Characterization of a folding intermediate from HIV‐1 ribonuclease H

• Published in: Protein science Vol. 7; no. 10; pp. 2164 - 2174
• Main Authors: Kern, Gunther, Handel, Tracy, Marqusee, Susan
• Format: Journal Article
• Language: English
• Published: Bristol Cold Spring Harbor Laboratory Press 01.10.1998
• Subjects: AIDS/HIV; Circular Dichroism; Deuterium - metabolism; Drug Design; Enzyme Inhibitors - chemistry; Enzyme Stability - drug effects; Guanidine - pharmacology; HIV-1 - enzymology; HIV‐1; Hydrogen - metabolism; hydrogen exchange; inhibitor; kinetic intermediate; Kinetics; Models, Molecular; Mutation - genetics; NMR; Protein Denaturation; Protein Folding; Protein Structure, Secondary; ribonuclease H; Ribonuclease H - chemistry; stopped flow; Viral Proteins - chemistry
• ISSN: 0961-8368; 1469-896X
• DOI: 10.1002/pro.5560071014

The RNase H domain from HIV‐1 (HIV RNase H) encodes an essential retroviral activity. Refolding of the isolated HIV RNase H domain shows a kinetic intermediate detectable by stopped‐flow far UV circular dichroism and pulse‐labeling H/D exchange. In this intermediate, strands 1, 4, and 5 as well as helices A and D appear to be structured. Compared to its homolog from Escherichia coli, the rate limiting step in refolding of HIV RNase H appears closer to the native state. We have modeled this kinetic intermediate using a C‐terminal deletion fragment lacking helix E. Like the kinetic intermediate, this variant folds rapidly and shows a decrease in stability. We propose that inhibition of the docking of helix E to this folding intermediate may present a novel strategy for anti HIV‐1 therapy.