Literature DB >> 20540927

Solvent-induced free energy landscape and solute-solvent dynamic coupling in a multielement solute.

P L San Biagio1, V Martorana, D Bulone, M B Palma-Vittorelli, M U Palma.   

Abstract

Molecular dynamics simulations using a simple multielement model solute with internal degrees of freedom and accounting for solvent-induced interactions to all orders in explicit water are reported. The potential energy landscape of the solute is flat in vacuo. However, the sole untruncated solvent-induced interactions between apolar (hydrophobic) and charged elements generate a rich landscape of potential of mean force exhibiting typical features of protein landscapes. Despite the simplicity of our solute, the depth of minima in this landscape is not far in size from free energies that stabilize protein conformations. Dynamical coupling between configurational switching of the system and hydration reconfiguration is also elicited. Switching is seen to occur on a time scale two orders of magnitude longer than that of the reconfiguration time of the solute taken alone, or that of the unperturbed solvent. Qualitatively, these results are unaffected by a different choice of the water-water interaction potential. They show that already at an elementary level, solvent-induced interactions alone, when fully accounted for, can be responsible for configurational and dynamical features essential to protein folding and function.

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Year:  2008        PMID: 20540927      PMCID: PMC1300523          DOI: 10.1016/S0006-3495(99)77083-9

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  15 in total

1.  Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble.

Authors:  B A Shoemaker; J Wang; P G Wolynes
Journal:  J Mol Biol       Date:  1999-04-02       Impact factor: 5.469

2.  The energy landscapes and motions of proteins.

Authors:  H Frauenfelder; S G Sligar; P G Wolynes
Journal:  Science       Date:  1991-12-13       Impact factor: 47.728

3.  Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.

Authors:  Y Duan; P A Kollman
Journal:  Science       Date:  1998-10-23       Impact factor: 47.728

4.  Collective properties of hydration: long range and specificity of hydrophobic interactions.

Authors:  V Martorana; D Bulone; P L San Biagio; M B Palma-Vittorelli; M U Palma
Journal:  Biophys J       Date:  1997-07       Impact factor: 4.033

5.  Hydration of an alpha-helical peptide: comparison of theory and molecular dynamics simulation.

Authors:  A E García; G Hummer; D M Soumpasis
Journal:  Proteins       Date:  1997-04

6.  A statistical mechanical description of biomolecular hydration.

Authors:  G Hummer; A E García; D M Soumpasis
Journal:  Faraday Discuss       Date:  1996       Impact factor: 4.008

Review 7.  Principles of protein folding--a perspective from simple exact models.

Authors:  K A Dill; S Bromberg; K Yue; K M Fiebig; D P Yee; P D Thomas; H S Chan
Journal:  Protein Sci       Date:  1995-04       Impact factor: 6.725

8.  Funnels, pathways, and the energy landscape of protein folding: a synthesis.

Authors:  J D Bryngelson; J N Onuchic; N D Socci; P G Wolynes
Journal:  Proteins       Date:  1995-03

Review 9.  Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics.

Authors:  T Lazaridis; G Archontis; M Karplus
Journal:  Adv Protein Chem       Date:  1995

10.  Interaction of explicit solvent with hydrophobic/philic/charged residues of a protein: residue character vs. conformational context.

Authors:  V Martorana; G Corongiu; M U Palma
Journal:  Proteins       Date:  1998-08-01
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  1 in total

1.  The role of solvent in protein folding and in aggregation.

Authors:  S M Vaiana; M Manno; A Emanuele; M B Palma-Vittorelli; M U Palma
Journal:  J Biol Phys       Date:  2001-06       Impact factor: 1.365

  1 in total

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