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35
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Huggins DJ, Payne MC. Assessing the accuracy of inhomogeneous fluid solvation theory in predicting hydration free energies of simple solutes. J Phys Chem B 2013; 117:8232-44. [PMID: 23763625 PMCID: PMC3756531 DOI: 10.1021/jp4042233] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Accurate
prediction of hydration free energies is a key objective
of any free energy method that is applied to modeling and understanding
interactions in the aqueous phase. Inhomogeneous fluid solvation theory
(IFST) is a statistical mechanical method for calculating solvation
free energies by quantifying the effect of a solute acting as a perturbation
to bulk water. IFST has found wide application in understanding hydration
phenomena in biological systems, but quantitative applications have
not been comprehensively assessed. In this study, we report the hydration
free energies of six simple solutes calculated using IFST and independently
using free energy perturbation (FEP). This facilitates a validation
of IFST that is independent of the accuracy of the force field. The
results demonstrate that IFST shows good agreement with FEP, with
an R2 coefficient of determination of
0.99 and a mean unsigned difference of 0.7 kcal/mol. However, sampling
is a major issue that plagues IFST calculations and the results suggest
that a histogram method may require prohibitively long simulations
to achieve convergence of the entropies, for bin sizes which effectively
capture the underlying probability distributions. Results also highlight
the sensitivity of IFST to the reference interaction energy of a water
molecule in bulk, with a difference of 0.01 kcal/mol changing the
predicted hydration free energies by approximately 2.4 kcal/mol for
the systems studied here. One of the major advantages of IFST over
perturbation methods such as FEP is that the systems are spatially
decomposed to consider the contribution of specific regions to the
total solvation free energies. Visualizing these contributions can
yield detailed insights into solvation thermodynamics. An insight
from this work is the identification and explanation of regions with
unfavorable free energy density relative to bulk water. These regions
contribute unfavorably to the hydration free energy. Further work
is necessary before IFST can be extended to yield accurate predictions
of binding free energies, but the work presented here demonstrates
its potential.
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Affiliation(s)
- David J Huggins
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 0HE, UK.
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36
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Pal S, Bandyopadhyay S. Effects of Protein Conformational Flexibilities and Electrostatic Interactions on the Low-Frequency Vibrational Spectrum of Hydration Water. J Phys Chem B 2013; 117:5848-56. [DOI: 10.1021/jp402662v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Somedatta Pal
- 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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37
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Pal S, Bandyopadhyay S. Importance of protein conformational motions and electrostatic anchoring sites on the dynamics and hydrogen bond properties of hydration water. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:1162-1173. [PMID: 23289748 DOI: 10.1021/la303959m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The microscopic dynamic properties of water molecules present in the vicinity of a protein are expected to be sensitive to its local conformational motions and the presence of polar and charged groups at the surface capable of anchoring water molecules through hydrogen bonds. In this work, we attempt to understand such sensitivity by performing detailed molecular dynamics simulations of the globular protein barstar solvated in aqueous medium. Our calculations demonstrate that enhanced confinement at the protein surface on freezing its local motions leads to increasingly restricted water mobility with long residence times around the secondary structures. It is found that the inability of the surface water molecules to bind with the protein residues by hydrogen bonds in the absence of protein-water (PW) electrostatic interactions is compensated by enhanced water-water hydrogen bonds around the protein with uniform bulklike behaviors. Importantly, it is further noticed that in contrast to the PW hydrogen bond relaxation time scale, the kinetics of the breaking and formation of such bonds are not affected on freezing the protein's conformational motions.
