1
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Dey P, Biswas P. Effect of caffeine on the aggregation of amyloid-β-A 3D RISM study. J Chem Phys 2024; 160:125101. [PMID: 38516974 DOI: 10.1063/5.0202636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024] Open
Abstract
Alzheimer's disease is a detrimental neurological disorder caused by the formation of amyloid fibrils due to the aggregation of amyloid-β peptide. The primary therapeutic approaches for treating Alzheimer's disease are targeted to prevent this amyloid fibril formation using potential inhibitor molecules. The discovery of such inhibitor molecules poses a formidable challenge to the design of anti-amyloid drugs. This study investigates the effect of caffeine on dimer formation of the full-length amyloid-β using a combined approach of all-atom, explicit water molecular dynamics simulations and the three-dimensional reference interaction site model theory. The change in the hydration free energy of amyloid-β dimer, with and without the inhibitor molecules, is calculated with respect to the monomeric amyloid-β, where the hydration free energy is decomposed into energetic and entropic components, respectively. Dimerization is accompanied by a positive change in the partial molar volume. Dimer formation is spontaneous, which implies a decrease in the hydration free energy. However, a reverse trend is observed for the dimer with inhibitor molecules. It is observed that the negatively charged residues primarily contribute for the formation of the amyloid-β dimer. A residue-wise decomposition reveals that hydration/dehydration of the side-chain atoms of the charged amino acid residues primarily contribute to dimerization.
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Affiliation(s)
- Priya Dey
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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2
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Dey P, Biswas P. Aggregation propensities of proteins with varying degrees of disorder. J Comput Chem 2023; 44:874-886. [PMID: 36468418 DOI: 10.1002/jcc.27049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 12/10/2022]
Abstract
The hydration thermodynamics of a globular protein (AcP), three intrinsically disordered protein regions (1CD3, 1MVF, 1F0R) and a fully disordered protein (α-synuclein) is studied by an approach that combines an all-atom explicit water molecular dynamics simulations and three-dimensional reference interaction site model (3D-RISM) theory. The variation in hydration free energy with percentage disorder of the selected proteins is investigated through its nonelectrostatic and electrostatic components. A decrease in hydration free energy is observed with an increase in percentage disorder, indicating favorable interactions of the disordered proteins with the solvent. This confirms the role of percentage disorder in determining the aggregation propensity of proteins which is measured in terms of the hydration free energy in addition to their respective mean net charge and mean hydrophobicity. The hydration free energy is decoupled into energetic and entropic terms. A residue-wise decomposition analysis of the hydration free energy for the selected proteins is evaluated. The decomposition shows that the disordered regions contribute more than the ordered ones for the intrinsically disordered protein regions. The dominant role of electrostatic interactions is confirmed from the residue-wise decomposition of the hydration free energy. The results depict that the negatively charged residues contribute more to the total hydration free energy for the proteins with negative mean net charge, while the positively charged residues contribute more for proteins with positive mean net charge.
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Affiliation(s)
- Priya Dey
- Department of Chemistry, University of Delhi, Delhi, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi, India
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3
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Maruyama Y, Takano H, Mitsutake A. Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory. Biophys Physicobiol 2019; 16:407-429. [PMID: 31984194 PMCID: PMC6975981 DOI: 10.2142/biophysico.16.0_407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/29/2019] [Indexed: 01/03/2023] Open
Abstract
Molecular dynamics simulation is a fruitful tool for investigating the structural stability, dynamics, and functions of biopolymers at an atomic level. In recent years, simulations can be performed on time scales of the order of milliseconds using special purpose systems. Since the most stable structure, as well as meta-stable structures and intermediate structures, is included in trajectories in long simulations, it is necessary to develop analysis methods for extracting them from trajectories of simulations. For these structures, methods for evaluating the stabilities, including the solvent effect, are also needed. We have developed relaxation mode analysis to investigate dynamics and kinetics of simulations based on statistical mechanics. We have also applied the three-dimensional reference interaction site model theory to investigate stabilities with solvent effects. In this paper, we review the results for designing amino-acid substitution of the 10-residue peptide, chignolin, to stabilize the misfolded structure using these developed analysis methods.
