Hironao Yamada

Designing the Binding Surface of Proteins to Construct Nano-fibers

In the field of nanotechnology, a variety of applications have been anticipated. We have been trying to design nano-fibers using proteins while maintaining their native structures. We try to use Lac repressor two-helix protein (LARFH), sulerythrin, and 3-isopropylmalate dehydrogenase (IPMDH) as adaptors for constructing nano-fibers. By making use of the α-helices outside of respective proteins, we are trying to form binding site between proteins: two α-helices of one protein are designed to form four-helix bundle with two α-helices of another protein. In addition, by introducing mutations in amino acids at the binding sites, hydrophobic and electrostatic interactions can be modified. The fiber may be produced upon mixing the two kinds of proteins. By umbrella sampling simulation, we have found that in the combination of LARFH-/-LARFH, hydrophobic interaction is enhanced in wild type, and electrostatic interaction is enhanced in variant. We also found high stability of IPMDH-/-IPMDH.

Structure and hydrogen bonds of cyclohexapeptide RA-VII by molecular dynamics simulations and quantum chemical calculations

Abstract We computationally examined the structure of anti-tumour bicyclic hexapeptide RA-VII. This peptide adopts three conformations (confs.), A, B and C, in dimethyl sulfoxide (DMSO). Although it was experimentally reported that the structure of conf. A is important for anti-tumour activity, the dynamics of confs. A, B and C are not well known. We performed quantum chemical calculations and molecular dynamics (MD) simulations of RA-VII in DMSO. The MD simulations indicated two different local stable structures for conf. C: a structure containing a bent 18-membered ring and another structure containing a rotated peptide bond between Tyr6 and d-Ala1. The root-mean-square fluctuation of the 14-membered ring for conf. A was larger than that for confs. B and C. Ala4 formed intramolecular hydrogen bonds more often in conf. A than in the other conformations. A large number of hydrogen bonds and large structural fluctuations are important for the anti-tumour activity of RA-VII. Our results for the structural change of conf. C and the analysis of the dynamics for confs. A, B and C may contribute to the design of new analogues of cyclic peptides.

Structural Study of Cell Attachment Peptide Derived from Laminin by Molecular Dynamics Simulation

Peptides with cell attachment activity are beneficial component of biomaterials for tissue engineering. Conformational structure is one of the important factors for the biological activities. The EF1 peptide (DYATLQLQEGRLHFMFDLG) derived from laminin promotes cell spreading and cell attachment activity mediated by α2β1 integrin. Although the sequence of the EF2 peptide (DFATVQLRNGFPYFSYDLG) is homologous sequence to that of EF1, EF2 does not promote cell attachment activity. To determine whether there are structural differences between EF1 and EF2, we performed replica exchange molecular dynamics (REMD) simulations and conventional molecular dynamics (MD) simulations. We found that EF1 and EF2 had β-sheet structure as a secondary structure around the global minimum. However, EF2 had variety of structures around the global minimum compared with EF1 and has easily escaped from the bottom of free energy. The structural fluctuation of the EF1 is smaller than that of the EF2. The structural variation of EF2 is related to these differences in the structural fluctuation and the number of the hydrogen bonds (H-bonds). From the analysis of H-bonds in the β-sheet, the number of H-bonds in EF1 is larger than that in EF2 in the time scale of the conventional MD simulation, suggesting that the formation of H-bonds is related to the differences in the structural fluctuation between EF1 and EF2. From the analysis of other non-covalent interactions in the amino acid sequences of EF1 and EF2, EF1 has three pairs of residues with hydrophobic interaction, and EF2 has two pairs. These results indicate that several non-covalent interactions are important for structural stabilization. Consequently, the structure of EF1 is stabilized by H-bonds and pairs of hydrophobic amino acids in the terminals. Hence, we propose that non-covalent interactions around N-terminal and C-terminal of the peptides are crucial for maintaining the β-sheet structure of the peptides.

