Molecular dynamics study on the hydrogen bond formation between α-hydrogen atom of L-Phe and N5 atom of FAD in the enzyme-substrate complex of the L-Phe oxidase reaction.

It is difficult to observe the structure of the enzyme-substrate complex (ES complex) experimentally, since the complex changes to the enzyme and its product during observation. The molecular dynamics (MD) approach is ideal to observe the structural change of enzyme and of substrate in the ES complex. Analyses on the complex of L-Phe oxidase with L-Phe by MD showed 1) the distance between the α-hydrogen atom of L-Phe and the N5 atom of isoalloxazine ring of FAD to be 2.64 ± 0.19 Å, and 2) the angle CA-HA-N5 atoms to be 141.5 ± 10.7°. This result clearly showed that the α-hydrogen atom forms the hydrogen bond with the N5 atom of isoalloxazine ring of FAD in the enzyme-substrate complex. Thus, the complex is ready for the hydrogen transfer from substrate to FAD in the key step of the oxidation of substrate by the enzyme.

Potential of mean force and umbrella sampling simulation for the transport of 5-oxazolidinone in heterotetrameric sarcosine oxidase.

The structure of heterotetrameric sarcosine oxidase (HSO) contains a highly complex system composed of a large cavity and tunnels, which are essential for the reaction and migration of the reactants, products, and intermediates. Previous geometrical analysis using the CAVER program has predicted that there are three possible tunnels, T1, T2, and T3, for the exit pathway of the iminium intermediate, 5-oxazolidinone (5-OXA), of the enzyme reaction. Previous molecular dynamics (MD) simulation of HSO has identified the regions containing the water channels from the density distribution of water. The simulation indicated that tunnel T3 is the most probable exit pathway of 5-OXA. In the present study, the potential of mean force (PMF) for the transport of 5-OXA through tunnels T1, T2, and T3 was calculated using umbrella sampling (US) MD simulations and the weighted histogram analysis method. The PMF profiles for the three tunnels support the notion that tunnel T3 is the exit pathway of 5-OXA, and that 5-OXA tends to stay at the middle of the tunnel. The maximum errors of the calculated PMF for the predicted exit pathway, tunnel T3, were estimated by repeating the US simulations using different sets of initial positions. The PMF profile was also calculated for the transport of glycine within T3. The PMF profiles from the US simulations were in good agreement with the previous predictions that 5-OXA escape through tunnel T3 and how glycine is released to the outside of HSO was discussed.

Visualizing the helical stacking of octahedral metallomesogens with a chiral core.

A combination of grazing-incidence X-ray diffraction and molecular dynamics simulation studies led to the visualization of the stacking structure of a helical columnar liquid crystal formed by enantiopure octahedral metallomesogens with ΔΛ chirality. The helical structure was elucidated as a hybrid of two major proposed structures.

Parallel Evolution of Two dmrt1-Derived Genes, dmy and dm-W, for Vertebrate Sex Determination.

Animal sex-determining genes, which bifurcate for female and male development, are diversified even among closely related species. Most of these genes emerged independently from various sex-related genes during species diversity as neofunctionalization-type genes. However, the common mechanisms of this divergent evolution remain poorly understood. Here, we compared the molecular evolution of two sex-determining genes, the medaka dmy and the clawed frog dm-W, which independently evolved from the duplication of the transcription factor-encoding masculinization gene dmrt1. Interestingly, we detected parallel amino acid substitutions, from serine (S) to threonine (T), on the DNA-binding domains of both ancestral DMY and DM-W, resulting from positive selection. Two types of DNA-protein binding experiments and a luciferase reporter assay demonstrated that these S-T substitutions could strengthen the DNA-binding abilities and enhance the transcriptional regulation function. These findings suggest that the parallel S-T substitutions may have contributed to the establishment of dmy and dm-W as sex-determining genes.

Comprehensive Understanding of Host- and Guest-Dependent Helix Inversion in Chiral Nematic Liquid Crystals: Experimental and Molecular Dynamics Simulation Study.

