Studying the effect of site-specific hydrophobicity and polarization on hydrogen bond energy of protein using a polarizable method

Chang G. Ji, Xudong Xiao, John Zhang

Research output: Contribution to journalArticle

Abstract

Quantification of backbone hydrogen bond energies in protein folding has remained elusive despite extensive theoretical and experimental investigations over the past 70 years. This is due to difficulties in experimental mutagenesis study as well as the lack of quantitatively reliable methods in theoretical calculation. Recent advance in experiment has enabled accurate measurement of site-specific backbone hydrogen bond energy in protein. In the present work, we developed an accurate and practical polarizable method to study site-specific hydrogen bond energies in the PIN WW domain. Excellent quantitative agreement between our calculated hydrogen bonding energy and recent experimental measurement is obtained. The direct comparison between theory and experiment helps uncover the microscopic mechanism of experimentally observed context dependent hydrogen bond contribution to protein stability in beta-sheet. In particular, our study reveals two effects that act in a cooperative manner to impact the strength of a hydrogen bond. One is the dynamic stability of the hydrogen bond determined by nearby solvent molecules, and the other is the polarization state of the hydrogen bond influenced by local electrostatic environment. The polar character of the hydrogen bond results in strong coupling between hydrophobic and polarization interactions in a cooperative manner. This nonadditive character in hydrogen bonding should help us better understand the microscopic mechanism in protein folding. Our study also investigated the possible structural effect of backbone amide to ester mutation which should be helpful to experimentalists using this technique in mutagenesis study.

Original languageEnglish (US)
Pages (from-to)2157-2164
Number of pages8
JournalJournal of Chemical Theory and Computation
Volume8
Issue number6
DOIs
StatePublished - Jun 12 2012

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Hydrophobicity
hydrophobicity
Hydrogen bonds
Polarization
hydrogen bonds
proteins
Proteins
polarization
mutagenesis
energy
Protein folding
Mutagenesis
folding
dynamic stability
hydrogen
mutations
amides
esters
Amides
electrostatics

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

Studying the effect of site-specific hydrophobicity and polarization on hydrogen bond energy of protein using a polarizable method. / Ji, Chang G.; Xiao, Xudong; Zhang, John.

In: Journal of Chemical Theory and Computation, Vol. 8, No. 6, 12.06.2012, p. 2157-2164.

Research output: Contribution to journalArticle

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