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251
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Sorenson JM, Hura G, Glaeser RM, Head-Gordon T. What can x-ray scattering tell us about the radial distribution functions of water? J Chem Phys 2000. [DOI: 10.1063/1.1319615] [Citation(s) in RCA: 305] [Impact Index Per Article: 12.2] [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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Choi IS, Weck M, Jeon NL, Whitesides GM. Mesoscale Folding: A Physical Realization of an Abstract, 2D Lattice Model for Molecular Folding. J Am Chem Soc 2000. [DOI: 10.1021/ja001874o] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Insung S. Choi
- Department of Chemistry and Chemical Biology Harvard University, 12 Oxford Street Cambridge, Massachusetts 02138
| | - Marcus Weck
- Department of Chemistry and Chemical Biology Harvard University, 12 Oxford Street Cambridge, Massachusetts 02138
| | - Noo Li Jeon
- Department of Chemistry and Chemical Biology Harvard University, 12 Oxford Street Cambridge, Massachusetts 02138
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology Harvard University, 12 Oxford Street Cambridge, Massachusetts 02138
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253
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Koh CA, Wisbey RP, Wu X, Westacott RE, Soper AK. Water ordering around methane during hydrate formation. J Chem Phys 2000. [DOI: 10.1063/1.1288818] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.0] [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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Barkema GT, Widom B. Model of hydrophobic attraction in two and three dimensions. J Chem Phys 2000. [DOI: 10.1063/1.482049] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [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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Carey C, Cheng YK, Rossky PJ. Hydration structure of the α-chymotrypsin substrate binding pocket: the impact of constrained geometry. Chem Phys 2000. [DOI: 10.1016/s0301-0104(00)00178-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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256
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257
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Eads CD. Simple Lattice Model for Solvation of Nonpolar Molecules in Hydrogen-Bonded Liquids. J Phys Chem B 2000. [DOI: 10.1021/jp993472c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Charles D. Eads
- Miami Valley Laboratories, The Procter & Gamble Company, P.O. Box 538707, Cincinnati, Ohio 45253-8707
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258
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Onuchic JN, Nymeyer H, García AE, Chahine J, Socci ND. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. ADVANCES IN PROTEIN CHEMISTRY 2000; 53:87-152. [PMID: 10751944 DOI: 10.1016/s0065-3233(00)53003-4] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- J N Onuchic
- Department of Physics, University of California at San Diego, La Jolla 92093-0319, USA
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259
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Abstract
A large number of thermodynamic data including the free energy, enthalpy, entropy, and heat capacity changes were collected for the denaturation of various proteins. Regression indicated that remarkable enthalpy-entropy compensation occurred in protein unfolding, which meant that the change in enthalpy was almost compensated by a corresponding change in entropy resulting in a smaller net free energy change. This behavior was proposed to result from the water molecule reorganization, which contributed significantly to the enthalpy and entropy changes but little to the free energy change in protein unfolding. It turned out that the enthalpy-entropy compensation could provide novel insights into the problem of enthalpy and entropy convergence in protein unfolding.
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Affiliation(s)
- L Liu
- Department of Chemistry, University of Science and Technology of China, Hefei, PR China
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260
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of CUNY, Convent Ave & 138th Street, New York, New York 10031
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261
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Southall NT, Dill KA. The Mechanism of Hydrophobic Solvation Depends on Solute Radius. J Phys Chem B 2000. [DOI: 10.1021/jp992860b] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Noel T. Southall
- Department of Pharmaceutical Chemistry, and Graduate Group in Biophysics, University of California at San Francisco, San Francisco, California 94143-1204
| | - Ken A. Dill
- Department of Pharmaceutical Chemistry, and Graduate Group in Biophysics, University of California at San Francisco, San Francisco, California 94143-1204
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262
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Garde S, Khare R, Hummer G. Microscopic density fluctuations and solvation in polymeric fluids. J Chem Phys 2000. [DOI: 10.1063/1.480705] [Citation(s) in RCA: 10] [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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263
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Abstract
Direct measurement of the thermodynamics of biomolecular interactions is now relatively easy. Interpretation of these thermodynamics in simple molecular terms is not. Recent work shows how the multiplicity of weak noncovalent interactions, and the inevitable enthalpy/entropy compensation that these interactions engender, lead to difficulties in teasing out the different components.
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Affiliation(s)
- A Cooper
- Chemistry Department, Glasgow University Glasgow, G12 8QQ, UK.
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264
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Pomès R, Eisenmesser E, Post CB, Roux B. Calculating excess chemical potentials using dynamic simulations in the fourth dimension. J Chem Phys 1999. [DOI: 10.1063/1.479622] [Citation(s) in RCA: 30] [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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265
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Sorenson JM, Hura G, Soper AK, Pertsemlidis A, Head-Gordon T. Determining the Role of Hydration Forces in Protein Folding. J Phys Chem B 1999. [DOI: 10.1021/jp990434k] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jon M. Sorenson
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720
| | - Greg Hura
- Graduate Group in Biophysics, University of California, Berkeley and Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Alan K. Soper
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, U.K
| | - Alexander Pertsemlidis
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75235-9038
| | - Teresa Head-Gordon
- Life Sciences Division & Physical Biosciences Division, Lawrence Berkeley, National Laboratory, Berkeley, California 94720
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266
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Gomez MA, Pratt LR, Hummer G, Garde S. Molecular Realism in Default Models for Information Theories of Hydrophobic Effects. J Phys Chem B 1999. [DOI: 10.1021/jp990337r] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. A. Gomez
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - L. R. Pratt
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - G. Hummer
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - S. Garde
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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267
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Garde S, García AE, Pratt LR, Hummer G. Temperature dependence of the solubility of non-polar gases in water. Biophys Chem 1999; 78:21-32. [PMID: 17030303 DOI: 10.1016/s0301-4622(99)00018-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/1998] [Revised: 01/18/1999] [Accepted: 01/18/1999] [Indexed: 10/17/2022]
Abstract
An explanation is provided for the experimentally observed temperature dependence of the solubility and the solubility minimum of non-polar gases in water. The influence of solute size and solute-water attractive interactions on the solubility minimum temperature is investigated. The transfer of a non-polar solute from the ideal gas into water is divided into two steps: formation of a cavity in water with the size and shape of the solute and insertion of the solute in this cavity which is equivalent to 'turning on' solute-water attractive interactions. This two step process divides the excess chemical potential of the non-polar solute in water into repulsive and attractive contributions, respectively. The reversible work for cavity formation is modeled using an information theory model of hydrophobic hydration. Attractive contributions are calculated by modeling the water structure in the vicinity of non-polar solutes. These models make a direct connection between microscopic quantities and macroscopic observables. Moreover, they provide an understanding of the peculiar temperature dependences of the hydration thermodynamics from properties of pure water; specifically, bulk water density and the water oxygen-oxygen radial distribution function.
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Affiliation(s)
- S Garde
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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