A protein molecule is a dielectric substance, so the binding of a ligand is expected to induce dielectric response in the protein molecule, considering that ligands are charged or polar in general. We previously reported that binding of adenosine triphosphate (ATP) to molecular motor myosin actually induces such a dielectric response in myosin due to the net negative charge of ATP. By this dielectric response, referred to as "dielectric allostery," spatially separated two regions in myosin, the ATP-binding region and the actin-binding region, are allosterically coupled. In this study, from the statistically stringent analyses of the extensive molecular dynamics simulation data obtained in the ATP-free and the ATP-bound states, we show that there exists the dielectric allostery that transmits the signal of ATP binding toward the distant lever-arm region. The ATP-binding-induced electrostatic potential change observed on the surface of the main domain induced a movement of the converter subdomain from which the lever arm extends. The dielectric response was found to be caused by an underlying large-scale concerted rearrangement of the electrostatic bond network, in which highly conserved charged/polar residues are involved. Our study suggests the importance of the dielectric property for molecular machines in exerting their function. Published by AIP Publishing.

Actin polymerization depends on the salt concentration, exhibiting a reentrant behavior: the polymerization is promoted by increasing KCl concentration up to 100 mM, and then depressed by further increase above 100 mM. We here investigated the physical mechanism of this reentrant behavior by calculating the polymerization energy, defined by the electrostatic energy change upon binding of an actin subunit to a filament, using an implicit solvent model based on the Poisson-Boltzmann (PB) equation. We found that the polymerization energy as a function of the salt concentration shows a non-monotonic reentrant-like behavior, with the minimum at about 100 mM (1:1 salt). By separately examining the salt concentration effect on the global electrostatic repulsion between the like-charged subunits and that on the local electrostatic attraction between the inter-subunit ionic-bond-forming residues in the filament, we clarified that the reentrant behavior is caused by the change in the balance between the two opposing electrostatic interactions. Our study showed that the non-specific nature of counterions, as described in the mean-field theory, plays an important role in the actin polymerization. We also discussed the endothermic nature of the actin polymerization and mentioned the effect of ATP hydrolysis on the G-F transformation, indicating that the electrostatic interaction is widely and intricately involved in the actin dynamics.

The generalize Born (GB) model is frequently used in MD simulations of biomolecular systems in aqueous solution. The GB model is usually based on the so-called Coulomb field approximation (CFA) for the energy density integration. In this study, we report that the GB model with CFA overdestabilizes the long-range electrostatic attraction between oppositely charged molecules (ionic bond forming two-helix system and kinesin-tubulin system) when the energy density integration cutoff, r(max), which is used to calculate the Born energy, is set to a large value. We show that employing large r(max), which is usually expected to make simulation results more accurate, worsens the accuracy so that the attraction is changed into repulsion. It is demonstrated that the overdestabilization is caused by the overestimation of the desolvation penalty upon binding that originates from CFA. We point out that the overdestabilization can be corrected by employing a relatively small cutoff (r(max) = 10-15 angstrom), affirming that the GB models, even with CFA, can be used as a powerful tool to theoretically study the protein-protein interaction, particularly on its dynamical aspect, such as binding and unbinding.

Protein uses allostery to execute biological function. The physical mechanism underlying the allostery has long been studied, with the focus on the mechanical response by ligand binding. Here, we highlight the electrostatic response, presenting an idea of "dielectric allostery". We conducted molecular dynamics simulations of myosin, a motor protein with allostery, and analyzed the response to ATP binding which is a crucial step in force-generating function, forcing myosin to unbind from the actin filament. We found that the net negative charge of ATP causes a large-scale, anisotropic dielectric response in myosin, altering the electrostatic potential in the distant actin-binding region and accordingly retracting a positively charged actin binding loop. A large-scale rearrangement of electrostatic bond network was found to occur upon ATP binding. Since proteins are dielectric and ligands are charged/polar in general, the dielectric allostery might underlie a wide spectrum of functions by proteins.

