Peptide conformational equilibria computed via a single-stage shifting protocol

F. Marty Ytreberg, Daniel Zuckerman

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

We study the conformational equilibria of two peptides using a novel statistical mechanics approach designed for calculating free energy differences between highly dissimilar conformational states. Our results elucidate the contrasting roles of entropy in implicitly solvated leucine dipeptide and decaglycine. The method extends earlier work by Voter and overcomes the notorious "overlap" problem in free energy computations by constructing a mathematically equivalent calculation with high conformational similarity. The approach requires only equilibrium simulations of the two states of interest, without the need for sampling transition states. We discuss possible extensions and optimizations of the approach.

Original languageEnglish (US)
Pages (from-to)9096-9103
Number of pages8
JournalJournal of Physical Chemistry B
Volume109
Issue number18
DOIs
StatePublished - May 12 2005
Externally publishedYes

Fingerprint

Dipeptides
Entropy
Jurisprudence
Mechanics
Leucine
Peptides
peptides
free energy
leucine
Free energy
statistical mechanics
Statistical mechanics
sampling
entropy
optimization
Sampling
simulation
decaglycine

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

Peptide conformational equilibria computed via a single-stage shifting protocol. / Ytreberg, F. Marty; Zuckerman, Daniel.

In: Journal of Physical Chemistry B, Vol. 109, No. 18, 12.05.2005, p. 9096-9103.

Research output: Contribution to journalArticle

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