Introduction
Human immunodeficiency virus, commonly known as HIV, is a retrovirus that causes AIDS. An enzyme called reverse transcriptase, found in this virus turns its RNA into DNA, and then the DNA is integrated into the host cell’s genome where viral RNA is transcribed and then translated into a long polyprotein.
A protease is an enzyme which cleaves proteins to their component peptides. The HIV-1 protease hydrolyzes viral polyproteins into functional protein products necessary for viral assembly as well as subsequent activity. The HIV-1 protease is a homodimer containing 99 amino acids in each identical chain. An axis of symmetry is formed by each monomer in the active protease. Monomers are stabilized by aliphatic residues in hydrophobic core and dimer by noncovalent interactions, hydrophobic packing of side chains and interactions involving catalytic residues. There are two cysteine residues in each monomer but they do not make disulfide bonds (1). The active site is located between identical subunits with characteristic Asp25-Thr26-Gly27 sequence common among aspartic proteases. These two Asp 25 residues from both monomer act as catalytic residues. (2)
Aim and Objectives
The ligand for IZI will be identified from the X-ray structure and comparative analysis in binding mode of 1IZI and Indinavir to the HIV-1 protease will be made in this project. The amino acid residues in the active site and those involved in binding the inhibitor will be identified and their interaction behavior will be studied. The functional groups that correspond to the P1, P1', P2, P2', P1-P3 groups will help to know if the groups in 1IZI also bind in the same way. The alternative binding sites if present will be discussed in brief.
Methods
Protein Databank Europe (PDBe) (3), a project for collecting, managing and distributing macromolecular structure data derived from Protein Data Bank was used to get the experimental details of the protein structures using PDB Id. The pdb entry files (1IZI and 2BPX) were read in BODIL(4) and 1IZI was superimposed on top of 2BPX using VERTAA(5) within BODIL. The ligand of our structure (structure assigned for the project) was selected from Structure Editor tree and active site was viewed displaying only the area of 7.0 Å radius within the ligand molecule.
Result:
The inhibitor-HIV-protease complex structure (Figure 1) was a mutant type with mutations in three amino acid residues (A71V, V82T, I84V) which was found in the pdb entry file. The chemical formula for the inhibitor is actually C38H47N5O7.However, in the structure I got from PDBe (Appendix 2) it is C38N5O7 i.e with no hydrogen atoms. There are altogether 17 amino acid residues and a water molecule that are involved in binding of the inhibitor. Among them, 4 amino acids, ASP25B, ASP25A, ASP30B, GLY48B and a water molecule HOH1002A form hydrogen bonding. GLY27B and GLY27A form electrostatic interaction. Remaining 11 residues make van-der-waals interactions; those residues are LEU23B, LEU23A, ALA28B, ASP29B, ILE47B, GLY48A, GLY49B, GLY49A, PRO81B and THR 82A. Each of the atoms of the inhibitor that are involved in binding or can make interaction with the amino acids nearby are presented in the table (appendix 1). This result was derived from PDBe where the possible bond lengths below 4Å and interaction type was obtained.
The structure of our structure was superimposed on top of 2BPX structure (WT indinavir) and the ligands along with their neighbouring amino acids that were 7Å in radius were selected to study the interaction mechanisms.
Discussion
The PDB entry file has mentioned that there are only 3 mutations(A71V, V82T, I84V) in our structure(1IZI) however, one more mutation (SER37ASN) was observed while doing pairwise alignment. They might be missing in the PDB file because they are located in the peripheral loop of the structure. The water molecule that is conserved in the binding site (WAT2002) that is also responsible in binding the inhibitor to amino acid residue and is thus not replaced while binding to the inhibitor (appendix 2). The functional group for P2(alkyl) and P1’(phenyl) are same in both the inhibitors. P1-P3 group in indinavir doesnot have correspondence with any groups as it is extended a bit and on the other hand, 1Q50 is extended a bit in the opposite side. However, they have maintained similar conformation in between.
References
1. Miyeko M, David M (2001) HIV-1 Protease CLU Biology Department. (http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/hiv_protease/molmast.htm)
3.Velankar S, Best C, Beuth B, Boutselakis CH, Cobely N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirishberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Saurez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ (2010) PDBe: Protein Data Bank in Europe. Nucleic Acids Research, 38, 308-317
4. Lehtonen JV, Still DJ, Rantanen VV, Ekholm J, Björklund D, Iftikhar Z, Huhtala M, Repo S, Jussila A, Jaakkola J, Pentikäinen O, Nyrönen T, Salminen T, Gyllenberg M and Johnson M (2004) BODIL: a molecular modeling environment for structure-function analysis and drug design. J Comput Aided Mol Des 18(6),401-419
5.Johnson MS, Overington JP (1993) A structural basis for the comparison of sequences: An evaluation of scoring methodologies. J. Mol. Biol. 233: 716-738
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