The intrinsically disordered protein (IDP) has distinct properties both physically and biologically: it often becomes folded when binding to the target and is frequently involved in signal transduction. The physical property seems to be compatible with the biological property where fast association and dissociation between IDP and the target are required. While fast association has been well studied, fueled by the fly-casting mechanism, the dissociation kinetics has received less attention. We here study how the intrinsic disorder affects the dissociation kinetics, as well as the association kinetics, paying attention to the interaction strength at the binding site (i.e., the quality of the "fly lure"). Coarse-grained molecular dynamics simulation of the pKID-KIX system, a well-studied IDP system, shows that the association rate becomes larger as the disorder-inducing flexibility that was imparted to the model is increased, but the acceleration is marginal and turns into deceleration as the quality of the fly lure is worsened. In contrast, the dissociation rate is greatly enhanced as the disorder is increased, indicating that intrinsic disorder serves for rapid signal switching more effectively through dissociation than association. (C) 2016 Wiley Periodicals, Inc.

© 2016 American Physical Society.Allostery is indispensable for a protein to work, where a locally applied stimulus is transmitted to a distant part of the molecule. While the allostery due to chemical stimuli such as ligand binding has long been studied, the growing interest in mechanobiology prompts the study of the mechanically stimulated allostery, the physical mechanism of which has not been established. By molecular dynamics simulation of a motor protein myosin, we found that a locally applied mechanical stimulus induces electrostatic potential change at distant regions, just like the piezoelectricity. This novel allosteric mechanism, "piezoelectric allostery", should be of particularly high value for mechanosensor/transducer proteins.

An important unresolved problem associated with actomyosin motors is the role of Brownian motion in the process of force generation. On the basis of structural observations of myosins and actins, the widely held lever-arm hypothesis has been proposed, in which proteins are assumed to show sequential structural changes among observed and hypothesized structures to exert mechanical force. An alternative hypothesis, the Brownian motion hypothesis, has been supported by single-molecule experiments and emphasizes more on the roles of fluctuating protein movement. In this study, we address the long-standing controversy between the lever-arm hypothesis and the Brownian motion hypothesis through in silico observations of an actomyosin system. We study a system composed of myosin II and actin filament by calculating free-energy landscapes of actin-myosin interactions using the molecular dynamics method and by simulating transitions among dynamically changing free-energy landscapes using the Monte Carlo method. The results obtained by this combined multi-scale calculation show that myosin with inorganic phosphate (P-i) and ADP weakly binds to actin and that after releasing P-i and ADP, myosin moves along the actin filament toward the strong-binding site by exhibiting the biased Brownian motion, a behavior consistent with the observed single-molecular behavior of myosin. Conformational flexibility of loops at the actin-interface of myosin and the N-terminus of actin subunit is necessary for the distinct bias in the Brownian motion. Both the 5.5-11 nm displacement due to the biased Brownian motion and the 3-5 nm displacement due to lever-arm swing contribute to the net displacement of myosin. The calculated results further suggest that the recovery stroke of the lever arm plays an important role in enhancing the displacement of myosin through multiple cycles of ATP hydrolysis, suggesting a unified movement mechanism for various members of the myosin family.

