In this study, we present a combined
analysis procedure between
atomistic molecular dynamics (MD) simulations and network topology
to obtain more understanding on the evolutionary consequences on protein
stability and substrate binding of the main protease enzyme of SARS-CoV2.
Communicability matrices of the protein residue networks (PRNs) were
extracted from MD trajectories of both Mpro enzymes in complex with
the nsp8/9 peptide substrate to compare the local communicability
within both proteases that would affect the enzyme function, along
with biophysical details on global protein conformation, flexibility,
and contribution of amino acid side chains to both intramolecular
and intermolecular interactions. The analysis displayed the significance
of the mutated residue 46 with the highest communicability gain to
the binding pocket closure. Interestingly, the mutated residue 134
with the highest communicability loss corresponded to a local structural
disruption of the adjacent peptide loop. The enhanced flexibility
of the disrupted loop connecting to the catalytic residue Cys145 introduced
an extra binding mode that brought the substrate in proximity and
could facilitate the reaction. This understanding might provide further
help in the drug development strategy against SARS-CoV2 and prove
the capability of the combined techniques of MD simulations and network
topology analysis as a “reverse” protein engineering
tool.
Mutations occurred within the binding pocket of enzymes directly modified the interaction network between an enzyme and its substrate. However, some mutations affecting the catalytic efficiency occurred far from the binding pocket and the explanation regarding mechanisms underlying the transmission of the mechanical signal from the mutated site to the binding pocket was lacking. In this study, network topology analysis was used to characterize and visualize the changes of interaction networks caused by site-directed mutations on a GH11 xylanase from our previous study. For each structure, coordinates from molecular dynamics (MD) trajectory were obtained to create networks of representative atoms from all protein and xylooligosaccharide substrate residues, in which edges were defined between pairs of residues within a cutoff distance. Then, communicability matrices were extracted from the network to provide information on the mechanical signal transmission from the number of possible paths between any residue pairs or local protein segments. The analysis of subgraph centrality and communicability clearly showed that site-direct mutagenesis at non-reducing or reducing ends caused binding pocket distortion close to the opposite ends and created denser interaction networks. However, site-direct mutagenesis at both ends cancelled the binding pocket distortion, while enhancing the thermostability. Therefore, the network topology analysis tool on the atomistic simulations of engineered proteins could play some roles in protein design for the minimization to the correction of binding pocket tilting, which could affect the functionality and efficacy of enzymes.
A series of atomistic molecular dynamics simulations were performed on the systems of gas molecules within an NVT ensemble, where the number of molecules, the volume and the temperature were controlled. For each simulation, simulated annealing technique was used to gradually vary the temperature and the change in gas pressure was measured within the simulation box at constant volume. Simulation results and regression analysis on the relationships between pressure and temperatures showed that two van der Waals parameters, representing interaction strength and effective size of the gas molecules, depended on shape, size and polarity of the molecules. This study provided an alternative way of demonstrating the basic thermodynamics of gas, and bridging the gap between information from microscopic and macroscopic scales.
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