251
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Kinoshita M, Hirata F. Analysis of salt effects on solubility of noble gases in water using the reference interaction site model theory. J Chem Phys 1997. [DOI: 10.1063/1.473519] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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252
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Matyushov DV, Schmid R, Ladanyi BM. A Thermodynamic Analysis of the π* and ET(30) Polarity Scales. J Phys Chem B 1997. [DOI: 10.1021/jp961609i] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dmitry V. Matyushov
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, and Institute of Inorganic Chemistry, Technical University of Vienna, Getreidemarkt 9, A-1060 Vienna, Austria
| | - Roland Schmid
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, and Institute of Inorganic Chemistry, Technical University of Vienna, Getreidemarkt 9, A-1060 Vienna, Austria
| | - Branka M. Ladanyi
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, and Institute of Inorganic Chemistry, Technical University of Vienna, Getreidemarkt 9, A-1060 Vienna, Austria
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253
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Qian H, Hopfield JJ. Entropy‐enthalpy compensation: Perturbation and relaxation in thermodynamic systems. J Chem Phys 1996. [DOI: 10.1063/1.472728] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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254
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Matyushov DV, Schmid R. A thermodynamic analysis of solvation in dipolar liquids. J Chem Phys 1996. [DOI: 10.1063/1.472333] [Citation(s) in RCA: 32] [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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255
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Åqvist J, Hansson T. On the Validity of Electrostatic Linear Response in Polar Solvents. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp953640a] [Citation(s) in RCA: 232] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johan Åqvist
- Department of Molecular Biology, Uppsala University, Biomedical Center, Box 590, S-75124 Uppsala, Sweden
| | - Tomas Hansson
- Department of Molecular Biology, Uppsala University, Biomedical Center, Box 590, S-75124 Uppsala, Sweden
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256
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Ashbaugh HS, Paulaitis ME. Entropy of Hydrophobic Hydration: Extension to Hydrophobic Chains. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952387b] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Henry S. Ashbaugh
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
| | - Michael E. Paulaitis
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
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257
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Re M, Laria D, Fernández-Prini R. Solvent structural contributions to the dissolution process of an apolar solute in water. Chem Phys Lett 1996. [DOI: 10.1016/0009-2614(95)01449-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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258
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Harris D, Loew G. Comparative study of free energies of solvation of phenylimidazole inhibitors of cytochrome P450cam by free energy simulation, AMSOL, and Poisson Boltzmann methods. J Comput Chem 1996. [DOI: 10.1002/(sici)1096-987x(199602)17:3<273::aid-jcc2>3.0.co;2-s] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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259
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Schmidt AB, Fine RM. Size effects in nonpolar solvation: lessons from two simple models. Biophys Chem 1996; 57:219-24. [PMID: 17023340 DOI: 10.1016/0301-4622(95)00060-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/1994] [Revised: 03/22/1995] [Accepted: 03/22/1995] [Indexed: 11/29/2022]
Abstract
Size dependence of the solute chemical potential mu(u) is examined using the Ornstein-Zernike equation for two models of the nonpolar solute-solvent interactions. Simple Lennard-Jones interactions are assumed in the first model while the Lennard-Jones potential is distributed over the solute volume in the second model similar to the Hamaker theory for the colloid dispersion forces. In both models, while mu(u) rises asymptotically as the third power of the solute size in agreement with asymptotic solution of the scaled particle theory, it increases faster at smaller sizes. Deviations from the cubic law are more pronounced at higher solvent densities and stronger molecular interactions. Within a relatively narrow size range typical for small organic molecules, mu(u) can be approximated with a polynomial of the third or even the second power. However, the latter approximation is less accurate and cannot be employed for extrapolation to the larger size region.
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Affiliation(s)
- A B Schmidt
- Biosym Technologies, Inc., 4 Century Dr., Parsippany, NJ 07054, USA
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260
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Dejaegere A, Karplus M. Analysis of Coupling Schemes in Free Energy Simulations: A Unified Description of Nonbonded Contributions to Solvation Free Energies. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952332+] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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261
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Boczko EM, Brooks CL. First-principles calculation of the folding free energy of a three-helix bundle protein. Science 1995; 269:393-6. [PMID: 7618103 DOI: 10.1126/science.7618103] [Citation(s) in RCA: 353] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The folding and unfolding of a three-helix bundle protein were explored with molecular-dynamics simulations, cluster analysis, and weighted-histogram techniques. The folding-unfolding process occurs by means of a "folding funnel," in which a uniform and broad distribution of conformational states is accessible outside of the native manifold. This distribution narrows near a transition region and becomes compact within the native manifold. Key thermodynamic steps in folding include initial interactions around the amino-terminal helix-turn-helix motif, interactions between helices I and II, and, finally, the docking of helix III onto the helix I-II subdomain. A metastable minimum in the calculated free-energy surface is observed at approximately 1.5 times the native volume. Folding-unfolding thermodynamics are dominated by the opposing influences of protein-solvent energy, which favors unfolding, and the overall entropy, which favors folding by means of the hydrophobic effect.
