Three dimensional molecular modeling studies in AIDS research using high performance computing facilities: a ternary complex of HIV-1 RT

Prem N.S. Yadav, Swamy Laxminarayan, Janardan S. Yadav, Virendra N. Pandey, Sunita Singh, Mukund J. Modak

Research output: Contribution to journalConference articlepeer-review

Abstract

We present here a complete three-dimensional molecular model structure of the ternary complex (Enzyme-DNA-dNTP) of human immunodeficiency virus-type 1 reverse transcriptase (HIV-1 RT) using high performance computer simulation and molecular modeling techniques. The Ca coordinates of the crystal structure of HIV-1 RT-DNA binary complex as well as biochemical properties of a number of mutant enzymes were used as the basis to model build a prepolymerase ternary complex in which Mg2 + ions are also accommodated. The side chains of amino acid residues interacting with the template and primer strands and those stabilizing the dNTP and Mg2+ ions in the active site pocket are clearly elucidated in the model. The structural information provided by this model should be useful in understanding the polymerase reaction mechanisms and should permit structure based drug design against HIV-1 RT.

Original languageAmerican English
Pages (from-to)1897-1898
Number of pages2
JournalAnnual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings
Volume5
StatePublished - 1996
EventProceedings of the 1996 18th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. Part 4 (of 5) - Amsterdam, Neth
Duration: Oct 31 1996Nov 3 1996

ASJC Scopus subject areas

  • Signal Processing
  • Biomedical Engineering
  • Computer Vision and Pattern Recognition
  • Health Informatics

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