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Zhong L, Li X, Duan M, Song Y, He N, Che L. Impacts of high hydrostatic pressure processing on the structure and properties of pectin. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111793] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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2
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Liu J, Li X, Hou J, Liu F. Electric-Field-Induced Interface Behavior of Dodecyl Sulfate with Large Organic Counterions: A Molecular Dynamics Study. J Phys Chem B 2020; 124:5498-5506. [PMID: 32520571 DOI: 10.1021/acs.jpcb.0c00129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Dodecyl sulfate with tetramethylammonium counterions has been employed to systematically investigate the influence of different static electric fields on molecular structural properties, surface tension, by adopting molecular dynamics (MD) simulations with IR and sum frequency generation (SFG) spectrum calculations. The results indicated that dodecyl sulfate (DS-) and large organic TMA+ counterions can form a mixed adsorption layer in which one head group of DS- is surrounded by two tetramethylammonium (TMA+) and one water molecule. Additionally, it was observed that the surface tension significantly decreases with the increasing static electric field strength since the surfactant stands straighter at the interface as the electric field increases. The result can be instructively adopted in the manufacturing field to control surface tension. Moreover, it was found that the SFG stretch intensities of methylene decrease and the stretch intensities of the methyl group increase with increasing static electric fields. The result indicated that the static electric fields can make DS- more orderly and upright at the interface.
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Affiliation(s)
- Jianchuan Liu
- CAS Key Laboratory of Organic Solids, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy Sciences, Beijing 100049, China
| | - Xun Li
- Institute of Linguistics, Shanghai International Studies University, Shanghai 201600, China
| | - Jian Hou
- University of Chinese Academy Sciences, Beijing 100049, China.,Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Fenghai Liu
- College of Physical and Electronics Engineering, Sichuan Normal University, Chengdu 610066, China
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3
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Biswas A, Mallik BS. Structure and stretching dynamics of water molecules around an amphiphilic amide from FPMD simulations: A case study of N,N-dimethylformamide. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112524] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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4
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Chattaraj KG, Paul S. Inclusion of Theobromine Modifies Uric Acid Aggregation with Possible Changes in Melamine–Uric Acid Clusters Responsible for Kidney Stones. J Phys Chem B 2019; 123:10483-10504. [DOI: 10.1021/acs.jpcb.9b08487] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India-781039
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5
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Min SH, Wijesinghe S, Berkowitz ML. Enhanced Cavitation and Hydration Crossover of Stretched Water in the Presence of C 60. J Phys Chem Lett 2019; 10:6621-6625. [PMID: 31609628 DOI: 10.1021/acs.jpclett.9b02511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We performed molecular dynamics simulations on systems containing stretched water and a C60 buckyball molecule. Our goals were to understand how the presence of the hydrophobic impurity influences the rate of cavitation in stretched water and how the change in pressure (an increase in the value of negative pressure) affects the nature of hydrophobic hydration. Our simulations show that the presence of a buckyball increases the rate of cavitation in water under negative pressure. When studying the influence of the degree of stretching on hydration, we observed that at pressures above -100 MPa the mechanism of hydrophobic hydration is the one that characterizes hydration of a small particle. At some pressure below -100 MPa, there is a crossover in the mechanism of hydration where dewetting occurs by forming cavities next to the surface of the buckyball, and this is characteristic of hydrophobic hydration of large particles.
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Affiliation(s)
- Sa Hoon Min
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Sidath Wijesinghe
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Max L Berkowitz
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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Hata H, Nishiyama M, Kitao A. Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129395. [PMID: 31302180 DOI: 10.1016/j.bbagen.2019.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Molecular dynamics (MD) simulation is well-recognized as a powerful tool to investigate protein structure, function, and thermodynamics. MD simulation is also used to investigate high pressure effects on proteins. For conducting better MD simulation under high pressure, the main issues to be addressed are: (i) protein force fields and water models were originally developed to reproduce experimental properties obtained at ambient pressure; and (ii) the timescale to observe the pressure effect is often much longer than that of conventional MD simulations. SCOPE OF REVIEW First, we describe recent developments in MD simulation methodologies for studying the high-pressure structure and dynamics of protein molecules. These developments include force fields for proteins and water molecules, and enhanced simulation techniques. Then, we summarize recent studies of MD simulations of proteins in water under high pressure. MAJOR CONCLUSIONS Recent MD simulations of proteins in solution under pressure have reproduced various phenomena identified by experiments using high pressure, such as hydration, water penetration, conformational change, helix stabilization, and molecular stiffening. GENERAL SIGNIFICANCE MD simulations demonstrate differences in the properties of proteins and water molecules between ambient and high-pressure conditions. Comparing the results obtained by MD calculations with those obtained experimentally could reveal the mechanism by which biological molecular machines work well in collaboration with water molecules.
