A combined 2d-nmr and molecular dynamics analysis of the structure of the actinomycin d: D(atgcat)2 complex

Steve Creighton, Barbara Rudolph, Terry Lybrand, U. C. Singh, Richard Shafer, Stephen Brown, Peter Kollman, David A. Case, Tariq Andrea

Research output: Contribution to journalArticle

23 Scopus citations

Abstract

We present a comparative analysis of an NMR experiment and molecular and harmonic dynamics simulations of an actinomycin D: D(ATGCA1)2 complex. A comparison of NOE measurements and l/R6 weighted proton-proton distances confirm the general correctness of the Actinomycin D·DNA model proposed by Sobell. There are, however, some substantial differences between the proton-proton distances inferred from the NOE results and the molecular and harmonic dynamics simulations. The remaining discrepancies could either come from contributions of other conformations to the average properties of the complex or from uncertainties in the NMR distance analysis. An analysis of the molecular dynamics helix properties, sugar puckers, hydrogen bonding, rms fluctuations and torsional properties are qualitatively consistent with those from previous simulations, but the presence of an intercalated drug leads to some new structural and dynamical features.

Original languageEnglish (US)
Pages (from-to)929-969
Number of pages41
JournalJournal of Biomolecular Structure and Dynamics
Volume6
Issue number5
DOIs
StatePublished - Jan 1 1989
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

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