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Affiliation(s)
- Yutaka Maruyama
- Architecture Development Team, FLAGSHIP 2020 Project, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Hiroshi Takano
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ayori Mitsutake
- Department of Physics, School of Science and Technology, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
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4
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Cao S, Konovalov KA, Unarta IC, Huang X. Recent Developments in Integral Equation Theory for Solvation to Treat Density Inhomogeneity at Solute–Solvent Interface. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Siqin Cao
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
| | - Kirill A. Konovalov
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
| | - Ilona Christy Unarta
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
- Bioengineering Graduate Programthe Hong Kong University of Science and TechnologyHong Kong of Chinese National EngineeringResearch Center for Tissue Restoration and Reconstructionthe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Xuhui Huang
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
- Bioengineering Graduate Programthe Hong Kong University of Science and TechnologyHong Kong of Chinese National EngineeringResearch Center for Tissue Restoration and Reconstructionthe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- HKUST‐Shenzhen Research Institute Hi‐Tech Park, Nanshan Shenzhen 518057 China
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5
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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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6
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Okumura H, Higashi M, Yoshida Y, Sato H, Akiyama R. Theoretical approaches for dynamical ordering of biomolecular systems. Biochim Biophys Acta Gen Subj 2017; 1862:212-228. [PMID: 28988931 DOI: 10.1016/j.bbagen.2017.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/30/2017] [Accepted: 10/04/2017] [Indexed: 01/21/2023]
Abstract
BACKGROUND Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. SCOPE OF REVIEW We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. MAJOR CONCLUSIONS The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. GENERAL SIGNIFICANCE These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Hisashi Okumura
- Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan; Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan.
| | - Masahiro Higashi
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Yuichiro Yoshida
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka 819-0395, Japan
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7
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Ratkova EL, Palmer DS, Fedorov MV. Solvation thermodynamics of organic molecules by the molecular integral equation theory: approaching chemical accuracy. Chem Rev 2015; 115:6312-56. [PMID: 26073187 DOI: 10.1021/cr5000283] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ekaterina L Ratkova
- †G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia.,‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany
| | - David S Palmer
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,§Department of Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, United Kingdom
| | - Maxim V Fedorov
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,∥Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde, John Anderson Building, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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8
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Zhang R, Chen J, Mi J. Evaluation of solvent effect on the amine-based CO2 absorbents by theory and experiment. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1637-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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Zhao S, Liu Y, Chen X, Lu Y, Liu H, Hu Y. Unified Framework of Multiscale Density Functional Theories and Its Recent Applications. MESOSCALE MODELING IN CHEMICAL ENGINEERING PART II 2015. [DOI: 10.1016/bs.ache.2015.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Liu Y, Zhao S, Wu J. A Site Density Functional Theory for Water: Application to Solvation of Amino Acid Side Chains. J Chem Theory Comput 2013; 9:1896-908. [DOI: 10.1021/ct3010936] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Liu
- Departments of Chemical and
Environmental Engineering and Mathematics, University of California,
Riverside, California 92521, United States
| | - Shuangliang Zhao
- State Key Laboratory of Chemical
Engineering, East China University of Science and Technology, Shanghai,
200238, P. R. China
| | - Jianzhong Wu
- Departments of Chemical and
Environmental Engineering and Mathematics, University of California,
Riverside, California 92521, United States
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11
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Xu M, Zhang C, Du Z, Mi J. Role of Interfacial Structure of Water in Polymer Surface Wetting. Macromolecules 2013. [DOI: 10.1021/ma301526a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Mengjin Xu
- The Key Laboratory of Carbon Fiber and Functional Polymers, Ministry
of Education, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Chen Zhang
- The Key Laboratory of Carbon Fiber and Functional Polymers, Ministry
of Education, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Zhongjie Du
- The Key Laboratory of Carbon Fiber and Functional Polymers, Ministry
of Education, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jianguo Mi
- State Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing
100029, China
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12
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Sato H. A modern solvation theory: quantum chemistry and statistical chemistry. Phys Chem Chem Phys 2013; 15:7450-65. [DOI: 10.1039/c3cp50247c] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Howard JJ, Pettitt BM. Integral equations in the study of polar and ionic interaction site fluids. JOURNAL OF STATISTICAL PHYSICS 2011; 145:441-466. [PMID: 22383857 PMCID: PMC3286808 DOI: 10.1007/s10955-011-0260-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this review article we consider some of the current integral equation approaches and application to model polar liquid mixtures. We consider the use of multidimensional integral equations and in particular progress on the theory and applications of three dimensional integral equations. The IEs we consider may be derived from equilibrium statistical mechanical expressions incorporating a classical Hamiltonian description of the system. We give example including salt solutions, inhomogeneous solutions and systems including proteins and nucleic acids.