Association of protein molecules constitutes the basis for the interaction network in a cell. Despite its fundamental importance, the thermodynamic aspect of protein protein binding, particularly the issues relating to the entropy change upon binding, remains elusive. The binding of actin and myosin, which are vital proteins in motility, is a typical example, in which two different binding mechanisms have been argued: the binding affinity increases with increasing temperature and with decreasing salt-concentration, indicating the entropy-driven binding and the enthalpy-driven binding, respectively. How can these thermodynamically different binding mechanisms coexist? To address this question, which is of general importance in understanding protein protein bindings, we conducted an in silico titration of the actin myosin system by molecular dynamics simulation using a residue-level coarse-grained model, with particular focus on the role of the electrostatic interaction. We found a good agreement between in silico and in vitro experiments on the salt-concentration dependence and the temperature dependence of the binding affinity. We then figured out how the two binding mechanisms can coexist: the enthalpy (due to electrostatic interaction between actin and myosin) provides the basal binding affinity, and the entropy (due to the orientational disorder of water molecules) enhances it at higher temperatures. In addition, we analyzed the actin myosin complex structures observed during the simulation and obtained a variety of weak-binding complex structures, among which were found an unusual binding mode suggested by an earlier experiment and precursor structures of the strong-binding complex proposed by electron microscopy. These results collectively indicate the potential capability of a residue-level coarse-grained model to simulate the association dissociation dynamics (particularly for transient weak-bindings) exhibited by larger and more complicated systems, as in a cell.

The phosphorylated kinase-inducible activation domain (pKID) adopts a helix-loop-helix structure upon binding to its partner KIX, although it is unstructured in the unbound state. The N-terminal and C-terminal regions of pKID, which adopt helices in the complex, are called, respectively, αA and αB. We performed all-atom multicanonical molecular dynamics simulations of pKID with and without KIX in explicit solvents to generate conformational ensembles. Although the unbound pKID was disordered overall, αA and αB exhibited a nascent helix propensity
the propensity of αA was stronger than that of αB, which agrees with experimental results. In the bound state, the free-energy landscape of αB involved two low free-energy fractions: native-like and non-native fractions. This result suggests that αB folds according to the induced-fit mechanism. The αB-helix direction was well aligned as in the NMR complex structure, although the αA helix exhibited high flexibility. These results also agree quantitatively with experimental observations. We have detected that the αB helix can bind to another site of KIX, to which another protein MLL also binds with the adopting helix. Consequently, MLL can facilitate pKID binding to the pKID-binding site by blocking the MLL-binding site. This also supports experimentally obtained results. © 2012 by the authors
licensee MDPI, Basel, Switzerland.

The actomyosin molecular motor, the motor composed of myosin II and actin filament, is responsible for muscle contraction, converting chemical energy into mechanical work. Although recent single molecule and structural studies have shed new light on the energy-converting mechanism, the physical basis of the molecular-level mechanism remains unclear because of the experimental limitations. To provide a clue to resolve the controversy between the lever-arm mechanism and the Brownian ratchet-like mechanism, we here report an in silico single molecule experiment of an actomyosin motor. When we placed myosin on an actin filament and allowed myosin to move along the filament, we found that myosin exhibits a unidirectional Brownian motion along the filament. This unidirectionality was found to arise from the combination of a nonequilibrium condition realized by coupling to the ATP hydrolysis and a ratchet-like energy landscape inherent in the actin-myosin interaction along the filament, indicating that a Brownian ratchet-like mechanism contributes substantially to the energy conversion of this molecular motor.

DNA-binding sites for SYCRP1, which is a regulatory protein of the cyanobacterium Synechocystis sp. PCC6803, were predicted for the whole genome sequence by estimating changes in the binding free energy (Delta Delta G(total)(A)) for SYCRP1 for those sites. The Delta Delta G(total)(A) values were calculated by summing Delta Delta G values derived from systematic single base-pair substitution experiments ( symmetrical and cooperative binding model). Of the calculated binding sites, 23 sites with a Delta Delta G(total)(A) value < 3.9 kcal.mol(-1) located upstream or between the ORFs were selected as putative binding sites for SYCRP1. In order to confirm whether SYCRP1 actually binds to these binding sites or not, 11 sites with the lowest Delta Delta G(total)(A) values were tested experimentally, and we confirmed that SYCRP1 binds to ten of the 11 sites with a Delta Delta G(total) value < 3.9 kcal mol(-1). The best correlation coefficient between Delta Delta G(total)(A)and the observed Delta Delta G(total) for binding of SYCRP1 to those sites was 0.78. These results suggest that the Delta Delta G values derived from systematic single base-pair experiments may be used to screen for potential binding sites of a regulatory protein in the genome sequence.

