高須 昌子

Alzheimer's disease is an irreversible neurological disorder for which there are no effective small molecule therapeutics. A phosphodiesterase 5 (PDE5) inhibitor is a candidate medicine for the treatment of Alzheimer's disease. Rutaecarpine, an indole alkaloid found in Euodiae Fructus, has inhibitory activity for PDE5. Euodiae Fructus contains more evodiamine than rutaecarpine. Therefore, we performed molecular dynamics simulations of the complex of PDE5 and evodiamine. The results showed that the PDE5 and (-)-evodiamine complexes were placed inside the reaction center compared to the case of PDE5 and (+)-evodiamine complex. The binding of (-)-evodiamine to PDE5 increased the root-mean-square deviation and radius of gyration of PDE5. In the PDE5 with (-)-evodiamine complex, the value of the root-mean-square fluctuation of the M-loop, which is thought to be important for activity, increased. This result suggests that (-)-evodiamine may have inhibitory activity.

The characteristic shape changes observed in the growth and division of L-form cells have been explained by several theoretical studies and simulations using a vesicle model in which the membrane area increases with time. In those theoretical studies, characteristic shapes such as tubulation and budding were reproduced in a non-equilibrium state, but it was not possible to incorporate deformations that would change the topology of the membrane. We constructed a vesicle model in which the area of the membrane increases using coarse-grained particles and analyzed the changes in the shape of growing membrane by the dissipative particle dynamics (DPD) method. In the simulation, lipid molecules were added to the lipid membrane at regular time intervals to increase the surface area of the lipid membrane. As a result, it was found that the vesicle deformed into a tubular shape or a budding shape depending on the conditions for adding lipid molecules. This suggests that the difference in the place where new lipid molecules are incorporated into the cell membrane during the growth of L-form cells causes the difference in the transformation pathway of L-form cells.

Experimental observations indicate that the repulsion of particles is a factor that induces the transformation of vesicles containing multiple particles. Metropolis Monte Carlo simulations are performed with two models in which repulsive particles are enclosed inside a vesicle. The distribution of the particles and the effective bending coefficient and surface tension of the membrane are analyzed. The shape and internal structure of the vesicle containing the particles are investigated as the vesicle volume is decreased. It is revealed that the repulsive interaction between particles produces a layered structure and stiffens the membrane. When particles repulsively interact over a long range, the membrane takes on a dumbbell form.

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.

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.

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.

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.

Proteins, which incorporate charged and hydrophobic amino acid residues, are useful as a material of nanotechnology. Among these proteins, IPMDH (3-isopropylmalate dehydrogenase), which has thermal stability, has potential as a material of nanofiber. In this study, we performed coarse-grained molecular dynamics simulation of IPMDH using MARTINI force fields, and we investigated the orientation for the binding of IPMDH. In simulation, we analyzed wild type of IPMDH and the mutated IPMDH proteins, where 13, 20, 27, 332, 335 and 338th amino acid residues are replaced by lysine residues which have positive charge and by glutamic acid residues which have negative charge. Since the binding of mutated IPMDH is advantageous compared with the binding of wild type for one orientation, we suggest that the Coulomb interaction for the binding of IPMDH is important.

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.

<p>2008年に酒井らによって開発されたTetra-polyethylene glycol(Tetra-PEG)ゲルは生体医療への応用が期待される高分子ゲルで、優れたネットワーク構造の均一性を誇る。我々はこの均一性と力学的強度との関係性を探ることを目的としている。本講演ではブラウン動力学法を用いてTetra-PEGゲルの形成過程をシミュレーションし、分子濃度によってネットワークの均一性がどのように変わるのかを検討する。</p>

<p>線毛を伸縮させて移動する（twitching運動）バクテリアには多くの種類が存在し，それぞれ特徴的な相違がみられる．特にバクテリアの形状や線毛の生える場所が異なると，それらの運動のメカニズムにも顕著な相違が表れることが知られている．本研究では，これらの違いがバクテリアの走化性に及ぼす影響を，シミュレーションモデルを用いて調べることを目的とする．</p>

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.

Telomeres, which consist of single-, double- and four-stranded DNA, shorten after each round of cell division. The repeated telomeric DNA sequence 5′-TTAGGG-3′ does not encode genetic information and is not replicated completely. We performed molecular dynamics (MD) simulations of telomeric single-stranded DNA (ssDNA) and protection of telomere 1 (POT1) for 100 ns. We calculated the distance between Cα (POT1) and O5’ (telomeric ssDNA) to verify the binding system for 100 ns MD. We then calculated the distance between the bases of the telomeric DNA ends and the root-mean-square deviation and gyration radius in the single and binding states. Moreover, we compared the root-mean-square fluctuations (RMSFs) between the single and binding states and calculated the number of hydrogen bonds between POT1 and telomeric DNA. There are many hydrogen bonds between Gln94 and the first guanine of the closest 5′-TTAGGG-3′ sequence in telomeric single-stranded DNA, and the RMSF between the single and binding states has a large difference between Gln94 and guanine. Overall, we found that Gln94 and guanine are important components of the binding system and are related to the stability of this system.

