Conformational ensembles by nmr and md simulations in model heptapeptides with select tri-peptide motifs

V. V. Krishnan, Timothy Bentley, Alina Xiong, Kalyani Maitra

Research output: Contribution to journalArticlepeer-review

Abstract

Both nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are routinely used in understanding the conformational space sampled by peptides in the solution state. To investigate the role of single-residue change in the ensemble of conformations sampled by a set of heptapeptides, AEVXEVG with X = L, F, A, or G, comprehensive NMR, and MD simulations were performed. The rationale for selecting the particular model peptides is based on the high variability in the occurrence of tri-peptide E*L between the transmembrane β-barrel (TMB) than in globular proteins. The ensemble of conformations sampled by E*L was compared between the three sets of ensembles derived from NMR spectroscopy, MD simulations with explicit solvent, and the random coil conformations. In addition to the estimation of global determinants such as the radius of gyra-tion of a large sample of structures, the ensembles were analyzed using principal component analysis (PCA). In general, the results suggest that the-EVL-peptide indeed adopts a conformational preference that is distinctly different not only from a random distribution but also from other peptides studied here. The relatively straightforward approach presented herein could help understand the conformational preferences of small peptides in the solution state.

Original languageEnglish (US)
Article number1364
Pages (from-to)1-12
Number of pages12
JournalInternational journal of molecular sciences
Volume22
Issue number3
DOIs
StatePublished - Feb 1 2021

Keywords

  • Conformation
  • Ensemble
  • MD
  • NMR
  • Peptide
  • Random coil

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

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