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Affiliation(s)
- E M Boczko
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
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262
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Lue L, Blankschtein D. Integral equations for interaction site fluids: The influence of connectivity constraints and auxiliary sites. J Chem Phys 1995. [DOI: 10.1063/1.469274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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263
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Wei D, Blum L. Solvation thermodynamic functions in the mean spherical approximation: Behavior near the solvent critical region. J Chem Phys 1995. [DOI: 10.1063/1.469469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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264
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Matyushov DV, Schmid R. Charge separation/recombination reactions in non-polar fluids: a molecular description. Mol Phys 1995. [DOI: 10.1080/00268979500100351] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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265
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Lazaridis T, Archontis G, Karplus M. Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics. ADVANCES IN PROTEIN CHEMISTRY 1995; 47:231-306. [PMID: 8561050 DOI: 10.1016/s0065-3233(08)60547-1] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- T Lazaridis
- Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA
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266
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267
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Boresch S, Archontis G, Karplus M. Free energy simulations: the meaning of the individual contributions from a component analysis. Proteins 1994; 20:25-33. [PMID: 7824520 DOI: 10.1002/prot.340200105] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A theoretical analysis is made of the decomposition into contributions from individual interactions of the free energy calculated by thermodynamic integration. It is demonstrated that such a decomposition, often referred to as "component analysis," is meaningful, even though it is a function of the integration path. Moreover, it is shown that the path dependence can be used to determine the relation of the contribution of a given interaction to the state of the system. To illustrate these conclusions, a simple transformation (Cl- to Br- in aqueous solution) is analyzed by use of the Reference Interaction Site Model-Hypernetted Chain Closure integral equation approach; it avoids the calculational difficulties of macromolecular simulation while retaining their conceptual complexity. The difference in the solvation free energy between chloride and bromide is calculated, and the contributions of the Lennard-Jones and electrostatic terms in the potential function are analyzed by the use of suitably chosen integration paths. The model is also used to examine the path dependence of individual contributions to the double free energy differences (delta delta G or delta delta A) that are often employed in free energy simulations of biological systems. The alchemical path, as contrasted with the experimental path, is shown to be appropriate for interpreting the effects of mutations on ligand binding and protein stability. The formulation is used to obtain a better understanding of the success of the Poisson-Boltzmann continuum approach for determining the solvation properties of polar and ionic systems.
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Affiliation(s)
- S Boresch
- Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138
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268
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Abstract
Using Widom's potential distribution theory (J. Chem. Phys. 39 (1963) 2808; J. Phys. Chem. 86 (1982) 869), a general and a special theorems are derived, by means of which one can judge whether a particular sub-process of an overall process will produce compensating changes in enthalpy and entropy. The enthalpy-entropy compensation phenomena that are observed in the transfer process of a hydrophobic molecule from a non-aqueous phase to water are examined in the light of these theorems. It is concluded that most sub-processes involved in the hydrophobic transfer process are compensating except one, that of inserting a cavity corresponding to the solute molecule in the liquid. The reason that this process is non-compensating, and therefore most responsible for the hydrophobicity, is traced to the hard core overlap between solvent and the solute molecules.
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Affiliation(s)
- B Lee
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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269
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Perkyns J, Pettitt BM. Integral equation approaches to structure and thermodynamics of aqueous salt solutions. Biophys Chem 1994; 51:129-42; discussion 142-6. [PMID: 7919031 DOI: 10.1016/0301-4622(94)00056-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Results for free energy, entropy, enthalpy and internal energy of solvation for monovalent ions in water have been studied by comparing DRISM theory results to those of RISM and ARISM theories. The greatly improved dielectric behavior in the DRISM case enabled the examination of realistically modeled salts at finite concentrations. The link between solvent structure and the entropy of solvent co-spheres was examined. Finally comparison with the Born free energy equation shows its virtues and flaws due to ignoring cavity formation and asymmetric solvation terms which together always contribute significantly to the free energy of hydration of ions.
