Constructing protein nano-fiber and estimation of the electronic state around metal ions

We aim to construct a nano‐fiber using proteins by mixing two kinds of proteins. The binding sites are expected to be formed between two α‐helices of one protein and two α‐helices of another protein. As model proteins, we use Lac repressor four helix protein (LARFH), sulerythrin, and 3‐isopropylmalate dehydrogenase. With these proteins, we performed molecular dynamics (MD) simulations with a coarse‐grained (CG) model. In MD simulations with the CG model for LARFH, we found that the molecules approached faster in the system where the mutant protein with positively charged amino acids was placed with the mutant protein with negatively charged amino acids than in the system containing two wild‐type protein molecules. In the system with the variants, the number of contact interfaces with the positive variant‐negative variant combination after 150 ns simulation is larger than that with the positive–positive variants combination or the negative–negative variants combination. Sulerythrin has two pairs of Fe2+ and Zn2+. Electronic structure calculation was performed around metal ions in sulerythrin. By electronic structure calculation for sulerythrin around metal ions, the electric charge and spin density were estimated. © 2012 Wiley Periodicals, Inc. Nano‐fiber can be self‐assembled by mixing two kinds of proteins. Binding between the two α‐helices of one protein and two α‐helices of second protein yields a four‐helix bundle, which is thermally stable. Coarse grained molecular dynamics simulations and electronic structure calculations are used to provide insight on this system, in particular, around their metal ions.