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Affiliation(s)
- Somedatta Pal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
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38
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Nayar D, Yadav HOS, Jabes BS, Chakravarty C. Relating Structure, Entropy, and Energy of Solvation of Nanoscale Solutes: Application to Gold Nanoparticle Dispersions. J Phys Chem B 2012; 116:13124-32. [DOI: 10.1021/jp307615f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Divya Nayar
- Department
of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | | | - B. Shadrack Jabes
- 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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39
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Jabes BS, Nayar D, Dhabal D, Molinero V, Chakravarty C. Water and other tetrahedral liquids: order, anomalies and solvation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:284116. [PMID: 22739063 DOI: 10.1088/0953-8984/24/28/284116] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In order to understand the common features of tetrahedral liquids with water-like anomalies, the relationship between local order and anomalies has been studied using molecular dynamics simulations for three categories of such liquids: (a) atomistic rigid-body models for water (TIP4P, TIP4P/2005, mTIP3P, SPC/E), (b) ionic melts, BeF(2) (TRIM model) and SiO(2) (BKS potential) and (c) Stillinger-Weber liquids parametrized to model water (mW) and silicon. Rigid-body, atomistic models for water and the Stillinger-Weber liquids show a strong correlation between tetrahedral and pair correlation order and the temperature for the onset of the density anomaly is close to the melting temperature. In contrast, the ionic melts show weaker and more variable degrees of correlation between tetrahedral and pair correlation metrics, and the onset temperature for the density anomaly is more than twice the melting temperature. In the case of water, the relationship between water-like anomalies and solvation is studied by examining the hydration of spherical solutes (Na(+), Cl(-), Ar) in water models with different temperature regimes of anomalies (SPC/E, TIP4P and mTIP3P). For both ionic and nonpolar solutes, the local structure and energy of water molecules is essentially the same as in bulk water beyond the second-neighbour shell. The local order and binding energy of water molecules are not perturbed by the presence of a hydrophobic solute. In the case of ionic solutes, the perturbation is largely localized within the first hydration shell. The binding energies for the ions are strongly dependent on the water models and clearly indicate that the geometry of the partial charge distributions, and the associated multipole moments, play an important role. However the anomalous behaviour of the water network has been found to be unimportant for polar solvation.
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Affiliation(s)
- B Shadrack Jabes
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
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40
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Sinha SK, Bandyopadhyay S. Conformational fluctuations of a protein-DNA complex and the structure and ordering of water around it. J Chem Phys 2012; 135:245104. [PMID: 22225189 DOI: 10.1063/1.3670877] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Protein-DNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue in this problem is how the protein recognizes the DNA and identifies its target base sequences. Water molecules present around the protein and DNA are also expected to play an important role in mediating the recognition process and controlling the structure of the complex. We have performed atomistic molecular dynamics simulations of an aqueous solution of the protein-DNA complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. The conformational fluctuations of the protein and DNA and the microscopic structure and ordering of water around them in the complex have been explored. In agreement with experimental studies, the calculations reveal conformational immobilization of the terminal segments of the protein on complexation. Importantly, it is discovered that both structural adaptations of the protein and DNA, and the subsequent correlation between them to bind, contribute to the net entropy loss associated with the complex formation. Further, it is found that water molecules around the DNA are more structured with significantly higher density and ordering than that around the protein in the complex.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur, India
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41
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Jana M, Bandyopadhyay S. Conformational flexibility of a protein-carbohydrate complex and the structure and ordering of surrounding water. Phys Chem Chem Phys 2012; 14:6628-38. [PMID: 22460826 DOI: 10.1039/c2cp24104h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein-carbohydrate non-covalent interactions are important to understand various biological processes in living organisms. One of the important issues in protein-carbohydrate binding is how the protein identifies the target carbohydrate and recognizes its conformational features. Surrounding water molecules are expected to play a critical role not only in mediating the recognition process but also in maintaining the structure of the complex. We carried out atomistic molecular dynamics (MD) simulations of an aqueous solution of the protein-carbohydrate complex formed between the hyaluronan binding domain (HABD) of the murine Cd44 protein and the octasaccharide hyaluronan (HA(8)). The conformational flexibilities of the protein and the carbohydrate, and the microscopic structure and ordering of water molecules around them in the complexed form have been explored. It is revealed that the formation of the complex is associated with significant immobilization of the monosaccharide units of the carbohydrate moiety that are involved in binding. Further, reduction in water densities around the binding residues of the two molecules in the complex with respect to their free forms clearly demonstrated that the recognition between the protein and the carbohydrate is facilitated by removal of a fraction of water molecules from regions around the binding domains.
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Affiliation(s)
- Madhurima Jana
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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42
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Sinha SK, Bandyopadhyay S. Local heterogeneous dynamics of water around lysozyme: a computer simulation study. Phys Chem Chem Phys 2012; 14:899-913. [DOI: 10.1039/c1cp22575h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Bhattacharjee N, Biswas P. Local order and mobility of water molecules around ambivalent helices. J Phys Chem B 2011; 115:12257-65. [PMID: 21916474 DOI: 10.1021/jp2066106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Water on a protein surface plays a key role in determining the structure and dynamics of proteins. Compared to the properties of bulk water, many aspects of the structure and dynamics of the water surrounding the proteins are less understood. It is interesting therefore to explore how the properties of the water within the solvation shell around the peptide molecule depend on its specific secondary structure. In this work we investigate the orientational order and residence times of the water molecules to characterize the structure, energetics, and dynamics of the hydration shell water around ambivalent peptides. Ambivalent sequences are identical sequences which display multiple secondary structures in different proteins. Molecular dynamics simulations of representative proteins containing variable helix, variable nonhelix, and conserved helix are also used to explore the local structure and mobility of water molecules in their vicinity. The results, for the first time, depict a different water distribution pattern around the conserved and variable helices. The water molecules surrounding the helical segments in variable helices are found to possess a less locally ordered structure compared to those around their corresponding nonhelical counterparts and conserved helices. The long conserved helices exhibit extremely high local residence times compared to the helical conformations of the variable helices, whereas the residence times of the nonhelical conformations of the variable helices are comparable to those of the short conserved helices. This differential pattern of the structure and dynamics of water molecules in the vicinity of conserved/variable helices may lend valuable insights for understanding the role of solvent effects in determining sequence ambivalency and help in improving the accuracy of water models used in the simulations of proteins.
