Molecular dynamics analysis of a ribonuclease C-peptide analogue

K. V. Soman, A. Karimi, D. A. Case

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1567-1580
Number of pages14
JournalBiopolymers
Volume33
Issue number10
StatePublished - Oct 1993
Externally publishedYes

Fingerprint

C-Peptide
Molecular Dynamics Simulation
Dynamic analysis
Peptides
Molecular dynamics
Hydrogen
Spectrum Analysis
Hydrogen bonds
Spectroscopy
Conformations
Protons
Amino acids
Amino Acids
Water
Computer simulation
ribonuclease C
Ribonucleases

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

Soman, K. V., Karimi, A., & Case, D. A. (1993). Molecular dynamics analysis of a ribonuclease C-peptide analogue. Biopolymers, 33(10), 1567-1580.

Molecular dynamics analysis of a ribonuclease C-peptide analogue. / Soman, K. V.; Karimi, A.; Case, D. A.

In: Biopolymers, Vol. 33, No. 10, 10.1993, p. 1567-1580.

Research output: Contribution to journalArticle

Soman, KV, Karimi, A & Case, DA 1993, 'Molecular dynamics analysis of a ribonuclease C-peptide analogue', Biopolymers, vol. 33, no. 10, pp. 1567-1580.
Soman KV, Karimi A, Case DA. Molecular dynamics analysis of a ribonuclease C-peptide analogue. Biopolymers. 1993 Oct;33(10):1567-1580.
Soman, K. V. ; Karimi, A. ; Case, D. A. / Molecular dynamics analysis of a ribonuclease C-peptide analogue. In: Biopolymers. 1993 ; Vol. 33, No. 10. pp. 1567-1580.
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