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Affiliation(s)
- Jesse J Howard
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003
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14
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Ratkova EL, Chuev GN, Sergiievskyi VP, Fedorov MV. An Accurate Prediction of Hydration Free Energies by Combination of Molecular Integral Equations Theory with Structural Descriptors. J Phys Chem B 2010; 114:12068-79. [DOI: 10.1021/jp103955r] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ekaterina L. Ratkova
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
| | - Gennady N. Chuev
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
| | - Volodymyr P. Sergiievskyi
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
| | - Maxim V. Fedorov
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
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15
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Palmer DS, Sergiievskyi VP, Jensen F, Fedorov MV. Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model. J Chem Phys 2010; 133:044104. [DOI: 10.1063/1.3458798] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Perkyns JS, Lynch GC, Howard JJ, Pettitt BM. Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories. J Chem Phys 2010; 132:064106. [PMID: 20151732 DOI: 10.1063/1.3299277] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Solvation forces dominate protein structure and dynamics. Integral equation theories allow a rapid and accurate evaluation of the effect of solvent around a complex solute, without the sampling issues associated with simulations of explicit solvent molecules. Advances in integral equation theories make it possible to calculate the angle dependent average solvent structure around an irregular molecular solution. We consider two methodological problems here: the treatment of long-ranged forces without the use of artificial periodicity or truncations and the effect of closures. We derive a method for calculating the long-ranged Coulomb interaction contributions to three-dimensional distribution functions involving only a rewriting of the system of integral equations and introducing no new formal approximations. We show the comparison of the exact forms with those implied by the supercell method. The supercell method is shown to be a good approximation for neutral solutes whereas the new method does not exhibit the known problems of the supercell method for charged solutes. Our method appears more numerically stable with respect to thermodynamic starting state. We also compare closures including the Kovalenko-Hirata closure, the hypernetted-chain (HNC) and an approximate three-dimensional bridge function combined with the HNC closure. Comparisons to molecular dynamics results are made for water as well as for the protein solute bovine pancreatic trypsin inhibitor. The proposed equations have less severe approximations and often provide results which compare favorably to molecular dynamics simulation where other methods fail.
