Coarse-Grained Molecular Dynamics Simulation of IPMDH Proteins

protein to study the effect of mutation to the binding sites of protein. We replace original amino acids on the surface by negatively or positively charged amino acids. We also study the effect of solvent to the binding of proteins. Our computational study may be useful for future experimental study of protein bindings. Making nano-fibers with proteins (1-3) is an interesting and challenging field. We have tried to construct nano-fibers while retaining native structure. We started with proteins which form 4-helix bundle structure (4) by two proteins, each having two helices. In our previous studies (5-6) of molecular dynamics simulation of all-atom model, we have found that IPMDH (3-isopropylmalate dehydrogenase) (7-9) is a good candidate for a building unit of constructing nano-fibers because of the high stability of the mutated IPMDH. In this study, we have performed molecular dynamics simulation of coarse-grained model of IPMDH proteins. We have introduced several mutations on the surface of IPMDH and found that the mutated IPMDHs are likely to make larger clusters than the wild-type IPMDH. 2. Simulation Model and Method We used coarse grained model of IPMDH with MARTINI force field (10), where one interaction point represents on average four heavy atoms. There are four kinds of interaction points in MARTINI force field: polar, nonpolar, apolar and charged. Using coarse grained model, we can perform simulation of long-time behavior of large scale system. To check the model, we calculated radial distribution function for both all-atom model and coarse grained model, and obtained similar results.