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Affiliation(s)
- Hiroaki Hata
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, 2-12-1 Meguro-ku, Tokyo 152-8550, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, 2-12-1 Meguro-ku, Tokyo 152-8550, Japan.
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7
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Parui S, Jana B. Factors Promoting the Formation of Clathrate-Like Ordering of Water in Biomolecular Structure at Ambient Temperature and Pressure. J Phys Chem B 2019; 123:811-824. [PMID: 30605607 DOI: 10.1021/acs.jpcb.8b11172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Clathrate hydrate forms when a hydrophobic molecule is entrapped inside a water cage or cavity. Although biomolecular structures also have hydrophobic patches, clathrate-like water is found in only a limited number of biomolecules. Also, while clathrate hydrates form at low temperature and moderately higher pressure, clathrate-like water is observed in biomolecular structure at ambient temperature and pressure. These indicate presence of other factors along with hydrophobic environment behind the formation of clathrate-like water in biomolecules. In the current study, we presented a systematic approach to explore the factors behind the formation of clathrate-like water in biomolecules by means of molecular dynamics simulation of a model protein, maxi, which is a naturally occurring nanopore and has clathrate-like water inside the pore. Removal of either confinement or hydrophobic environment results in the disappearance of clathrate-like water ordering, indicating a coupled role of these two factors. Apart from these two factors, clathrate-like water ordering also requires anchoring groups that can stabilize the clathrate-like water through hydrogen bonding. Our results uncover crucial factors for the stabilization of clathrate-like ordering in biomolecular structure which can be used for the development of new biomolecular structure promoting clathrate formation.
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Affiliation(s)
- Sridip Parui
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Biman Jana
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
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8
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Parui S, Jana B. Molecular Insights into the Unusual Structure of an Antifreeze Protein with a Hydrated Core. J Phys Chem B 2018; 122:9827-9839. [PMID: 30286600 DOI: 10.1021/acs.jpcb.8b05350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The primary driving force for protein folding is the formation of a well-packed, anhydrous core. However, recently, the crystal structure of an antifreeze protein, maxi, has been resolved where the core of the protein is filled with water, which apparently contradicts the existing notion of protein folding. Here, we have performed standard molecular dynamics (MD) simulation, replica exchange MD (REMD) simulation, and umbrella sampling using TIP4P water at various temperatures (300, 260, and 240 K) to explore the origin of this unusual structural feature. It is evident from standard MD and REMD simulations that the protein is found to be stable at 240 K in its unusual state. The core of protein has two layers of semi-clathrate water separating the methyl groups of alanine residues from different helical strands. However, with increasing temperature (260 and 300 K), the stability decreases as the core becomes dehydrated, and methyl groups of alanine are tightly packed driven by hydrophobic interactions. Calculation of the potential of mean force by an umbrella sampling technique between a pair of model hydrophobes resembling maxi protein at 240 K shows the stabilization of second solvent-separated minima (SSM), which provides a thermodynamic rationale of the unusual structural feature in terms of weakening of the hydrophobic interaction. Because the stabilization of SSMs is implicated for cold denaturation, it suggests that the maxi protein is so designed by nature where the cold denatured-like state becomes the biologically active form as it works near or below the freezing point of water.