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Affiliation(s)
- John S Perkyns
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003, USA
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17
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Chuev GN, Fedorov MV, Chiodo S, Russo N, Sicilia E. Hydration of ionic species studied by the reference interaction site model with a repulsive bridge correction. J Comput Chem 2008; 29:2406-15. [DOI: 10.1002/jcc.20979] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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18
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Griebel M, Jager L. The BGY3dM model for the approximation of solvent densities. J Chem Phys 2008; 129:174511. [DOI: 10.1063/1.2991296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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19
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Roth R, Harano Y, Kinoshita M. Morphometric approach to the solvation free energy of complex molecules. PHYSICAL REVIEW LETTERS 2006; 97:078101. [PMID: 17026275 DOI: 10.1103/physrevlett.97.078101] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Indexed: 05/12/2023]
Abstract
We show that the solvation free energy of a complex molecule such as a protein can be calculated using only four geometrical measures of the molecular structure and corresponding thermodynamical coefficients. We compare results from this morphometric approach to those obtained by an elaborate statistical-mechanical theory in liquid state physics for a large variety of different structures of protein G and find excellent agreement. Since the computational time is drastically reduced, the new approach provides a practical and efficient way for calculating the solvation free energy which can be employed when this quantity has to be calculated for a large number of structures, as in a simulation study of protein folding.
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Affiliation(s)
- Roland Roth
- Max-Planck-Institut für Metallforschung, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
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20
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Harano Y, Kinoshita M. Crucial importance of translational entropy of water in pressure denaturation of proteins. J Chem Phys 2006; 125:24910. [PMID: 16848614 DOI: 10.1063/1.2217011] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present statistical thermodynamics of pressure denaturation of proteins, in which the three-dimensional integral equation theory is employed. It is applied to a simple model system focusing on the translational entropy of the solvent. The partial molar volume governing the pressure dependence of the structural stability of a protein is expressed for each structure in terms of the excluded volume for the solvent molecules, the solvent-accessible surface area (ASA), and a parameter related to the solvent-density profile formed near the protein surface. It is argued that the entropic effect originating from the translational movement of water molecules plays critical roles in the pressure-induced denaturation. We also show that the exceptionally small size of water molecules among dense liquids in nature is crucial for pressure denaturation. An unfolded structure, which is only moderately less compact than the native structure but has much larger ASA, is shown to turn more stable than the native one at an elevated pressure. The water entropy for the native structure is higher than that for the unfolded structure in the low-pressure region, whereas the opposite is true in the high-pressure region. Such a structure is characterized by the cleft and/or swelling and the water penetration into the interior. In another solvent whose molecular size is 1.5 times larger than that of water, however, the inversion of the stability does not occur any longer. The random coil becomes relatively more destabilized with rising pressure, irrespective of the molecular size of the solvent. These theoretical predictions are in qualitatively good agreement with the experimental observations.
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Affiliation(s)
- Yuichi Harano
- International Innovation Center, Kyoto University, Uji, Kyoto 611-0011, Japan
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21
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Abstract
We show that even in the complete absence of potential energies among the atoms in a protein-aqueous solution system, there is a physical factor that favors the folded state of the protein. It is a gain in the translational entropy (TE) of water originating from the translational movement of water molecules. An elaborate statistical-mechanical theory is employed to analyze the TE of water in which a protein or peptide with a prescribed conformation is immersed. It is shown that if the number of residues is sufficiently large, the TE gain is powerful enough to compete with the conformational-entropy loss upon folding. For protein G we have tested over 100 compact conformations generated by a computer simulation with the all-atom potentials as well as the native structure. A significant finding is that the largest TE is attained in the native structure. The translational movement of water molecules is quite effective in achieving the tight packing in the interior of a natural protein. These results are true only when the solvent is water whose molecular size is the smallest among the ordinary liquids in nature.
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Affiliation(s)
- Yuichi Harano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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22
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Dudowicz J, Freed KF, Shen MY. Hydration structure of met-enkephalin: A molecular dynamics study. J Chem Phys 2003. [DOI: 10.1063/1.1531612] [Citation(s) in RCA: 10] [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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23
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Kinoshita M, Imai T, Kovalenko A, Hirata F. Improvement of the reference interaction site model theory for calculating the partial molar volume of amino acids and polypeptides. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)01129-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Harano Y, Imai T, Kovalenko A, Kinoshita M, Hirata F. Theoretical study for partial molar volume of amino acids and polypeptides by the three-dimensional reference interaction site model. J Chem Phys 2001. [DOI: 10.1063/1.1369138] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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