Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR experiments

Daniel S. Weinstock, Chitra Narayanan, Anthony K. Felts, Michael Andrec, Ronald M. Levy, Kuen Phon Wu, Jean Baum

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

Abstract

Replica exchange molecular dynamics simulations are used to generate a set of 20 structural ensembles between 270 and 690 K for the G peptide corresponding to residues 41-56 of the B1 domain of protein G. Each of the structural ensembles is then compared with experimental NMR chemical shift, J-coupling, and NOE data we recorded for the peptide. We show that the peptide ensembles in the middle of the simulation temperature range provide the best fit to the low temperature (278 K) experimental NMR data, thereby providing a set of models for visualizing the large amount of structural heterogeneity present in the experimental ensemble and also providing information that can be used to help calibrate effective potentials employed for peptide modeling.

Original languageEnglish (US)
Pages (from-to)4858-4859
Number of pages2
JournalJournal of the American Chemical Society
Volume129
Issue number16
DOIs
StatePublished - Apr 25 2007

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

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