We study the early process of gelation using our model of 5 particles and 9 particles in a monomer. We compare our models and obtain slower reaction for model of 9 particles. We also study the effect of random force and obtain slower reaction with random force but more extended structure.

γS-crystallin maintains transparency of the crystalline lens and increases the refraction index of lens. γS-G18V is a mutant γS-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 γS-WT and γS-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.

Vesicles containing charged colloids show peculiar shape deformation under certain conditions. However, its physical mechanism is not clear. We have performed Monte Carlo simulation for a model of closed triangulated membrane and encapsulated hard spheres. We analyzed vesicular shapes and encapsulated hard spheres by using diffusion coefficient, change of area difference and volume, and the radial distribution of hard spheres from the membrane. The discussion of our results can be used as the foundation for understanding of the complex behavior of vesicles containing colloids.

<br /> <br /> Telomeres play a central role in determining longevity of a cell. Our study focuses on the interaction between telomeric guanines and TRF1 as a means to observe the telomeric based mechanism of the genome protection. In this research, we performed molecular dynamics simulations of a telomeric DNA and TRF1. Our results show a stable structure with a high affinity for the specific protein. Additionally, we calculated the distance between guanines and the protein in their complex state. From this comparison, we found the calculated values of distance to be very similar, and the angle of guanines in their complex states was larger than that in their single state.

The objective of this study is to design the binding interface between proteins that form protein–protein complex. We chose a 4-helix bundle motif as a scaffold for forming the intermolecular binding. Based on this motif, we designed several binding interfaces including some charged and hydrophobic amino acid residues. Molecular dynamics (MD) simulations were performed to explore appropriate amino acid arrangements for the binding interface. We found binding interfaces that may be suitable for inducing the intermolecular binding.

Laminin is one of the components of the basement membrane and has diverse biological activities. Several functional peptides (EF1-EF5) are identified from LG4 modules of laminin alpha 1–5 chains. Thus, we perform conformation analysis of EF1 and EF2 using molecular dynamics simulations. In this study, we perform structure sampling with NPT ensemble (300 K, 1 bar). Our results show that EF1 peptide has β-sheet structure in water, and EF2 peptide does not have. Likewise, the EF2 peptide has unstable structure compared with the EF1 peptide in water.

We have performed molecular dynamics simulation of coarse-grained model of IPMDH 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.

A dynamics model of bacterial twitching motility is devised. A bacterial body is bound on a plane surface and driven by multiple type IV pili (TFP) which are appendages of the bacterium. The drag force following Stokes’ law also applies to the bacterial body in the viscous fluid. By using the individual model, the numerical simulations are performed and the velocities and the rotational velocity of the bacterial body are investigated. From the results of the simulations, a rapid motion with rotationcalled slingshot, which was found in P. aeruginosa, is reproduced. There is a possibility that the slingshot motion may be carried out widely in many species of bacteria having TFP.

We study the effect of the tails of H3 and H4 histones in the nucleosomes, where DNA and histones are packed in the form of chromatin. We perform molecular dynamics simulations of the complex of DNA and histones and calculate the mean square displacement and the gyration radius of the complex of DNA and histones for the cases with tails intact and the cases with tails missing. Our results show that the H3 tails are important for the motion of the histones. We also find that the motion of one tail is affected by other tails, although the tails are distanced apart, suggesting the correlated motion in biological systems.

Docking of two protein molecules is induced by intermolecular interactions. Our purposes in this study are: designing binding interfaces on the two proteins, which specifically interact to each other; and inducing intermolecular interactions between the two proteins by mixing them. A 4-helix bundle structure was chosen as a scaffold on which binding interfaces were created. Based on this scaffold, we designed binding interfaces involving charged and nonpolar amino acid residues. We performed molecular dynamics (MD) simulation to identify suitable amino acid residues for the interfaces. We chose YciF protein as the scaffold for the protein-protein docking simulation. We observed the structure of two YciF protein molecules (I and II), and we calculated the distance between centroids (center of gravity) of the interfaces’ surface planes of the molecules I and II. We found that the docking of the two protein molecules can be controlled by the number of hydrophobic and charged amino acid residues involved in the interfaces. Existence of six hydrophobic and five charged amino acid residues within an interface were most suitable for the protein-protein docking.