Junichi Higo

Energy landscape of a peptide consisting of α‐helix, 310‐helix, β‐turn, β‐hairpin, and other disordered conformations

The energy landscape of a peptide [Ace‐Lys‐Gln‐Cys‐Arg‐Glu‐Arg‐Ala‐Nme] in explicit water was studied with a multicanonical molecular dynamics simulation, and the AMBER parm96 force field was used for the energy calculation. The peptide was taken from the recognition helix of the DNA‐binding protein, c‐Myb. A rugged energy landscape was obtained, in which the random‐coil conformations were dominant at room temperature. The CD spectra of the synthesized peptide revealed that it is in the random state at room temperature. However, the 300 K canonical ensemble, Q(300K), contained α‐helix, 310‐helix, β‐turn, and β‐hairpin structures with small but notable probabilities of existence. The complete α‐helix, imperfect α‐helix, and random‐coil conformations were separated from one another in the conformational space. This means that the peptide must overcome energy barriers to form the α‐helix. The overcoming process may correspond to the hydrogen‐bond rearrangements from peptide–water to peptide–peptide interactions. The β‐turn, imperfect 310‐helix, and β‐hairpin structures, among which there are no energy barriers at 300 K, were embedded in the ensemble of the random‐coil conformations. Two types of β‐hairpin with different β‐turn regions were observed in Q(300K). The two β‐hairpin structures may have different mechanisms for the β‐hairpin formation. The current study proposes a scheme that the random state of this peptide consists of both ordered and disordered conformations. In contrast, the energy landscape obtained from the parm94 force field was funnel like, in which the peptide formed the helical conformation at room temperature and random coil at high temperature.

FLEXIBLE DOCKING OF A LIGAND PEPTIDE TO A RECEPTOR PROTEIN BY MULTICANONICAL MOLECULAR DYNAMICS SIMULATION

Abstract A new method for flexible docking by multicanonical molecular dynamics simulation is presented. The method was applied to the binding of a short proline-rich peptide to a Src homology 3 (SH3) domain. The peptide and the side-chains at the ligand binding cleft of SH3 were completely flexible and the large number of possible conformations and dispositions of the peptide were sampled. The reweighted canonical resemble at 300 K resulted in only a few predominant binding modes, one of which was similar to the complex crystal structure. The inverted peptide orientation was also observed in the other binding modes.

A Free-Energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from Detailed All-Atom Computations

The N-terminal repressor domain of neural restrictive silencer factor (NRSF) is an intrinsically disordered protein (IDP) that binds to the paired amphipathic helix (PAH) domain of mSin3. An NMR experiment revealed that the minimal binding unit of NRSF is a 15-residue segment that adopts a helical structure upon binding to a cleft of mSin3. We computed a free-energy landscape of this system by an enhanced conformational sampling method, all-atom multicanonical molecular dynamics. The simulation started from a configuration where the NRSF segment was fully disordered and distant from mSin3 in explicit solvent. In the absence of mSin3, the disordered NRSF segment thermally fluctuated between hairpins, helices, and bent structures. In the presence of mSin3, the segment bound to mSin3 by adopting the structures involved in the isolated state, and non-native and native complexes were formed. The free-energy landscape comprised three superclusters, and free-energy barriers separated the superclusters. The native complex was located at the center of the lowest free-energy cluster. When NRSF landed in the largest supercluster, the generated non-native complex moved on the landscape to fold into the native complex, by increasing the interfacial hydrophobic contacts and the helix content. When NRSF landed in other superclusters, the non-native complex overcame the free-energy barriers between the various segment orientations in the binding cleft of mSin3. Both population-shift and induced-fit (or induced-folding) mechanisms work cooperatively in the coupled folding and binding. The diverse structural adaptability of NRSF may be related to the hub properties of the IDP.

Two‐component multicanonical Monte Carlo method for effective conformation sampling

A multicanonical algorithm, which is one of the most powerful conformation‐sampling methods to obtain the density of states described by a component (i.e., the total potential energy), was extended to obtain the density of states described by two components. This method was tested on a simplified model for bacteriorhodopsin, which is a membrane protein consisting of seven helices. Two kinds of simulation were done by adopting different sets of two components: in one set, the components were the site‐specific and the non–site‐specific energies between helices; and, in the other set, the total potential energy and the end‐to‐end distance (distance between the first and the seventh helices) were used. In both simulations, a wide and flat probability distribution was obtained, showing the efficiency of the two‐component method. A variety of applications may be possible by effectively selecting the two components, such as the van der Waals and electrostatic energies, the intermolecular and intramolecular interactions, the solute–solute and solute–solvent interactions, or an energy and a reaction coordinate. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 2086–2092, 1997

Conformational transition states of a β‐hairpin peptide between the ordered and disordered conformations in explicit water

