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Toward Temperature-DependentCoarse-Grained Potentialsof Side-Chain Interactions for Protein Folding Simulations. II. MolecularDynamics Study of Pairs of Different Types of Interactions in Waterat Various Temperatures.

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Title: Toward Temperature-DependentCoarse-Grained Potentialsof Side-Chain Interactions for Protein Folding Simulations. II. MolecularDynamics Study of Pairs of Different Types of Interactions in Waterat Various Temperatures.
Authors: Sobolewski, Emil1, Ołdziej, Stanisław1, Wiśniewska, Marta1, Liwo, Adam1, Makowski, Mariusz1
Source: Journal of Physical Chemistry B. Jun2012, Vol. 116 Issue 23, p6844-6853. 10p.
Subjects: Protein folding -- Computer simulation, Temperature effect, Molecular dynamics, Protein-protein interactions, Water, Entropy
Abstract: By means of molecular dynamics simulations of 15 pairsof moleculesselected to model the interactions of nonpolar, nonpolar and polar,nonpolar and charged, polar, and polar and charged side chains inwater, we determined the potentials of mean force (PMFs) of pairsof interacting molecules in water as functions of distance betweenthe interacting particles or their distance and orientations at threetemperatures: 283, 323, and 373 K, respectively. The systems werefound to fall into the following four categories as far as the temperaturedependence of the PMF is concerned: (i) pairs for which associationis entropy-driven, (ii) pairs for which association is energy-driven,(iii) pairs of positively charged solute molecules, for which associationis energy-driven with unfavorable entropy change, and (iv) the remainingsystems for which temperature dependence is weak. For each pair ofPMFs, entropic and energetic contributions have been discussed. [ABSTRACT FROM AUTHOR]
Copyright of Journal of Physical Chemistry B is the property of American Chemical Society and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Toward Temperature-DependentCoarse-Grained Potentialsof Side-Chain Interactions for Protein Folding Simulations. II. MolecularDynamics Study of Pairs of Different Types of Interactions in Waterat Various Temperatures.
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  Data: <searchLink fieldCode="JN" term="%22Journal+of+Physical+Chemistry+B%22">Journal of Physical Chemistry B</searchLink>. Jun2012, Vol. 116 Issue 23, p6844-6853. 10p.
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  Data: <searchLink fieldCode="DE" term="%22Protein+folding+--+Computer+simulation%22">Protein folding -- Computer simulation</searchLink><br /><searchLink fieldCode="DE" term="%22Temperature+effect%22">Temperature effect</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+dynamics%22">Molecular dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22Protein-protein+interactions%22">Protein-protein interactions</searchLink><br /><searchLink fieldCode="DE" term="%22Water%22">Water</searchLink><br /><searchLink fieldCode="DE" term="%22Entropy%22">Entropy</searchLink>
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  Data: By means of molecular dynamics simulations of 15 pairsof moleculesselected to model the interactions of nonpolar, nonpolar and polar,nonpolar and charged, polar, and polar and charged side chains inwater, we determined the potentials of mean force (PMFs) of pairsof interacting molecules in water as functions of distance betweenthe interacting particles or their distance and orientations at threetemperatures: 283, 323, and 373 K, respectively. The systems werefound to fall into the following four categories as far as the temperaturedependence of the PMF is concerned: (i) pairs for which associationis entropy-driven, (ii) pairs for which association is energy-driven,(iii) pairs of positively charged solute molecules, for which associationis energy-driven with unfavorable entropy change, and (iv) the remainingsystems for which temperature dependence is weak. For each pair ofPMFs, entropic and energetic contributions have been discussed. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Journal of Physical Chemistry B is the property of American Chemical Society and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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      – Type: doi
        Value: 10.1021/jp212593h
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      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 10
        StartPage: 6844
    Subjects:
      – SubjectFull: Protein folding -- Computer simulation
        Type: general
      – SubjectFull: Temperature effect
        Type: general
      – SubjectFull: Molecular dynamics
        Type: general
      – SubjectFull: Protein-protein interactions
        Type: general
      – SubjectFull: Water
        Type: general
      – SubjectFull: Entropy
        Type: general
    Titles:
      – TitleFull: Toward Temperature-DependentCoarse-Grained Potentialsof Side-Chain Interactions for Protein Folding Simulations. II. MolecularDynamics Study of Pairs of Different Types of Interactions in Waterat Various Temperatures.
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            NameFull: Sobolewski, Emil
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            NameFull: Ołdziej, Stanisław
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            NameFull: Wiśniewska, Marta
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            NameFull: Liwo, Adam
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            NameFull: Makowski, Mariusz
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              M: 06
              Text: Jun2012
              Type: published
              Y: 2012
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              Value: 116
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            – TitleFull: Journal of Physical Chemistry B
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