To construct a new model of the propagation mechanism of infectious scrapie-type prion protein (PrPsc), here we conducted a disruption simulation of a PrPsc nonamer using structure-based molecular dynamics simulation method based on a hypothetical PrPsc model structure. The simulation results showed that the nonamer disrupted in cooperative manners into monomers via two significant intermediate states: (1) a nonamer with a partially unfolded surface trimer and (2) a hexamer and three monomers. Dimers and trimers were rarely observed. Then, we propose a new PrPsc propagation mechanism where a hexamer plays an essential role as a minimum infectious unit. (c) 2007 Elsevier Inc. All rights reserved.

We report the results of molecular dynamics simulations of the protein myosin carried out with an elastic network model. Quenching the system, we observe glassy behavior of a density correlation function and a density response function that are often investigated in structure glasses and spin glasses. In the equilibrium, the fluctuation-response relation, a representative relation of the fluctuation-dissipation theorem, holds that the ratio of the density correlation function to the density response function is equal to the temperature of the environment. Weshow that, in the quenched system that we study, this relation can be violated. In the case that this relation does not hold, this ratio can be regarded as an effective temperature. We find that this effective temperature of myosin is higher than the temperature of the environment. We discuss the relation between this effective temperature and energy transduction that occurs after ATP hydrolysis in the myosin molecule.

What granularity is needed to carry out computer simulations of biomolecular reactions/motions? This is one of the central issues of the in silico biomolecular computing. In this paper, we addressed this issue by studying model granularity dependence of the native structure dynamics of protein molecules. We conducted molecular dynamics simulations employing three different protein models: the model with full atomic details and two coarse - grained models in which only C α atoms interacting with each other through simple potentials are considered. In addition to the observed agreement among the three models in terms of isotropic thermal fluctuation, principal component analysis showed that the coarse-grained models can also reproduce the anisotropy (or directionality) of the fluctuation, particularly of collective modes having relevance to molecular function. This indicates that the dependence of the essential dynamics of a protein molecule on the model granularity is weak, although it was also shown that incorporation of the Lennard - Jones-type potential into the harmonic-potential-based coarse-grained model improves the reproducibility to some degree, and that a plastic nature of structural dynamics observed in the full atomic model transforms into an elastic one in the coarse-grained models. The coarse-grained model can be applied to a molecular motor system, which may lead to a new view of biomolecular computing in the context of biological physics. © 2004 Kluwer Academic Publishers.

The cAMP receptor protein SYCRP1 in cyanobacterium Synechoeystis sp. PCC 6803 is a regulatory protein that binds to the consensus DNA sequence (5'-AAATGTGATCTAGATCACATTT-3') for the cAMP receptor protein CRP in Escherichia coli. Here we examined the effects of systematic single base-pair substitutions at positions 4-8 (TGTGA) of the consensus sequence on the specific binding of SYCRP1. The consensus sequence exhibited the highest affinity, and the effects of base-pair substitutions at positions 5 and 7 were the most deleterious. The result is similar to that previously reported for CRP, whereas there were differences between SYCRP1 and CRP in the rank order of affinity for each substitution. (C) 2004 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

An in vitro domainal shuffling strategy for protein evolution was proposed in (J. Kolkman and W. Stemmer, Nat. Biotech. 19 (423) 2001). Due to backhybridization, however this method appears unlikely to be an efficient means of iteratively generating massive libraries of combinatorially shuffled genes. Recombination at the domain level (30-300 residues) also appears too coarse to support the evolution of proteins with substantially new folds. In this work, the module (10-25 residues long) and pseudomodule are adopted as the fundamental units of protein structure. Each protein is modelled as an N to C-terminal tour of a digraph composed of pseudomodules. An in vitro method based on PNA-mediated Whiplash PCR (PWPCR), RNA-protein fusion, and restriction-based recombination, XWPCR is then presented for evolving proteins with a high affinity for a given motif, subject to the constraint that each corresponds to a walk on the pseudomodule digraph of interest. Simulations predict that PWPCR is an efficient method of producing massive, shuffled gene libraries encoding for proteins as long as roughly 600 residues.

