Molecular dynamics analysis of a ribonuclease C‐peptide analogue

Kizhake V. Soman, Afshin Karimi, David A. Case

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


We have carried out a nanosecond molecular dynamics simulation of an analogue of the ribonuclease C‐peptide in water. The overall conformation has an extended region for the first three amino acids connected to an α‐helix for residues 4–13, and this basic structure is preserved throughout the simulation, with helical hydrogen bonds present 87% of the time, on average. The final helical hydrogen bond is spontaneously broken and re‐formed several times, providing a detailed picture of such winding/unwinding events. The simulation was used to estimate the effects of internal motion on proton nuclear Overhauser effect spectroscopy (NOESY) intensities for several classes of important cross peaks. Within the helical regions, the effects of internal motion vary only a little from one residue to another for backbone–backbone cross peaks, and the relevant correlation functions reach plateau values within about 50 ps. The spectral simulations show, however, that it may be difficult to establish a close quantitative connection between NOESY cross‐peak volumes and measures of helical content. © 1993 John Wiley & Sons, Inc.

Original languageEnglish (US)
Pages (from-to)1567-1580
Number of pages14
Issue number10
StatePublished - Oct 1993
Externally publishedYes

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry


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