MATLAB process for validating amino acids on CD4 involving in DARPin binding site from ZDOCK molecular docking database

Abstract

Human immunodeficiency virus (HIV) inherits the active mutation, which promotes the viral survival in human and is the main hurdle of vaccine development. The mutations on HIV surface i.e. CD4 binding site on HIV gp120, causes the escaping from the immune-surveillance but still retains the infectivity for CD4+ T cells. Formerly, Designed Ankyrin Repeat Protein (DARPin) technology has been innovated to inhibit the HIV infection. The CD4-specific DARPin specifically excludes the adhesion step of HIV to CD4 molecule and efficiently prevents HIV infection in vitro by competing with gp120, however, not in vivo. Therefore, insight into the interaction between DARPin and CD4 molecules will provide the information to improve the interaction affinity of DARPin for in vivo purpose. The binding activity can be modified by directly defining the key amino acid residues of CD4-specific DARPin and replacing them with other possible residues. To discover the remarkable CD4's residues, a molecular docking software i.e. ZDOCK was used to predict the complex structures between CD4 and DARPin. In this study, the candidate residues of CD4-specific DARPin were identified by the residues of CD4 molecule involving in gp120 interaction. The defined DARPin poses that interrelated with them were then extracted. The MATLAB software was implemented to generate the assigned screening criteria for recruiting the most relevant binding residues in eleven complex-structure-candidates derived from ZDOCK. The invented data processing methodology will assist the molecular simulation researchers to rapidly and precisely define important residues.