Investigating hydrogen production enzymes using gaming GPUs

Abstract

Hydrogen production is crucial to use hydrogen as an energy source. Hydrogenase, an enzyme found in green algae, plays a key role in this process. The function of an enzyme is determined by its structure, and the structure of hydrogenase suggests that certain residues in the proton transfer pathway (PTP) are critical for its function. Simulation results from the initial study support the hypothesis that mutations in these residues can alter enzymatic activity by changing the dynamics of amino acids in the proton transfer pathway. The goal of the current study was to understand which structural and geometric features of the PTP in hydrogenase affect its efficiency in hydrogen production, and to predict mutations that could improve this efficiency. To investigate the relationship between protein structure/dynamics and function in this enzyme, molecular dynamics simulations and various analysis techniques, including GPU cards and cloud computing, have been used to study eight variations of hydrogenase. Based on the data, mutations in the PTP of the protein can affect its dynamics and might be linked to changes in its efficiency. The C299A has similar structure and behavior to the normal protein, but the loss of a key sulfur atom in its structure significantly reduces its effectiveness. The charged D variant of C299 had higher activity than the neutral S variant while both had different behavior than the Wildtype. It paves way for future expansion to other variants, lengthening of simulation time, establishment of complete structure and functional relationships, and prediction of activity enhanceable amino acid in silico mutagenesis.