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Journal of Biomolecular Structure and Dynamics Volume 6, 1989 - Issue 5
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Original Articles

A Combined 2D-NMR and Molecular Dynamics Analysis of the Structure of the Actinomycin D: d(ATGCAT)2 Complex

Steve Creighton Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143
,
Barbara Rudolph Department of Chemistry, University of California, Davis, 95616
,
Terry Lybrand Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143
,
U. C. Singh Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143
,
Richard Shafer Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143
,
Stephen Brown Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143
,
Peter Kollman Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143
,
David A. Case Department of Chemistry, University of California, Davis, 95616
&
Tariq Andrea Shell Research Laboratories, Modesto, CA
 show all
Pages 929-969 | Received 21 May 1987, Published online: 15 May 2012
 
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Abstract

We present a comparative analysis of an NMR experiment and molecular and harmonic dynamics simulations of an actinomycin D: d(ATGCAT)2 complex. A comparison of NOE measurements and 1/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.

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