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J. Biol. Chem., Vol. 281, Issue 7, 4173-4182, February 17, 2006

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Identification of Amino Acids in HIV-1 and Avian Sarcoma Virus Integrase Subsites Required for Specific Recognition of the Long Terminal Repeat Ends^*

Aiping Chen, Irene T. Weber, Robert W. Harrison^¶, and Jonathan Leis¹

From the Department of Microbiology and Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611 and the Departments of Biology and ^¶Computer Science, Georgia State University, Atlanta, Georgia 30303

A tetramer model for HIV-1 integrase (IN) with DNA representing 20 bp of the U3 and U5 long terminal repeats (LTR) termini was assembled using structural and biochemical data and molecular dynamics simulations. It predicted amino acid residues on the enzyme surface that can interact with the LTR termini. A separate structural alignment of HIV-1, simian sarcoma virus (SIV), and avian sarcoma virus (ASV) INs predicted which of these residues were unique. To determine whether these residues were responsible for specific recognition of the LTR termini, the amino acids from ASV IN were substituted into the structurally equivalent positions of HIV-1 IN, and the ability of the chimeras to 3 ' process U5 HIV-1 or ASV duplex oligos was determined. This analysis demonstrated that there are multiple amino acid contacts with the LTRs and that substitution of ASV IN amino acids at many of the analogous positions in HIV-1 IN conferred partial ability to cleave ASV substrates with a concomitant loss in the ability to cleave the homologous HIV-1 substrate. HIV-1 IN residues that changed specificity include Val⁷², Ser¹⁵³, Lys¹⁶⁰–Ile¹⁶¹, Gly¹⁶³–Val¹⁶⁵, and His¹⁷¹–Leu¹⁷². Because a chimera that combines several of these substitutions showed a specificity of cleavage of the U5 ASV substrate closer to wild type ASV IN compared with chimeras with individual amino acid substitutions, it appears that the sum of the IN interactions with the LTRs determines the specificity. Finally, residues Ser¹⁵³ and Val⁷² in HIV-1 IN are among those that change in enzymes that develop resistance to naphthyridine carboxamide- and diketo acid-related inhibitors in cells. Thus, amino acid residues involved in recognition of the LTRs are among these positions that change in development of drug resistance.

Received for publication, September 28, 2005 , and in revised form, November 16, 2005.

^* This work was supported in part by United States Public Health Service Grants CA52047 (to J. L.), GM62920, and GM065762, the Georgia Cancer Coalition, and the Georgia Research Alliance (to I. T. W. and R. W. H.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental material.

¹ To whom correspondence should be addressed: Dept. of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611. Tel.: 312-503-1166; Fax: 312-503-2790; E-mail: j-leis{at}northwestern.edu.

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