Studies Of The HIV Protease And Dna Polymerase

Environmental Health Sciences

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Abstract

Summary of Work: The objective of these studies is to apply state of the art molecular simulation methodology as an adjunct to experimental structure-function studies of the HIV-1 Reverse Transcriptase. In this year we carried out a number of studies aimed at characterizing the level of accuracy attainable with our simulation methodology. These studies revealed to us the critical importance of the DNA force field used. Although the DNA simulations carried out in recent years are of unprecedented accuracy, some shortcomings are still apparent. We also began work to improve the form of these force fields. The hope is that next generation force fields will be better able to reproduce the known sequence-dependent structural features which are thought to influence the processivity and fidelity of HIV-1 RT catalyzed DNA replication. We carried out simulations to characterize the effect of mutations of Asn to Asp at positions 255 and 265 within helix H of the polymerase on binding and processivity of RT on an RNA template, DNA primer hybrid substrate. Our simulations pointed out the importance of interactions with the 2'OH group on RNA.