Beyond Bioinformatics

Title

Paradigm development: Comparative and predictive 3D modeling of HIV-1 Virion Infectivity Factor (vif)

Authors

Seetharaaman Balaji ^{1, 2*}, Rangaswamy Kalpana ³ and Paul Shapshak ⁴

Affiliation

¹  Previous: Lecturer, Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamilnadu, India; ² Present: Research Associate, Bioinformatics, Indian Institute of Spices Research, Calicut, Kerala, India; ³ Lecturer, Bioinformatics, CMS college of Arts & Science, Bharathiar University, Coimbatore, Tamilnadu, India; ⁴ Research Professor, Department of Psychiatry and Behavioral Sciences, University of Miami Miller Medical School, Miami, Florida 33136

Email

blast_balaji@rediffmail.com; * Corresponding author

Article Type

Hypothesis

Date

received October 04, 2006; revised December 04, 2006; accepted December 05, 2006; published online December 06, 2006

Abstract

Obtaining structural information about Vif is of interest for several reasons that include the study of the interaction of Vif with APOBEC3G, a resistance factor. Vif is a potential drug target and its function is essential for the HIV-1 infectivity process. To study Vif mechanism of action, we need to decipher its structure. Pivotal in this approach is the painstaking prediction of its protein structure. The three-dimensional (3D) crystal structure for Vif has not been established. In order to understand its mechanism of action, information on the structure of Vif is very much needed. Therefore we undertook this study based on the hypothesis that information from structurally homologous proteins can be used to predict the 3D structure of Vif by computer modeling and threading. As a result the structure of HIV-1 Vif has been modeled and deposited in the theoretical models section and accepted with the PDB code 1VZF. Here, we present the results of the comparative modeling strategy we used to predict the 3D structure of Vif.

Keywords

Vif; HIV-1; 3D structure; computer modeling; threading

Citation

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics Publishing Group

Copyright

Publisher

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.