Baek Kim, Ph.D.

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1. Research Projects in Progress

(A)

Enzymology of HIV-1 reverse transcriptase: Molecular evolution and mutagenesis of lentiviruses

HIV-1 reverse transcriptase is the most error-prone DNA polymerases among known replication DNA polymerases. Our research primarily focuses on mechanistic and structural understanding of the error-prone active site of HIV-1 RT. Other RTs with high fidelity such as MuLV RT is also studied for identifying molecular elements that contribute to the fidelity difference between HIV-1 and MuLV RTs. For this study we employ both pre-steady and steady state kinetic analyses as well as other well established fidelity assays such as M13 lacZ? forward mutation assay and gel-based misincorporation assay. Next, we also focus on the contribution of the RT fidelity in HIV-1 genomic mutagenesis, evolution and escape using various virological methodologies. This study is currently being supported by NIH R01 AI049781.

(B)

Modification of viral DNA polymerases for designing new oncolytic viruses: Based on our HIV-1 RT studies, we recently established a new concept for constructing oncolytic viruses. The DNA polymerase mutants with reduced dNTP binding affinity are active only at the high dNTP concentrations. In addition, it has been well-established that all cancer cells with uncontrolled cell cycle have highly elevated dNTP concentrations than normal cells due to their fast cell division phenotype. We hypothesize that adenovirus containing mutant DNA polymerase with reduced dNTP binding affinity replicates specifically in the cells with elevated dNTP concentrations such as cancer cells. We employ thermo-stable Pfu DNA polymerase, which, together with adenovirus DNA polymerase, belongs to the same alpha-like DNA polymerase family to screen mutant with reduced dNTP binding affinity. This study is being supported by NCI CA122213 (Pancreatic cancer) and DOD BC060381 (breast cancer).

(C) HIV-1 and macrophage reservoirs: Research Activities on understanding roles of HIV-1 Tat protein in 1) DNA damage signal induction, 2) activation of dNTP biosynthesis, and 3) viral reverse transcription kinetics in human macrophages. These research projects focus on testing the Vpr functions as a HIV target. This research activity includes collaborations with Dr. Stephen Dewhurst and Dr. Vicente Planelles (University of Utah). The R01 support for this project was recently reviewed and approved for funding (AI077401).

(D) Recombination and HIV-1 evolution: Research activities on identifying molecular determinants of lentiviral recombination. These studies focus on roles of RT processivity, viral cis-acting sequences (secondary structures) and RT polymerase kinetics in viral recombination frequency. These research activities include collaborations with Dr. Robert A. Bambara (Baek Kim, Co-PI, NIH GM049573)

(E) Fidelity of avian influenza virus RNA polymerases: Research activities on examining enzymatic fidelity of avian and H5N1 influenza RNA polymerases, and its role in viral evolution and host adaptation. This project is a part of NIH contract awarded to NY Influenza Center of Excellence (Co-PI, NIH HHSN26620077778C).

Current Appointments

• Professor - Department of Microbiology and Immunology (SMD)
• Professor - Cancer Center (SMD)

Lab Website

http://baekkimlab.com/