Multibody correlations in the hydrophobic solvation of glycine peptides

Robert C. Harris, Justin A. Drake, Bernard Pettitt

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔGvdw) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔGvdw, as well as its attractive (ΔGatt) and repulsive (ΔGrep) components, was not simply a linear function of A. We found that the surface tensions, γrep, γatt, and γvdw, gotten from ΔGrep, ΔGatt, and ΔGvdw against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysis to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γrep. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γrep for the intact decaglycines. Finally, γatt for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γvdw (-74 and -56 cal/mol/Å2 for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔGvdw favors extended rather than compact structures for decaglycine. We find that ΔGrep and ΔGvdw have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.

Original languageEnglish (US)
Article number22D525
JournalJournal of Chemical Physics
Volume141
Issue number22
DOIs
StatePublished - Dec 14 2014

Fingerprint

Solvation
glycine
Glycine
peptides
solvation
Atoms
Peptides
Free energy
Alkanes
free energy
atoms
alanine
Alanine
alkanes
configurations
folding
field theory (physics)
Surface tension
Conformations
solutes

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Multibody correlations in the hydrophobic solvation of glycine peptides. / Harris, Robert C.; Drake, Justin A.; Pettitt, Bernard.

In: Journal of Chemical Physics, Vol. 141, No. 22, 22D525, 14.12.2014.

Research output: Contribution to journalArticle

@article{34160714edde44818234113b353fe7e1,
title = "Multibody correlations in the hydrophobic solvation of glycine peptides",
abstract = "Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔGvdw) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔGvdw, as well as its attractive (ΔGatt) and repulsive (ΔGrep) components, was not simply a linear function of A. We found that the surface tensions, γrep, γatt, and γvdw, gotten from ΔGrep, ΔGatt, and ΔGvdw against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysis to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γrep. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γrep for the intact decaglycines. Finally, γatt for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γvdw (-74 and -56 cal/mol/{\AA}2 for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔGvdw favors extended rather than compact structures for decaglycine. We find that ΔGrep and ΔGvdw have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.",
author = "Harris, {Robert C.} and Drake, {Justin A.} and Bernard Pettitt",
year = "2014",
month = "12",
day = "14",
doi = "10.1063/1.4901886",
language = "English (US)",
volume = "141",
journal = "Journal of Chemical Physics",
issn = "0021-9606",
publisher = "American Institute of Physics Publising LLC",
number = "22",

}

TY - JOUR

T1 - Multibody correlations in the hydrophobic solvation of glycine peptides

AU - Harris, Robert C.

AU - Drake, Justin A.

AU - Pettitt, Bernard

PY - 2014/12/14

Y1 - 2014/12/14

N2 - Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔGvdw) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔGvdw, as well as its attractive (ΔGatt) and repulsive (ΔGrep) components, was not simply a linear function of A. We found that the surface tensions, γrep, γatt, and γvdw, gotten from ΔGrep, ΔGatt, and ΔGvdw against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysis to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γrep. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γrep for the intact decaglycines. Finally, γatt for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γvdw (-74 and -56 cal/mol/Å2 for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔGvdw favors extended rather than compact structures for decaglycine. We find that ΔGrep and ΔGvdw have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.

AB - Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔGvdw) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔGvdw, as well as its attractive (ΔGatt) and repulsive (ΔGrep) components, was not simply a linear function of A. We found that the surface tensions, γrep, γatt, and γvdw, gotten from ΔGrep, ΔGatt, and ΔGvdw against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysis to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γrep. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γrep for the intact decaglycines. Finally, γatt for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γvdw (-74 and -56 cal/mol/Å2 for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔGvdw favors extended rather than compact structures for decaglycine. We find that ΔGrep and ΔGvdw have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.

UR - http://www.scopus.com/inward/record.url?scp=84914127080&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84914127080&partnerID=8YFLogxK

U2 - 10.1063/1.4901886

DO - 10.1063/1.4901886

M3 - Article

C2 - 25494796

AN - SCOPUS:84914127080

VL - 141

JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

SN - 0021-9606

IS - 22

M1 - 22D525

ER -