A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the "unfolding". While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.

Noe, F., Daidone, I., Smith, J., Di Nola, A., Amadei, A. (2008). Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, 112(35), 11155-11163 [10.1021/jp801391t].

Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation

AMADEI, ANDREA
2008-01-01

Abstract

A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the "unfolding". While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.
2008
Pubblicato
Rilevanza internazionale
Articolo
Sì, ma tipo non specificato
Settore CHIM/02 - CHIMICA FISICA
English
Con Impact Factor ISI
Amines; Chlorine compounds; Conformations; Electrostriction; Entropy; Hydrophobicity; Molecular dynamics; Molecular mechanics; Nanofluidics; Offshore oil well production; Protein folding; Quantum chemistry; Solvents; Thermodynamics; Trellis codes; Configurational entropy; Conformational states; Conformational thermodynamics; Experimental studies; Hydration water; Hydrophobic effects; Microscopic structures; Molar entropies; Molecular dynamics simulation; Orientational orders; Peptide folding; Quasi-Gaussian; Dynamics; fluorescent dye; MR121 oxazine fluorophore; oxazine derivative; peptide; solvent; article; chemical structure; chemistry; drug effect; electric conductivity; entropy; metabolism; protein conformation; protein folding; reproducibility; Electric Conductivity; Entropy; Fluorescent Dyes; Models, Molecular; Oxazines; Peptides; Protein Conformation; Protein Folding; Reproducibility of Results; Solvents
Noe, F., Daidone, I., Smith, J., Di Nola, A., Amadei, A. (2008). Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, 112(35), 11155-11163 [10.1021/jp801391t].
Noe, F; Daidone, I; Smith, J; Di Nola, A; Amadei, A
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2108/23742
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