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Affiliation(s)
- J Perkyns
- Chemistry Department University of Houston, TX 77204-5641
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270
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271
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Madan B, Lee B. Role of hydrogen bonds in hydrophobicity: the free energy of cavity formation in water models with and without the hydrogen bonds. Biophys Chem 1994; 51:279-86; discussion 286-9. [PMID: 7919039 DOI: 10.1016/0301-4622(94)00049-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The free energies of cavity formation in water with and without hydrogen bonding potential were computed from the results of a set of Monte Carlo simulation calculations on pure liquid TIP4P water model and on the same model but with the electrostatic charges turned off (Lennard-Jones liquid). The free energies of cavity formation in the Lennard-Jones liquids are higher than or approximately equal to those in TIP4P water, depending, respectively, on whether the Lennard-Jones size parameter sigma is set equal to 3.15 A, which is the value of sigma for TIP4P water, or to 2.8 A, which is the commonly assumed value for the oxygen-oxygen distance between two hydrogen-bonded water molecules. This result indicates that changes in the hydrogen-bonded structure of water and/or in the orientational degree of freedom of water are not essential features in the production of the large free energy change upon cavity formation.
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Affiliation(s)
- B Madan
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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272
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273
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Lau FT, Karplus M. Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant. J Mol Biol 1994; 236:1049-66. [PMID: 8120886 DOI: 10.1016/0022-2836(94)90011-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Alchemical molecular dynamics simulations are performed to determine the difference in the free energy of binding of the tyrosine substrate between the wild type of tyrosyl-tRNA synthetase (TyrRS) from Bacillus stearothermophilus and the mutant Tyr169-->Phe. The results are of general interest because the Tyr169 hydroxyl group interacts with the ammonium group of the substrate in a manner corresponding to that found in other amino acid binding proteins (e.g. the Asp receptor of the chemotactic bacterium Salmonella typhimurium and class I major histocompatibility complex molecules). The calculated free-energy change due to the Tyr169-->Phe mutation is 3.4 kcal/mol (the statistical error is +/- 0.5 kcal/mol) in satisfactory agreement with the experimental value of 3(+/- 0.5) kcal/mol. By use of thermodynamic integration, the contribution of the different terms to the free energy change are estimated. The path dependence of such a decomposition is discussed and it is suggested that the alchemical choice is of primary interest for understanding the interactions involved. There are large protein contributions to the alchemical free energy difference of the bound and free enzyme that cancel in the overall result. Due to this cancellation, the essential interactions contributing to the free-energy change are those between the OH group of Tyr169 and water in the free enzyme and those between the OH group of Tyr169 and the ammonium group of the substrate in the bound system. The results thus support simple models based on a balance of hydrogen bonding interactions.
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Affiliation(s)
- F T Lau
- Department of Chemistry, Harvard University, Cambridge, MA 02138
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274
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Lue L, Blankschtein D. Proper integral equations for interaction‐site fluids: Exact free‐energy expressions. J Chem Phys 1994. [DOI: 10.1063/1.466441] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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275
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Olender R, Nitzan A. Lattice theory of solvation and dissociation in macromolecular fluids. I. Mean field approximation. J Chem Phys 1994. [DOI: 10.1063/1.466935] [Citation(s) in RCA: 14] [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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276
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Guillot B, Guissani Y. A computer simulation study of the temperature dependence of the hydrophobic hydration. J Chem Phys 1993. [DOI: 10.1063/1.465634] [Citation(s) in RCA: 300] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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277
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Zeng J, Hush N, Reimers J. Enthalpy of hydration and partial molar specific volume as criteria for evaluation of intermolecular potentials. NPT-ensemble Monte Carlo calculations for dilute neon in water. Chem Phys Lett 1993. [DOI: 10.1016/0009-2614(93)85558-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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278
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Rashin AA. Aspects of protein energetics and dynamics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1993; 60:73-200. [PMID: 8362069 DOI: 10.1016/0079-6107(93)90017-e] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- A A Rashin
- Biosym Technologies Inc, Parsippany, NJ 07054
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279
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Hirata F. Interaction‐site representation of the Smoluchowski–Vlasov equation: The space–time correlation functions in a molecular liquid. J Chem Phys 1992. [DOI: 10.1063/1.462797] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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280
