Recombinant HIV type 1 (CM235/CRF01_AE) Glycoprotein 120 (a.a. 30-498) [His]

Acquired immune deficiency syndrome (AIDS) is one of the most lethal infectious diseases influencing human community. While fusion of HIV-1 and host cell membranes, viral envelope glycoprotein gp120 is dissociated and a cascade of refolding events is initiated in the viral fusion protein gp41. To promote formation of the co-receptor binding site on the gp120 and initial attachment, HIV-1 employs CD4 as its primary receptor. Ibalizumab, a humanized, anti-CD4 monoclonal antibody for HIV-1 infection, was investigated in silico to design a potential improved antibody. Computer-aided antibody engineering has been successful in the design of new biologics for disease diagnosis and therapeutic interventions. Here, crystal structure of CD4 along with monoclonal antibody Ibalizumab was explored. Thr30, Ser31, Asn52, Tyr53, Asn98 and Tyr99 in heavy chain of Ibalizumab were mutated with 19 standard amino acid residues using computational methods. A set of 720 mutant macromolecules were designed, and binding affinity of these macromolecules to CD4 was evaluated through Ag-Ab docking, binding free-energy calculations, and hydrogen binding estimation. In comparison to Ibalizumab, seven designed theoretical antibody demonstrated better result in all assessments. Therefore, these newly designed macromolecules were proposed as potential antibodies to serve as therapeutic options for HIV infection.

Proprotein convertase subtilisin/kexin 9 (PCSK9) is a key regulator of lipid metabolism by degrading liver LDL receptors. Structural studies have provided molecular details of PCSK9 function. However, the N-terminal acidic stretch of the PCSK9 prodomain (Q31-T60) has eluded structural investigation, since it is in a disordered state. The interest in this region is intensified by the presence of human missense mutations associated with low and high LDL-c levels (E32K, D35Y, and R46L, respectively), as well as two posttranslationally modified sites, sulfated Y38 and phosphorylated S47. Herein we show that a segment within this region undergoes disorder-to-order transition. Experiments with acidic stretch-derived peptides demonstrated that the folding is centered at the segment Y38-L45, which adopts an alpha-helix as determined by NMR analysis of free peptides and by X-ray crystallography of peptides in complex with antibody 6E2 (Ab6E2). In the Fab6E2-peptide complexes, the structured region features a central 2 1/4-turn alpha-helix and encompasses up to 2/3 of the length of the acidic stretch, including the missense mutations and posttranslationally modified sites. Experiments with helix-breaking proline substitutions in peptides and in PCSK9 protein indicated that Ab6E2 specifically recognizes the helical conformation of the acidic stretch. Therefore, the observed quantitative binding of Ab6E2 to native PCSK9 from various cell lines suggests that the disorder-to-order transition is a true feature of PCSK9 and not limited to peptides. Because the helix provides a constrained spatial orientation of the missense mutations and the posttranslationally modified residues, it is probable that their biological functions take place in the context of an ordered conformational state. (C) 2018 Elsevier Ltd. All rights reserved.