The all-atom and the Ising-based models have both played their own roles to help our understanding of helix-coil transition. In this study, we address to what degree these two theoretical models can be consistent with each other in the nonstationary regime, complementing the preceding equilibrium study. We conducted molecular dynamics simulations of an all-atom model polyalanine chain and Monte Carlo simulations of a corresponding kinetic Ising chain. Nonstationary properties of each model were characterized through power spectrum, Allan variance, and autocorrelation analyses regarding the time course of a system order parameter. A clear difference was indicated between the two models: the Ising-based model showed a Lorentzian spectrum in the frequency domain and a single exponential form in the time domain, whereas the all-atom model showed a 1/f spectrum and a stretched exponential form. The observed stretched exponential form is in agreement with a very recent T-jump experiment. The effect of viscous damping on helix-coil dynamics was also studied. A possible source of the observed difference between the two models is discussed by considering the potential energy landscape, and the idea of dynamical disorder was introduced into the original Glauber model in the hope of bridging the gap between the two models. Other possible sources, e. g., the limitations of the Ising framework and the validity of the Markovian dynamics assumption, are also discussed. (C) 2003 American Institute of Physics.

To describe the polypeptide helix-coil transition, while the Ising-based theory has been playing the principal role for 40 years, we can now make use of computer simulation using the so-called "all-atom model" that is far more precise than the Ising-based model. In this study, by conducting molecular dynamics (MD) simulations of helix-coil transition exhibited by a short polyalanine chain, we investigated how the MD simulation results and the Ising-based theoretical values coincide with each other, placing a focus on their equilibrium statistical mechanical properties. Several important physical properties, such as temperature-dependent helix ratio, distribution of the helix-residue number, position-dependent helix ratio, and pair-correlation between residue states were taken up as the proving grounds on which we made a comparison between the all-atom model simulation and the Ising-based theory. As an overall trend, we realized that the Ising-based theoretical results agreed with the all-atom simulation results at least qualitatively, suggesting that the Ising-based model, though very simple, extracts the essence of the phenomenon with respect to the equilibrium properties. On the other hand we found some quantitative disagreements between them. The origins of the observed disagreements are discussed by going into details of the all-atom model. (C) 2002 American Institute of Physics.

We present a molecular dynamics study of the alpha-helix formation in a system consisting of a 15-residue poly(L-alanine) and surrounding water molecules. By applying a relatively high temperature, we observed the alpha-helix formation several times during a 17-ns run, and reversible helix-coil transitions were also observed. The alpha-helix formations were usually initiated by the beta-tum structures. A crank-shaft-like motion of the peptide was included in the folding process. In the formed alpha-helical domains, substantial 3(10)-helix formations were found especially at the termini, as observed by the NMR study. The folding time scale at room temperature estimated from our simulation was found to lie in the range of 100ns, which is in accord with the time scale of the T-jump experiments. The total energy of the whole system was lower in the alpha-helix state than in the random-coil state by 20.4 +/- 4.8 kcal/mol, which is consistent with the experimental value obtained by calorimetry. This energy decrease in forming the alpha-helix was mainly caused by the Coulombic energy and the torsional energy.

We report on molecular dynamics simulations of the helix-coil transition of a polypeptide. The simulated transition was two-state-like and similar to the solid-liquid-like transition that has been observed in computer simulations of an atomic cluster. At the transition temperature, the polypeptide chain fluctuated between a helical and a random-coil state, and we observed 1/f fluctuation through potential-energy fluctuations. The origin of the observed 1/f fluctuation is discussed, considering the underlying potential-energy landscape.