The conformational transition states of a β‐hairpin peptide in explicit water were identified from the free energy landscapes obtained from the multicanonical ensemble, using an enhanced conformational sampling calculation. The β‐hairpin conformations were significant at 300 K in the landscape, and the typical nuclear Overhauser effect signals were reproduced, consistent with the previously reported experiment. In contrast, the disordered conformations were predominant at higher temperatures. Among the stable conformations at 300 K, there were several free energy barriers, which were not visible in the landscapes formed with the conventional parameters. We identified the transition states around the saddle points along the putative folding and unfolding paths between the β‐hairpin and the disordered conformations in the landscape. The characteristic features of these transition states are the predominant hydrophobic contacts and the several hydrogen bonds among the side‐chains, as well as some of the backbone hydrogen bonds. The unfolding simulations at high temperatures, 400 K and 500 K, and their principal component analyses also provided estimates for the transition state conformations, which agreed well with those at 400 K and 500 K deduced from the current free energy landscapes at 400 K and 500 K, respectively. However, the transition states at high temperatures were much more widely distributed on the landscape than those at 300 K, and their conformations were different.

Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: On the correlation between crystal water sites, solvent density, and solvent dipole

The hydration structure of human lysozyme was studied with cryogenic X‐ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 Å provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1‐ns simulation trajectories: the solvent density reflecting the time‐averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long‐distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration.

Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules.

We propose a framework to describe the cooperative orientational motions of water molecules in liquid water and around solute molecules in water solutions. From molecular dynamics (MD) simulation a new quantity “site-dipole field” is defined as the averaged orientation of water molecules that pass through each spatial position. In the site-dipole field of bulk water we found large vortex-like structures of more than 10 Å in size. Such coherent patterns persist more than 300 ps although the orientational memory of individual molecules is quickly lost. A 1-ns MD simulation of systems consisting of two amino acids shows that the fluctuations of site-dipole field of solvent are pinned around the amino acids, resulting in a stable dipole-bridge between side-chains of amino acids. The dipole-bridge is significantly formed even for the side-chain separation of 14 Å, which corresponds to five layers of water. The way that dipole-bridge forms sensitively depends on the side-chain orientations and thereby explains the specificity in the solvent-mediated interactions between biomolecules.

Peptide free‐energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

The C96 and AMBER95 force fields were compared with small model peptides Ac‐(Ala)n‐NMe (Ac = CH3CO, NMe = NHCH3, n=2 and 3) in vacuo and in TIP3P water by computing the free‐energy profiles using multicanonical molecular dynamics method. The C96 force field is a modified version of the AMBER95 force field, which was adjusted to reproduce the energy difference between extended β‐ and constrained α‐helical energies for the alanine tetrapeptide, obtained by the high level ab initio MO method. The slight modification resulted in a large difference in the free energy profiles. The C96 force field prefers relatively extended conformers, whereas the AMBER95 force field favors turn conformations.

Enhanced conformational diversity search of CDR‐H3 in antibodies: Role of the first CDR‐H3 residue

Through a conformation search by a simulation calculation, the relationships between the amino acid sequences and the conformations of the third complementarity‐determining region of the antibody heavy chain (CDR‐H3) were investigated to characterize the large conformational varieties of antibodies. Here, we focused on the structural role of the first CDR‐H3 residue, and we selected two antibodies, 28B4 and PLG, whose CDR‐H3 conformations are significantly different, having Trp and Gly at the first position, respectively. Multicanonical molecular dynamics simulations, with the advantage of enhanced sampling efficiency, were performed for the CDR‐H3 fragments of 28B4 and PLG, and a modified CDR‐H3 model of 28B4, where the first Trp residue was substituted with Gly. When the first CDR‐H3 residue is Trp, almost all of the observed CDR‐H3 loops were bent at the first residue. In contrast, when the first residue is Gly, large varieties of loop conformations were observed. The structural role of this Gly residue is discussed from the perspective of the other antibody structures in the database. When the surrounding residues were included in the calculations, CDR‐H3 loop structures similar to those in the crystal structures were reproduced as the major conformations for both the 28B4 and PLG antibodies. Proteins 1999;37:683–696. ©1999 Wiley‐Liss, Inc.

Free-energy landscape of a chameleon sequence in explicit water and its inherent α/β bifacial property

A sequence in yeast MATα2/MCM1/DNA complex that folds into α‐helix or β‐hairpin depending on the surroundings has been known as “chameleon” sequence. We obtained the free‐energy landscape of this sequence by using a generalized‐ensemble method, multicanonical molecular dynamics simulation, to sample the conformational space. The system was expressed with an all‐atom model in explicit water, and the initial conformation for the simulation was a random one. The free‐energy landscape demonstrated that this sequence inherently has an ability to form either α or β structure: The conformational distribution in the landscape consisted of two α‐helical clusters with different packing patterns of hydrophobic residues, and four β‐hairpin clusters with different strand–strand interaction patterns. Narrow pathways connecting the clusters were found, and analysis on the pathways showed that a compact structure formed at the N‐terminal root of the chameleon sequence controls the cluster‐cluster transitions. The free‐energy landscape indicates that a small conditional change induces α‐β transitions. Additional unfolding simulations done with replacing amino acids showed that the chameleon sequence has an advantage to form an α‐helix. Current study may be useful to understand the mechanism of diseases resulting from abnormal chain folding, such as amyloid disease.