HIV-1 envelope accessible surface and polarity: clade, blood, and brain 


Gopichandran Sowmya1, 2, Gunasagaran Shamini1, 2, Sathyanarayanan Anita1, Meena Sakharkar3, Venkat Mathura4, 5, Hector Rodriguez6, Andrew J Levine7, 8, Elyse Singer7, 8, Deborah Commins7, 9, Charurut Somboonwit10, 11, John T Sinnott10, 11, Harcharan S Sidhu2, Ganapathy Rajaseger12, Peter Natesan Pushparaj13, Pandajarasamme Kangueane1, 2, Paul Shapshak11, 14* 


1Biomedical Informatics, Pondicherry 607402, India; 2Aimst University, 08100 Semeling, Malaysia; 3Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan; 4Archer Pharmaceuticals, Sarasota, Florida, USA; 5Roskamp Institute, 2040 Whitfield Avenue, Sarasota, FL 34243, US; 6Department of Biology, University of Miami, Coral Gables, FL 33146; 7National Neurological AIDS Bank, UCLA School of Medicine, Westwood, CA 90095; 8Department of Neurology, UCLA School of Medicine, Westwood, CA 90095; 9Department of Neuropathology, USC Keck School of Medicine, Los Angeles, CA90089; 10Clinical Research Unit, Hillsborough Health Department, Tampa, Florida 33602; 11Division of Infectious Disease and International Medicine, Tampa General Hospital, USF Health, Tampa, FL 33601; 12Defense Science Organization National Laboratories, Singapore; 13Glasgow Biomedical Research Centre, Faculty of Medicine, Univ. of Glasgow, Glasgow, UK; 14Department of Psychiatry & Behavioral Medicine, University of South Florida, College of Medicine, Tampa, FL 33613 

Email; *Corresponding author

Article Type




Received March 9, 2011; Accepted March 11, 2011; Published March 22, 2011



The human immunodeficiency virus type-1 (HIV-1) gp160 (gp120-gp41 complex) trimer envelope (ENV) protein is a potential vaccine candidate for HIV/AIDS. HIV-1 vaccine development has been problematic and charge polarity as well as sequence variation across clades may relate to the difficulties. Further obstacles are caused by sequence variation between blood and brain-derived sequences, since the brain is a separate compartment for HIV-1 infection. We utilize a three-dimensional residue measure of solvent exposure, accessible surface area (ASA), which shows that major segments of gp120 and gp41 known structures are solvent exposed across clades. We demonstrate a large percent sequence polarity for solvent exposed residues in gp120 and gp41. The range of sequence polarity varies across clades, blood, and brain from different geographical locations. Regression analysis shows that blood and brain gp120 and gp41 percent sequence polarity range correlate with mean Shannon entropy. These results point to the use of protein modifications to enhance HIV-1 ENV vaccines across multiple clades, blood, and brain. It should be noted that we do not address the issue of protein glycosylation here; however, this is an important issue for vaccine design and development.  


HIV-1, clades, blood, brain, accessible surface area, compositional polarity, Shannon entropy, gp120, gp41, gp120-gp41 complex, gp160, ENV, trimer, vaccine.


Sowmya et al. Bioinformation 6(2): 48-56 (2011)

Edited by

F Chiappelli






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.