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Affiliation(s)
- Sridip Parui
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Biman Jana
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
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9
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Dubey V, Kumar N, Daschakraborty S. Importance of Solvents’ Translational–Rotational Coupling for Translational Jump of a Small Hydrophobic Solute in Supercooled Water. J Phys Chem B 2018; 122:7569-7583. [DOI: 10.1021/acs.jpcb.8b03177] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vikas Dubey
- Department of Chemistry, Indian Institute of Technology Patna, Patna 801103, Bihar, India
| | - Nitesh Kumar
- Department of Chemistry, Indian Institute of Technology Patna, Patna 801103, Bihar, India
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10
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The opposing effect of urea and high pressure on the conformation of the protein β-hairpin: A molecular dynamics simulation study. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.12.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Parui S, Jana B. Pairwise Hydrophobicity at Low Temperature: Appearance of a Stable Second Solvent-Separated Minimum with Possible Implication in Cold Denaturation. J Phys Chem B 2017; 121:7016-7026. [DOI: 10.1021/acs.jpcb.7b02676] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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12
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13
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Dixit M, Hajari T, Tembe B. The effect of urea and taurine osmolytes on hydrophobic association and solvation of methane and neopentane molecules. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.08.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Effect of glycine betaine on the hydrophobic interactions in the presence of denaturant: A molecular dynamics study. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.12.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Yang J, Powers JR. Effects of High Pressure on Food Proteins. HIGH PRESSURE PROCESSING OF FOOD 2016. [DOI: 10.1007/978-1-4939-3234-4_18] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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16
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Martín EI, Martínez JM, Sánchez Marcos E. Theoretical study on the hydrophobic and hydrophilic hydration on large solutes: The case of phthalocyanines in water. J Chem Phys 2015; 143:044502. [DOI: 10.1063/1.4927003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Elisa I. Martín
- Departamento de Química Física, Universidad de Sevilla, E-41012 Sevilla, Spain
- Departamento de Ingeniería Química, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - José M. Martínez
- Departamento de Química Física, Universidad de Sevilla, E-41012 Sevilla, Spain
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17
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Paul S, Paul S. Exploring the Counteracting Mechanism of Trehalose on Urea Conferred Protein Denaturation: A Molecular Dynamics Simulation Study. J Phys Chem B 2015; 119:9820-34. [DOI: 10.1021/acs.jpcb.5b01576] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Subrata Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India-781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India-781039
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18
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Sharma B, Paul S. Understanding the Role of Temperature Change and the Presence of NaCl Salts on Caffeine Aggregation in Aqueous Solution: From Structural and Thermodynamics Point of View. J Phys Chem B 2015; 119:6421-32. [DOI: 10.1021/jp512336n] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Bhanita Sharma
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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19
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Karmakar A, Chandra A. Ab initio molecular dynamics studies of hydrogen bonded structure, molecular motion, and frequency fluctuations of water in the vicinity of azide ions. J Chem Phys 2015; 142:164505. [DOI: 10.1063/1.4918579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Anwesa Karmakar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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20
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Oshima H, Kinoshita M. Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water. J Chem Phys 2015; 142:145103. [DOI: 10.1063/1.4917075] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hiraku Oshima
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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21
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Bankura A, Chandra A. Proton transfer through hydrogen bonds in two-dimensional water layers: A theoretical study based on ab initio and quantum-classical simulations. J Chem Phys 2015; 142:044701. [DOI: 10.1063/1.4905495] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Arindam Bankura
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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23
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24
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Bartosik A, Wiśniewska M, Makowski M. Potentials of mean force for hydrophobic interactions between hydrocarbons in water solution: dependence on temperature, solute shape, and solute size. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3387] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Angelika Bartosik
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
| | - Marta Wiśniewska
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
| | - Mariusz Makowski
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
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25
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Paul S, Paul S. Effects of the temperature and trehalose concentration on the hydrophobic interactions of a small nonpolar neopentane solute: a molecular dynamics simulation study. RSC Adv 2014. [DOI: 10.1039/c4ra03678f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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26
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Kim H, Keasler SJ, Chen B. A nucleation-based method to study hydrophobic interactions under confinement: enhanced hydrophobic association driven by energetic contributions. J Phys Chem B 2014; 118:6875-84. [PMID: 24853272 DOI: 10.1021/jp5027459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel simulation approach was developed and applied to the study of hydrophobic interactions for a small hydrophobic solute pair under confinement. In this method, the aggregation-volume-bias Monte Carlo algorithm, developed originally for nucleation studies, is used to evaluate the association free energy with water molecules for a methane pair through the gradual addition of water molecules into a nanometer-sized sphere. Through a thermodynamic cycle, this method allows for a convenient examination of the free energy difference between two different solvated configurations without sampling any of the configurations in between. The potential of mean force (PMF) for a methane pair under confinement obtained from this method reveals that the stability of the contact pair configuration can be enhanced compared to that in bulk water, which is in agreement with previous studies. Also, constraining the center of this methane pair at the center of this confined volume yields a PMF with a metastable solvent separated configuration, resembling more closely the PMF from the bulk-phase system compared to previous studies in which this solvent-separated minimum was found to be completely absent. A combination with histogram reweighting enables the study of this association behavior at different thermodynamic conditions without additional simulations. From a comprehensive thermodynamic analysis, it is evident that such hydrophobic association, known to be entropically driven in the bulk-phase system at ambient conditions, is entropically favorable only when a suitable range of solvent molecules is added to the confined system. More importantly, the energetic contributions are a favorable factor that explains the enhanced hydrophobic association toward the high number of solvent molecules.
