Conversation 11: No. 1

category image Volume: Conversation 11
Issue Number 1
May 2000
ISBN 0-940030-80-2

Relating the Structure of HIV-1 Reverse Transcriptaseto Its Processing Step

By treating an enzyme as a coarse-grained uniform block of material, utilizing only the a-Carbon positions, the normal modes of motion can be obtained. For reverse transcriptase the slower of these motions are suggestive of being involved in the processing step, where the RNA or DNA strand is copied onto a new DNA strand at a polymerase site, and the RNA strand is subsequently cut up at the distant Ribonuclease H site. The slowest mode of motion involves hinge bending about a site midway between the polymerase and Ribonuclease H sites, suggesting that it can push or pull the RNA strand between these two sites. Pulling the nucleic acid strand would require tight binding to the RNase H site. The next slowest mode involves a hinge that opens and closes the protein like a clamp, which could facilitate the release of the nucleic acids for their step-wise progression. The third mode could rotate the substrate. An overall description of the step-wise processing step would involve close coordination among these steps. Results suggest that the smaller p51 subunit serves only as ballast to support the various modes of motion involving the different parts of the p66 subunit.

R. L. Jernigan1
Ivet Bahar1,2
David G. Covell3
Ali Rana Atilgan2
Burak Erman4
and Daniel T. Flatow1

1Molecular Structure Section
Laboratory of Experimental and Computational Biology
Division of Basic Sciences
National Cancer Institute
National Institutes of Health
MSC 5677
Bethesda, MD 20892-5677
2 Polymer Research Center and School of Engineering
Bogazici University and TUBITAK Advanced Polymeric Materials Research Center
Bebek 80815, Istanbul, Turkey
3Frederick Cancer Research and Development Center
National Cancer Institute
Science Applications International Corporation
Frederick MD 21702, USA
4Sabanci University
Sabanci Center
Istanbul 80745, Turkey


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