Nematic liquid crystals (LCs) are known to transform into chiral nematic LCs with helical structures upon doping with enantiomeric compounds (called chiral dopants or guests). Here, we investigated the mechanism of host LC- and guest-dependent helix inversion by using octahedral metal complexes as guests. The helical twisting powers (HTPs/µm-1) of eight metal complexes with Δ, Λ chirality were examined in five nematic LC hosts. For example, Δ-[Ru(acac)2(trop)] (Ru-trop, Hacac = 2,4-pentanedione, Htrop = tropolone) induces a left-handed ( M) helix upon doping with N-(4-methoxybenzylidene)-4-butylaniline (MBBA), whereas it induces an opposite right-handed ( P) helix in 4-cyano-4'-pentylbiphenyl (5CB). The monobrominated complex of Ru-trop, Δ-[Ru(acac)2(Brtrop)] (Ru-Br1trop, HBr1trop = 5-bromotropolone), induces P helices in both MBBA and 5CB, whereas the dibrominated complex, Δ-[Ru(acac)2(Br2trop)] (Ru-Br2trop, HBr2trop = 3,7-dibromotroplone) induces M helices in both the media. The molecular dynamics simulation performed in parallel confirmed the drastic effect of the bromo groups on the microscopic ordering direction of guests in nematics. Further, HTPs of all Δ isomers of metal complexes investigated were found to shift in the positive direction as the dielectric constant anisotropy (Δε) of the host LCs increases (and vice versa for Λ isomers). These experimental and calculated results highlight the interplay of steric (excluded volume effect) and electrostatic (dipole-dielectric body) interactions between the host LCs and guest metal complexes.

CAPLIB: A New Program Library for the Modeling and Analysis of Icosahedrally Symmetric Viral Capsids.

A new program library named "CAPLIB" was developed for the modeling and analysis of icosahedrally symmetric virus capsids. CAPLIB is equipped with the mathematical data of 60 rotation matrices of icosahedral symmetry, 15 planes bisecting the entire capsid structure, and a table summarizing how the 60 asymmetric units (cells) are partitioned by the planes. CAPLIB contains the function to determine the cell numbers of atoms from the atomic positions and the function to determine the rotation axes and angles from the rotation matrices. Using CAPLIB, it is possible to generate the structure of any selected protein unit within the entire capsid by rotating a single protein unit structure. CAPLIB can classify Protein Data Bank files of capsids with the directions of rotation axes, rotate the protein structure onto the standard position, and perform various deformations of the entire capsid. The interface to the molecular graphics software, PyMOL, was also developed for efficient modeling of capsids.

Molecular Dynamics Simulations to Determine the Structure and Dynamics of Hepatitis B Virus Capsid Bound to a Novel Anti-viral Drug.

Hepatitis B virus (HBV) chronically infects millions of people worldwide and is a major cause of serious liver diseases, including liver cirrhosis and liver cancer. In our previous study, in silico screening was used to isolate new anti-viral compounds predicted to bind to the HBV capsid. Four of the isolated compounds have been reported to suppress the cellular multiplication of HBV experimentally. In the present study, molecular dynamics simulations of the HBV capsid were performed under rotational symmetry boundary conditions, to clarify how the structure and dynamics of the capsid are affected at the atomic level by the binding of one of the isolated compounds, C13. Two simulations of the free HBV capsid, two further simulations of the capsid-C13 complex, and one simulation of the capsid-AT-130 complex were performed. For statistical confidence, each set of simulations was repeated by five times, changing the simulation conditions. C13 continued to bind at the predicted binding site during the simulations, supporting the hypothesis that C13 is a capsid-binding compound. The structure and dynamics of the HBV capsid were greatly influenced by the binding and release of C13, and these effects were essentially identical to those seen for AT-130, indicating that C13 likely inhibits the function of the HBV capsid.

Analysis of water channels by molecular dynamics simulation of heterotetrameric sarcosine oxidase.

A precise 100-ns molecular dynamics simulation in aquo was performed for the heterotetrameric sarcosine oxidase bound with a substrate analogue, dimethylglycine. The spatial region including the protein was divided into small rectangular cells. The average number of the water molecules locating within each cell was calculated based on the simulation trajectory. The clusters of the cells filled with water molecules were used to determine the water channels. The narrowness of the channels, the average hydropathy indices of the residues of the channels, and the number of migration events of water molecules through the channels were consistent with the selective transport hypothesis whereby tunnel T3 is the pathway for the exit of the iminium intermediate of the enzyme reaction.