Evaluation of the protein interfaces that form an intermolecular four-helix bundle as studied by computer simulation

Rational design of protein surface is important for creating higher order protein structures, but it is still challenging. In this study, we designed in silico the several binding interfaces on protein surfaces that allow a de novo protein–protein interaction to be formed. We used a computer simulation technique to find appropriate amino acid arrangements for the binding interface. The protein–protein interaction can be made by forming an intermolecular four-helix bundle structure, which is often found in naturally occurring protein subunit interfaces. As a model protein, we used a helical protein, YciF. Molecular dynamics simulation showed that a new protein–protein interaction is formed depending on the number of hydrophobic and charged amino acid residues present in the binding surfaces. However, too many hydrophobic amino acid residues present in the interface negatively affected on the binding. Finally, we found an appropriate arrangement of hydrophobic and charged amino acid residues that induces a protein–protein interaction through an intermolecular four-helix bundle formation.

Structural Analysis of Metal-Binding Peptides Using Molecular Dynamics

Proteins that specifically bind metals have been the target of the research for developing new organic-inorganic hybrid materials. Some amino acid sequences that bind metal have been reported, and the structures of proteins and peptides are considered responsible for binding to metal. The purpose of this study is to identify molecular structures responsible for binding metals. We performed molecular dynamics simulations and structural analyses of metal-binding peptides. The most frequently appearing structure of each peptide was identified. Combined with the previous experimental results, peptides with a stable, specific bent structure were suggested to have strong binding abilities. Peptides with a different bent structure have been suggested to be responsible for weak binding ability.

Simulation Study for Wild-Type and C101F Mutant of LIM2 Domain in FHL1

Myopathy is a rare disease lacking a fundamental therapy. Several genetic factors are involved in myopathy; those caused by mutations in FHL1 are rare. We performed molecular dynamics simulation of the LIM2 domain in FHL1 (four and a half LIM domain protein 1). We simulated a partial system consisting of only the LIM2 domain for the wild-type and C101F mutant to confirm the structural stability. We found that structural changes and fluctuations were larger for the mutant type than for the wild-type. Therefore, mutant type structures are unstable in water when the mutations are in residues constituting the zinc finger. Similar results were observed in the simulation of the LIM1+LIM2 domain.

Coarse-Grained Molecular Dynamics Simulation of Sulerythrin and LARFH for Producing Protein Nanofibers

Artificial creation of fibers utilizing proteins has been a target of bionanotechnology. Yagi et al. succeeded in designing artificial protein fibers using two types of proteins: LARFH and sulerythrin. Binding interfaces were designed for sulerythrin and LARFH by introducing mutations, and the fibrous structures were confirmed by atomic force microscopy. However, branching was observed in the fibrous structure, possibly because of non-specific interactions between the proteins. In this study, we analyzed the behavior and binding sites of sulerythrin mutants and LARFH mutants using coarse-grained molecular dynamics (MD) simulation. Binding simulations were performed for a system of one sulerythrin and one LARFH, and also of two sulerythrin molecules and four LARFH molecules. These results suggested that glutamic acids originally possessed by sulerythrin contribute to non-specific binding at sites other than the designed interfaces.

Structure and hydrogen bonds of γS-crystallin and γS-G18V studied by molecular dynamics simulation

The γS-crystallin protein maintains transparency and increases the reflection index of the eye lens. Here, γS−G18V, a mutant of γS-crystallin, was studied, in which the 18th residue, glycine, is replaced by valine. This mutation is associated with childhood-onset cortical cataract. Mutated γS-crystallin forms cross-links with other proteins in the eye lens and leads to aggregation at a temperature lower than that for γS-crystallin. In this study, structural analysis of γS-crystallin and γS−G18V was performed by molecular dynamics simulation. It was found that cysteine residues around the area where the mutation is introduced are arranged at the solvent side with less hydrogen bonds than in the case of γS−WT.

Molecular Dynamics Simulation of γS-WT and γS-G18V

S-crystallin maintains transparency of the crystalline lens and increases the refraction index of lens. S-G18V is a mutant S-crystallin in which 18th glycine is replaced by valine. This protein is related to childhood-onset cortical cataract. In this paper, we study the fluctuation of residues and dihedral angles, and investigate the difference between S-WT and S-G18V by using molecular dynamics simulation. In the result of RMSF, we found large difference around the mutation point. In addition, differences of dihedral angles of cysteins were found in this area.

Molecular dynamics simulation of coarse grained models of gel and proteins

Polymers and proteins have both similarities and differences with conformation and order formation. We perform molecular dynamics simulation of gelation process and also of aggregation of proteins. By discussing the results of the simulation, we obtain some insight into the difference of order formation of polymers and proteins.