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Affiliation(s)
- Hyunmi Kim
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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27
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Oshima H, Kinoshita M. Effects of sugars on the thermal stability of a protein. J Chem Phys 2014; 138:245101. [PMID: 23822280 DOI: 10.1063/1.4811287] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It is experimentally known that the heat-denaturation temperature of a protein is raised (i.e., its thermal stability is enhanced) by sugar addition. In earlier works, we proposed a physical picture of thermal denaturation of proteins in which the measure of the thermal stability is defined as the solvent-entropy gain upon protein folding at 298 K normalized by the number of residues. A multipolar-model water was adopted as the solvent. The polyatomic structures of the folded and unfolded states of a protein were taken into account in the atomic detail. A larger value of the measure implies higher thermal stability. First, we show that the measure remains effective even when the model water is replaced by the hard-sphere solvent whose number density and molecular diameter are set at those of real water. The physical picture is then adapted to the elucidation of the effects of sugar addition on the thermal stability of a protein. The water-sugar solution is modeled as a binary mixture of hard spheres. The thermal stability is determined by a complex interplay of the diameter of sugar molecules dC and the total packing fraction of the solution η: dC is estimated from the volume per molecule in the sugar crystal and η is calculated using the experimental data of the solution density. We find that the protein is more stabilized as the sucrose or glucose concentration becomes higher and the stabilization effect is stronger for sucrose than for glucose. These results are in accord with the experimental observations. Using a radial-symmetric integral equation theory and the morphometric approach, we decompose the change in the measure upon sugar addition into two components originating from the protein-solvent pair and protein-solvent many-body correlations, respectively. Each component is further decomposed into the excluded-volume and solvent-accessible-surface terms. These decompositions give physical insights into the microscopic origin of the thermal-stability enhancement by sugar addition. As an example, the higher stability of the native state relative to that of the unfolded state is found to be attributable primarily to an increase in the solvent crowding caused by sugar addition. Due to the hydrophilicity of sugar molecules, the addition of sugar by a larger amount or that with a larger molecular size leads to an increase in η which is large enough to make the solvent crowding more serious.
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Affiliation(s)
- Hiraku Oshima
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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28
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Paul S, Paul S. Trehalose Induced Modifications in the Solvation Pattern of N-Methylacetamide. J Phys Chem B 2014; 118:1052-63. [DOI: 10.1021/jp407782x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Subrata Paul
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam, India-781039
| | - Sandip Paul
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam, India-781039
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Paul S, Paul S. The influence of trehalose on hydrophobic interactions of small nonpolar solute: A molecular dynamics simulation study. J Chem Phys 2013; 139:044508. [DOI: 10.1063/1.4816521] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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31
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Sarma R, Paul S. Trimethylamine-N-oxide’s Effect on Polypeptide Solvation at High Pressure: A Molecular Dynamics Simulation Study. J Phys Chem B 2013; 117:9056-66. [DOI: 10.1021/jp405202j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rahul Sarma
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, India-781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, India-781039
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32
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Yadav VK, Chandra A. Dynamics of supercritical methanol of varying density from first principles simulations: Hydrogen bond fluctuations, vibrational spectral diffusion, and orientational relaxation. J Chem Phys 2013; 138:224501. [DOI: 10.1063/1.4808034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Rana MK, Chandra A. Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet. J Chem Phys 2013; 138:204702. [DOI: 10.1063/1.4804300] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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34
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A first principles simulation study of vibrational spectral diffusion in aqueous NaBr solutions: Dynamics of water in ion hydration shells. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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35
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Sarma R, Paul S. Crucial Importance of Water Structure Modification on Trimethylamine N-Oxide Counteracting Effect at High Pressure. J Phys Chem B 2013; 117:677-89. [DOI: 10.1021/jp311102v] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rahul Sarma
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, India-781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, India-781039
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36
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Rana MK, Chandra A. Solvation structure of nanoscopic hydrophobic solutes in supercritical water: Results for varying thickness of hydrophobic walls, solute–solvent interaction and solvent density. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Effect of pressure on the solution structure and hydrogen bond properties of aqueous N-methylacetamide. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Sarma R, Paul S. Effect of trimethylamine-N-oxide on pressure-induced dissolution of hydrophobic solute. J Chem Phys 2012; 137:114503. [DOI: 10.1063/1.4752104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Sarma R, Paul S. The effect of aqueous solutions of trimethylamine-N-oxide on pressure induced modifications of hydrophobic interactions. J Chem Phys 2012; 137:094502. [DOI: 10.1063/1.4748101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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