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Molecular dynamics studies of U1A-RNA complexes

Published online by Cambridge University Press:  01 February 1999

CAROLINA M. REYES  and
PETER A. KOLLMAN
CAROLINA M. REYES
Affiliation:
Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, California 94143-0446, USA
PETER A. KOLLMAN
Affiliation:
Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, California 94143-0446, USA
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Abstract

The U1A protein binds to a hairpin RNA and an internal-loop RNA with picomolar affinities. To probe the molecular basis of U1A binding, we performed state-of-the-art nanosecond molecular dynamics simulations on both complexes. The good agreement with experimental structures supports the protocols used in the simulations. We compare the dynamics, hydrogen-bonding occupancies, and interfacial flexibility of both complexes and also describe a rigid-body motion in the U1A–internal loop complex that is not observed in the U1A–hairpin simulation. We relate these observations to experimental mutational studies and highlight their significance in U1A binding affinity and specificity.

Keywords

molecular dynamics simulationsnucleic acidsPIE-RNARNA–protein interactions
Type
Research Article
Information
RNA , Volume 5 , Issue 2 , February 1999 , pp. 235 - 244
Copyright
1999 RNA Society

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