Exploring the concerted mechanistic pathway for HIV-1 PR-substrate revealed by umbrella sampling simulation

HIV-1 protease (HIV-1 PR) is an essential enzyme for the replication process of its virus, and therefore considered an important target for the development of drugs against the acquired immunodeficiency syndrome (AIDS). Our previous study shows that the catalytic mechanism of subtype B/C-SA HIV-1 PR follows a one-step concerted acyclic hydrolysis reaction process using a two-layered ONIOM B3LYP/6-31++G(d,p) method. This present work is aimed at exploring the proposed mechanism of the proteolysis catalyzed by HIV-1 PR and to ensure our proposed mechanism is not an artefact of a single theoretical technique. Hence, we present umbrella sampling method that is suitable for calculating potential mean force (PMF) for non-covalent ligand/substrate-enzyme association/dissociation interactions which provide thermodynamic details for molecular recognition. The free activation energy results were computed in terms of PMF analysis within the hybrid QM(DFTB)/MM approach. The theoretical findings suggest that the proposed mechanism corresponds in principle with experimental data. Given our observations, we suggest that the QM/MM MD method can be used as a reliable computational technique to rationalize lead compounds against specific targets such as the HIV-1 protease.

Using steered molecular dynamics to study the interaction between ADP and the nucleotide-binding domain of yeast Hsp70 protein Ssa1

Genetics experiments have identified six mutations located in the subdomain IA (A17V, R23H, G32D, G32S, R34K, V372I) of Ssa1 that influence propagation of the yeast [PSI⁺] prion. However, the underlining molecular mechanisms of these mutations are still unclear. The six mutation sites are present in the IA subdomain of the nucleotide-binding domain (NBD). The ATPase subdomain IA is a critical mediator of inter-domain allostery in Hsp70 molecular chaperones, so the mutation and changes in this subdomain may influence the function of the substrate-binding domain. In addition, ADP release is a rate-limiting step of the ATPase cycle and dysregulation of the ATPase cycle influences the propagation of the yeast [PSI⁺] prion. In this work, steered molecular dynamics (SMD) simulations were performed to explore the interaction between ADP and NBD. Results suggest that during the SMD simulations, hydrophobic interactions are predominant and variations in the binding state of ADP within the mutants is a potential reason for in vivo effects on yeast [PSI⁺] prion propagation. Additionally, we identify the primary residues in the ATPase domain that directly constitute the main hydrophobic interaction network and directly influence the ADP interaction state with the NBD of Ssa1. Furthermore, this in silico analysis reaffirms the importance of previously experimentally-determined residues in the Hsp70 ATPase domain involved in ADP binding and also identifies new residues potentially involved in this process.

Immobilization and unbinding investigation of the antigen-antibody complex using theoretical and experimental techniques

Experimental results for the antibody known as immunoglobulin G - IgG interacting with phenobarbital were obtained via atomic force microscopy (AFM) and thereafter investigated using computer simulation modeling tools. Using molecular dynamics simulation and docking calculations, the energetically stable configurations of an immobilized antibody over a silicon surface were searched. Six stable configurations of the immobilized antibody over the silicon nitride surface covered by linker molecules were found. Although, only three of them (P1, P2, P5) maintained the Fragment antigen binding available for antigen interaction. Therefore, these configurations were equilibrated after reaching 100 ns molecular dynamics trajectory. The average interaction energy between the surface and the immunoglobulin G - IgG antibody in the P1, P2 and P5 configurations were -62.4 ± 2.4 kcal/mol; -54.3 ± 5.7 kcal/mol, and -360.9 ± 4.2 kcal/mol respectively. Phenobarbital was docked within the Fab domain of P1, P2, and P5 immobilized configurations and equilibrated with molecular dynamics for binding energy estimation. Then, steered molecular dynamics was performed to evaluate unbinding energy pathway between phenobarbital and IgG in each of the three-oriented IgG configurations. No significant differences were observed in the rupture force values (EP1 = 591 ± 13 pN, EP2 = 605 ± 18 pN, and EP5 = 610 ± 45 pN). In comparison, the average AFM experimental results were (641.6 ± 363.3 pN). Therefore, it is worth noting that P5 is the configuration with highest protein-surface interaction. Therefore, the force value calculated for the P5 orientation is statistically more favorable and it is the one to be compared to the experimental data. The agreement between experimental and theoretical results indicates a favorable presented for this study opening new perspectives for antigen-antibody evaluation.