Discrimination of HIV-1 and HIV-2 Reverse Transcriptase Proteins Using Chou’s PseAAC

Abstract

Reverse transcriptase (RT) is an important enzyme for retrovirus replication in susceptible target cells. RT of HIV-1 is one of the key targets for anti-HIV drugs. In contrast, HIV-2 RT reveals a basic resistance to non-nucleoside RT inhibitors (NNRTIs). In the present study, a comparison of different aspects of RT proteins in HIV-1 and HIV-2 such as pseudo amino acid composition (PseAAC), conventional amino acid composition (AAC), physicochemical properties, secondary structures and structural motifs has been performed. Statistical analysis and support vector machine (SVM) algorithm have been used for final comparison of two RT protein groups. The results demonstrate that AAC of four amino acids (Ala, Leu, Gln and Ser), molecular weight and percentage of alpha helix of RT proteins are significantly different between these two types. Classification based on the concept of PseAAC also showed 100% accuracy and highlighted that pseudo pI and pseudo pKa values are significant differences between two RT groups. In conclusion, the results indicate that the computational techniques can provide useful information for comparing HIV-1 and HIV-2 RTs. Our results may also explain the dissimilarity between the susceptibility of HIV-1 and HIV-2 to different drugs. © 2017, Shiraz University.