Structure and dynamics of the GH loop of the foot-and-mouth disease virus capsid.

The GH loop of VP1 of the foot-and-mouth disease virus capsid is important because it is a major antigenic site and an integrin recognition site. The GH loop is disordered in all X-ray structures of the capsid except for serotype O under reduced conditions in which the loop lies on the capsid surface. Although the structure of the capsid-integrin complex has not yet been determined, the GH loop is known to protrude from the capsid surface when the capsid is bound with an antigen-binding fragment (Fab). To clarify the structure and dynamics of the GH loop under natural unreduced conditions before binding to integrins or Fab fragments, we performed molecular dynamics simulation of 16.3 ns long under rotational symmetry boundary conditions for the capsid of serotype O using the X-ray structure of the reduced capsid for the initial coordinates. When the disulfide bond at the base of the GH loop was formed by the molecular mutation method, the loop protruded into the surrounding water, as reported for Fab-capsid complexes, and fluctuated like a tentacle. After equilibration, the GH loop overlapped the surface of the capsid but continued to fluctuate, being directed toward a 2-fold axis. The conformational change of the GH loop after formation of the disulfide bond was explained by a model of elastic tube. The side chains of arginine and aspartic acid of the integrin recognition residues (RGD tripeptide) extended in opposite directions, and the residues on the C-terminal side of the RGD tripeptide formed a hydrophobic cluster in close proximity of the arginine residue of the tripeptide.

Analysis of low-frequency phonons in guanosine dihydrate based on molecular dynamics simulations.

Fourier analysis, using the atomic trajectory calculated by molecular dynamics simulation at 300 K, is applied to the study of low-frequency phonons of guanine dihydrate. The vibrational modes of guanine bases are analyzed, and the optically active modes associated with the guanine moieties are extracted. There are a few significant peaks in the low-frequency region. A possible assignment of the Raman active mode near 27 cm(-1), whose origin would be common to the S-mode of DNA double helices, is discussed.

Crystal water dynamics of guanosine dihydrate: analysis of atomic displacement parameters, time profile of hydrogen-bonding probability, and translocation of water by MD simulation.

The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism.

Motion of an antiviral compound in a rhinovirus capsid under rotational symmetry boundary conditions.

A molecular dynamics (MD) simulation of a complex of a rhinovirus protein shell referred to as a "capsid" and an anti-rhinovirus drug, WIN52084s, was performed under the rotational symmetry boundary conditions. For the simulation, the energy parameters of WIN52084s in all-atom approximations were determined by ab initio calculations using a 6-31G* basis set and the two-conformational two-stage restricted electrostatic potential fit method. The motion of WIN52084s and the capsid was focused on in the analysis of the trajectory of the simulation. The root mean square deviations of WIN52084s from the X-ray structure were decomposed to conformational, translational, and rotational components. The translation was further decomposed to radial, longitudinal, and lateral components. The conformation of WIN52084s was rigid, but moving in the pocket. The easiest path of motion for WlN52084s was on the longitudinal line, providing a track for the binding process required of the anti-rhinovirus drug to enter the pocket. The conformation of the pocket was also preserved in the simulation, although the position of the pocket in the capsid fluctuated in the lateral and radial directions.

Dynamic characteristics of a peptide-binding groove of human HLA-A2 class I MHC molecules: normal mode analysis of the antigen peptide-class I MHC complex.

Class I major histocompatibility complex (MHC) binds antigen peptides with various sequences. We performed a normal mode analysis of HLA-A2 MHC that binds three peptides with different affinity. HLA-A2 MHC has a peptide-binding groove composed of two alpha-helices (residue 49-84, residue 140-179). Some residues in the center of the groove showed an increase in fluctuations and some residue pairs between two helix groups showed a negative change in correlations by removing the antigen peptide. The extent of the fluctuation and correlation changes correlated well with the experimental ranking of the three peptides in binding affinity. Some definite anti-correlative motions were found between two helix groups in low frequency modes (<50 cm(-1)) by removing the antigen peptide. We propose that the above anti-correlative motions play an important role to bind the antigen peptide, especially in obtaining a "dynamic fit."