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44
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Nayar D, Agarwal M, Chakravarty C. Comparison of Tetrahedral Order, Liquid State Anomalies, and Hydration Behavior of mTIP3P and TIP4P Water Models. J Chem Theory Comput 2011; 7:3354-67. [PMID: 26598167 DOI: 10.1021/ct2002732] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The relationship between local tetrahedral order, tagged particle potential energy, and coordination number is studied for mTIP3P and TIP4P models of water in the bulk as well as in the neighborhood of a small peptide. The tendency of water molecules with different binding or tagged particle potential energies to occupy environments with different degrees of disorder can be effectively illustrated by constructing tetrahedral order distributions and corresponding entropy metrics conditional on restricted ranges of local binding energy. At the state point corresponding to the onset of the density anomaly, the correlation between tetrahedral entropy versus tagged potential energy is strong and virtually identical for mTIP3P and TIP4P. In TIP4P, this correlation is retained up to temperatures as high as 300 K, while it is lost by 250 K in mTIP3P. In the 250-300 K regime that is important for biomolecular simulations, mTIP3P behaves essentially as a simple liquid while TIP4P shows the density and related anomalies characteristic of water. We also study the number of water molecules, the tetrahedral order, and the tagged molecule potential energies for water molecules as a function of the distance from the peptide for the 16-residue β-hairpin fragment of 2GB1 in mTIP3P and TIP4P solvents. The hydration shell coordination profiles (n(r)) of the number of water molecules are almost identical in the two solvents, but the radial variation in the local energies and local order show significant differences. The residue-wise variation in the tagged potential energy of water molecules within the first hydration shell is qualitatively similar in the two models. A comparison of the tetrahedral order distributions of water molecules lying at different distances from the biomolecular solute shows that the perturbation in the local tetrahedral order distributions of the bulk solvent due to the presence of the solute is marginal. Thus, in the 250-300 K regime, the mTIP3P and TIP4P water models show qualitatively different behavior in terms of the relationship between tetrahedral order and local energy, but as solvents in the neighborhood of a biomolecular solute, the differences between the two models are only quantitative and not qualitative.
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Affiliation(s)
- Divya Nayar
- Department of Chemistry, Indian Institute of Technology-Delhi , New Delhi 110016, India
| | - Manish Agarwal
- 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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45
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Masella M, Borgis D, Cuniasse P. Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects. J Comput Chem 2011; 32:2664-78. [DOI: 10.1002/jcc.21846] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 03/23/2011] [Accepted: 04/29/2011] [Indexed: 12/25/2022]
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46
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Bhattacharjee N, Biswas P. Structure of hydration water in proteins: a comparison of molecular dynamics simulations and database analysis. Biophys Chem 2011; 158:73-80. [PMID: 21665349 DOI: 10.1016/j.bpc.2011.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 05/07/2011] [Accepted: 05/08/2011] [Indexed: 11/15/2022]
Abstract
Hydration layer water molecules play important structural and functional roles in proteins. Despite being a critical component in biomolecular systems, characterizing the properties of hydration water poses a challenge for both experiments and simulations. In this context we investigate the local structure of hydration water molecules as a function of the distance from the protein and water molecules respectively in 188 high resolution protein structures and compare it with those obtained from molecular dynamics simulations. Tetrahedral order parameter of water in proteins calculated from previous and present simulation studies show that the potential of bulk water overestimates the average tetrahedral order parameter compared to those calculated from crystal structures. Hydration waters are found to be more ordered at a distance between the first and second solvation shell from the protein surface. The values of the order parameter decrease sharply when the water molecules are located very near or far away from the protein surface. At small water-water distance, the values of order parameter of water are very low. The average order parameter records a maximum value at a distance equivalent to the first solvation layer with respect to the water-water radial distribution and asymptotically approaches a constant value at large distances. Results from present analysis will help to get a better insight into structure of hydration water around proteins. The analysis will also help to improve the accuracy of water models on the protein surface.