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Papazyan A, Maroncelli M. Simulations of solvation in a Brownian dipole lattice. J Chem Phys 1991. [DOI: 10.1063/1.461203] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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281
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Shemetulskis NE, Loring RF. Electronic absorption spectra in a polar fluid: Theory and simulation. J Chem Phys 1991. [DOI: 10.1063/1.461718] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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282
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Guillot B, Guissani Y, Bratos S. A computer‐simulation study of hydrophobic hydration of rare gases and of methane. I. Thermodynamic and structural properties. J Chem Phys 1991. [DOI: 10.1063/1.460815] [Citation(s) in RCA: 129] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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283
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284
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Tobias DJ, Sneddon SF, Brooks CL. Reverse turns in blocked dipeptides are intrinsically unstable in water. J Mol Biol 1990; 216:783-96. [PMID: 2258940 DOI: 10.1016/0022-2836(90)90399-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have carried out molecular dynamics simulations to study the conformational equilibria of two blocked dipeptides, Ac-Ala-Ala-NHMe and trans-Ac-Pro-Ala-NHMe, in water (Ac, amino-terminal blocking group COCH3; NHMe, carboxy-terminal blocking group NHCH3). Using specialized sampling techniques we computed free-energy surfaces as functions of a conformation co-ordinate that corresponds to hydrogen-bonded reverse turns at small values and to extended conformations at large values. The free-energy difference between hydrogen-bonded reverse turn conformations and extended conformations, determined from the equilibrium constants for reverse turn unfolding, is approximately -5 kcal/mole for Ac-Ala-Ala-NHMe, and -10 kcal/mole for Ac-Pro-Ala-NHMe. These results demonstrate that reverse turns in blocked dipeptides are intrinsically unstable in water. That is, in the absence of strongly stabilizing sequence-specific inter-residue interactions involving side-chains and/or charged terminal groups, the extended conformations of small peptides are highly favored in solution. By thermodynamically decomposing the free-energy differences, we found that the peptide-water entropy is the primary reason for the exceptional stability of the extended conformations of both peptides, and that the differences between the two peptides are primarily due to differences in the peptide-water interactions. In addition, we assessed the "proline effect" on the conformational equilibria by comparing the differences in configurational entropies between the reverse turn and extended conformations of the two peptides. As expected, the extended conformation of the Pro-Ala peptide is destabilized by reduced configurational entropy, but the effect is negligible in the blocked dipeptides. Finally, we compared our results with the results of several other experimental studies to identify some of the specific interactions that may be responsible for stabilizing reverse turns in small peptides in solution.
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Affiliation(s)
- D J Tobias
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
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285
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Wei D, Patey GN. Dynamics of molecular liquids: A comparison of different theories with application to wave vector dependent dielectric relaxation and ion solvation. J Chem Phys 1990. [DOI: 10.1063/1.459704] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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286
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Yu H, Roux B, Karplus M. Solvation thermodynamics: An approach from analytic temperature derivatives. J Chem Phys 1990. [DOI: 10.1063/1.458538] [Citation(s) in RCA: 113] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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287
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Tobias DJ, Brooks CL. The thermodynamics of solvophobic effects: A molecular‐dynamics study of n‐butane in carbon tetrachloride and water. J Chem Phys 1990. [DOI: 10.1063/1.457951] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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288
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Gao J, Kuczera K, Tidor B, Karplus M. Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. Science 1989; 244:1069-72. [PMID: 2727695 DOI: 10.1126/science.2727695] [Citation(s) in RCA: 209] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A molecular dynamics simulation method is used to determine the contributions of individual amino acid residues and solvent molecules to free energy changes in proteins. Its application to the hemoglobin interface mutant Asp G1(99) beta----Ala shows that some of the contributions to the difference in the free energy of cooperativity are as large as 60 kilocalories (kcal) per mole. Since the overall free energy change is only -5.5 kcal/mole (versus the experimental value of -3.4 kcal/mole), essential elements of the thermodynamics are hidden in the measured results. By exposing the individual contributions, the free energy simulation provides new insights into the origin of thermodynamic changes in mutant proteins and demonstrates the role of effects beyond those usually considered in structural analyses.
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Affiliation(s)
- J Gao
- Department of Chemistry, Harvard University, Cambridge, MA 02138
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