Molecular Dynamics of Proteins: Applications in Complement and CRISPR-Cas9

Molecular dynamics (MD) is a simulation technique that has been utilized to analyze biomolecular systems. Classical MD simulations and constant pH MD simulations have been applied to observe the behavior of components involved in two biomolecular systems of interest, the complement system and CRISPR-Cas9. The complement system is a defense mechanism part of the innate immune system. Complement associated diseases, such as paroxysmal nocturnal hemoglobinuria and atypical hemolytic uremic syndrome, are treated with complement inhibitors. Monoclonal antibody, eculizumab, is used as treatment for these diseases and functions as an inhibitor of complement component 5 (C5). A next generation version of eculizumab has also been developed known as ravulizumab, resulting from mutations within the heavy chain of eculizumab. MD simulations elucidated key residues involved in intermolecular interactions between complement inhibitors, eculizumab and ravulizumab, and C5. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 is part of the bacterial adaptive immune system that functions as a genome editing tool. The HNH domain of CRISPR-Cas9 is involved in DNA cleavage. Through classical MD simulations, residues near the catalytic center of the HNH domain were observed. Mutations were applied to several residues within the HNH domain. The wild type structure was compared to different mutated structures to analyze the effect of the mutations. Distances between residues and RMSD were calculated. Constant pH MD simulations determined pKa values for histidine for the wild type and mutated structures. Taken together, our simulations clarified mechanisms and function of the complement and CRISPR-Cas systems, helping fundamental understanding and engineering