Dinucleotides docking to scorpion polypeptide toxins: a molecular modeling method for protein functional site recognition

Molecular mechanism of the protective effect of monomer polyvinylpyrrolidone on antioxidants - experimental and computational studies

We previously developed a lutein-polyvinylpyrrolidone (PVP) complex with improved aqueous saturation solubility and stability, though the conjugation mechanism is still unclear. In this paper, experiments with astaxanthin-PVP complex and curcumin-PVP complex were carried out, which indicated that PVP could improve the solubility and stability of astaxanthin and curcumin. We aimed to construct a computational model capable of understanding the protective effect in complexes formed between PVP and antioxidants, through which the binding mode of PVP and antioxidants was investigated with molecular modelling in order to obtain the interactions, binding energy, binding site and surface area between PVP and antioxidants. Solubility enhancement was attributed to the H-bonds between PVP and antioxidants, and the saturation solubility was curcumin > lutein > astaxanthin. Binding energy, binding site and surface area were beneficial for the stability of complex, and the stability enhancement was lutein > astaxanthin > curcumin. The experimental results were in agreement with the computational results. Furthermore, we established a method for the exploration of a similar system with other polymer complexes. Additionally, the proposed PVP model could predict the interactions between PVP and various ligands, such as antioxidants and drugs.

Identification of human immunodeficiency virus type 1 (HIV-1) gp120-binding sites on scavenger receptor cysteine rich 1 (SRCR1) domain of gp340

BACKGROUND

gp340, a member of scavenger receptor cysteine rich family encoded by Deleted in Malignant Brain Tumors 1 (DMBT1), is an important component in innate immune defense. The first scavenger receptor cysteine rich domain (SRCR1) of gp340 has been shown to inhibit HIV-1 infection through binding to the N-terminal flank of the V3 loop of HIV-1 gp120.

RESULTS

Through homology modeling and docking analysis of SRCR1 to a gp120-CD4-X5 antibody complex, we identified three loop regions containing polar or acidic residues that directly interacted with gp120. To confirm the docking prediction, a series of over-lapping peptides covering the SRCR1 sequence were synthesized and analyzed by gp120-peptide binding assay. Five peptides coincide with three loop regions showed the relative high binding index. An alanine substitution scan revealed that Asp34, Asp35, Asn96 and Glu101 in two peptides with the highest binding index are the critical residues in SRCR1 interaction with gp120.

CONCLUSION

We pinpointed the vital gp120-binding regions in SRCR1 and narrowed down the amino acids which play critical roles in contacting with gp120.