Characterization of the 'helix clamp' motif of HIV-1 reverse transcriptase using MALDI-TOF MS and surface plasmon resonance

Shanhua Lin, Sheree Long, Suzanne M. Ramirez, Robert J. Cotter, Amina S. Woods

Research output: Contribution to journalArticle

Abstract

A helix-turn-helix motif in the crystal structure of human immunodeficiency virus type I reverse transcriptase (HIV-1 RT) was proposed to be a conserved nucleic acid binding domain among several nucleotide polymerizing enzymes (Hermann, T.; Meier, T.; Gotte, M.; Heumann, H. Nucleic Acids Res. 1994, 22, 4625 4633). The sequence of this domain is homologous to 259KLVGKL(X)16KLLR284 of HIV-1 RT, which acts as a 'helix clamp' grasping the template primer (T-P) complex. We characterized the helix clamp motif using MALDI-TOF MS and surface plasmon resonance (BIAcore). Our studies showed that the 'helix clamp' has a nucleic acid binding function that may not be sequence specific. This evidence suggests that ionic interactions between the helix clamp and oligonucleotide backbone are not solely responsible for binding. Secondary and tertiary structures of the protein may also play a significant role in nucleic acid binding. The association and dissociation constants, k(a) and k(d), for the binding of single-stranded oligonucleotide to the helix clamp were determined to be 7.03 x 103 M-1 s-1 and 1.22 x 103 s-1, respectively.

Original languageEnglish (US)
Pages (from-to)2635-2640
Number of pages6
JournalAnalytical chemistry
Volume72
Issue number11
DOIs
StatePublished - Jun 1 2000

ASJC Scopus subject areas

  • Analytical Chemistry

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