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Agarwal M, Alam MP, Chakravarty C. Thermodynamic, diffusional, and structural anomalies in rigid-body water models. J Phys Chem B 2011; 115:6935-45. [PMID: 21553909 DOI: 10.1021/jp110695t] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural, density, entropy, and diffusivity anomalies of the TIP4P/2005 model of water are mapped out over a wide range of densities and temperatures. The locus of temperatures of maximum density (TMD) for this model is very close to the experimental TMD locus for temperatures between 250 and 275 K. Four different water models (mTIP3P, TIP4P, TIP5P, and SPC/E) are compared with the TIP4P/2005 model in terms of their anomalous behavior. For all the water models, the density regimes for anomalous behavior are bounded by a low-density limit at around 0.85-0.90 g cm(-3) and a high-density limit at about 1.10-1.15 g cm(-3). The onset temperatures of the density anomaly in the various models show a much greater variation, ranging from 202 K for mTIP3P to 289 K for TIP5P. The order maps for the various water models are qualitatively very similar with the structurally anomalous regions almost superimposable in the q(tet)-τ plane. Comparison of the phase diagrams of water models with the region of liquid-state anomalies shows that the crystalline phases are much more sensitive to the choice of water models than the liquid state anomalies; for example, SPC/E and TIP4P/2005 show qualitatively similar liquid state anomalies but very different phase diagrams. The anomalies in the liquid in all the models occur at much lower pressures than those at which the melting line changes from negative to positive slope. The results in this study demonstrate several aspects of structure-entropy-diffusivity relationships of water models that can be compared with experiment and used to develop better atomistic and coarse-grained models for water.
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Affiliation(s)
- Manish Agarwal
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi, India
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Jana M, Bandyopadhyay S. Hydration properties of α-, β-, and γ-cyclodextrins from molecular dynamics simulations. J Phys Chem B 2011; 115:6347-57. [PMID: 21510684 DOI: 10.1021/jp2013946] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Atomistic molecular dynamics (MD) simulations of α-, β-, and γ-cyclodextrins (ACD, BCD, and GCD) in aqueous solutions have been performed. Detailed analyses were carried out to compare the microscopic properties of water confined within the cavities of these macromolecules and in the hydration layers around them. It is noticed that reduced tetrahedral ordering of water in and around the CD molecules are associated with their restricted motions. Interestingly, unlike the translational motions, the rotational motions of cavity water molecules are found to be highly dependent on cavity dimensions. Additionally, it is found that severely hindered rotational motion of cavity water molecules is the origin of drastically restricted structural relaxation of hydrogen bonds involving those water molecules. It is demonstrated that the geometrical constraints within the cavities of the CD molecules enhance the rate of reformation of broken hydrogen bonds, thereby resulting in rapid establishment of the breaking and reformation equilibria for hydrogen bonds involving cavity water molecules.
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Affiliation(s)
- Madhurima Jana
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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Sinha SK, Bandyopadhyay S. Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules. J Chem Phys 2011; 134:115101. [DOI: 10.1063/1.3560442] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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de Oliveira AB, Salcedo E, Chakravarty C, Barbosa MC. Entropy, diffusivity and the energy landscape of a waterlike fluid. J Chem Phys 2010; 132:234509. [PMID: 20572723 DOI: 10.1063/1.3429254] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics simulations and instantaneous normal mode (INM) analysis of a fluid with core-softened pair interactions and waterlike liquid-state anomalies are performed to obtain an understanding of the relationship between thermodynamics, transport properties, and the potential energy landscape. Rosenfeld scaling of diffusivities with the thermodynamic excess and pair correlation entropy is demonstrated for this model. The INM spectra are shown to carry information about the dynamical consequences of the interplay between length scales characteristic of anomalous fluids, such as bimodality of the real and imaginary branches of the frequency distribution. The INM spectral information is used to partition the liquid entropy into two contributions associated with the real and imaginary frequency modes; only the entropy contribution from the imaginary branch captures the nonmonotonic behavior of the excess entropy and diffusivity in the anomalous regime of the fluid.
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Affiliation(s)
- Alan Barros de Oliveira
- Departamento de Física, Universidade Federal de Ouro Preto, Ouro Preto, MG 35400-000, Brazil.
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