Hiroshi Fujisaki

Minimum free energy path of ligand-induced transition in adenylate kinase.

Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme.

Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins

Without invoking the Markov approximation, we derive formulas for vibrational energy relaxation (VER) and dephasing for an anharmonic system oscillator using a time-dependent perturbation theory. The system-bath Hamiltonian contains more than the third order coupling terms since we take a normal mode picture as a zeroth order approximation. When we invoke the Markov approximation, our theory reduces to the Maradudin-Fein formula which is used to describe the VER properties of glass and proteins. When the system anharmonicity and the renormalization effect due to the environment vanishes, our formulas reduce to those derived by and Mikami and Okazaki [J. Chem. Phys. 121, 10052 (2004)] invoking the path-integral influence functional method with the second order cumulant expansion. We apply our formulas to VER of the amide I mode of a small amino-acid like molecule, N-methylacetamide, in heavy water.

Dynamical aspects of quantum entanglement for weakly coupled kicked tops

We investigate how the dynamical production of quantum entanglement for weakly coupled, composite quantum systems is influenced by the chaotic dynamics of the corresponding classical system, using coupled kicked tops. The linear entropy for the subsystem (a kicked top) is employed as a measure of entanglement. A perturbative formula for the entanglement production rate is derived. The formula contains a correlation function that can be evaluated only from the information of uncoupled tops. Using this expression and the assumption that the correlation function decays exponentially which is plausible for chaotic tops, it is shown that the increment in the strength of chaos does not enhance the production rate of entanglement when the coupling is weak enough and the subsystems (kicked tops) are strongly chaotic. The result is confirmed by numerical experiments. The perturbative approach is also applied to a weakly chaotic region, where tori and chaotic sea coexist in the corresponding classical phase space, to reexamine a recent numerical study that suggests an intimate relationship between the linear stability of the corresponding classical trajectory and the entanglement production rate.

Quantum dynamics of N-methylacetamide studied by the vibrational configuration interaction method

Vibrational energy transfer of the amide I mode of N-methylacetamide (NMA) is studied theoretically using the vibrational configuration interaction method. A quartic force field of NMA is constructed at the B3LYP/6-31G+(d) level of theory and its accuracy is checked by comparing the resulting anharmonic frequencies with available theoretical and experimental values. Quantum dynamics calculations for the amide I mode excitation clarify the dominant energy transfer pathways, which sensitively depend on the anharmonic couplings among vibrational modes. A ratio of the anharmonic coupling to the frequency mismatch is employed to predict and interpret the dominant energy flow pathways.

Dynamic treatment of vibrational energy relaxation in a heterogeneous and fluctuating environment

A computational approach to describe the energy relaxation of a high-frequency vibrational mode in a fluctuating heterogeneous environment is outlined. Extending previous work [H. Fujisaki, Y. Zhang, and J. E. Straub, J. Chem. Phys. 124, 144910 (2006)], second-order time-dependent perturbation theory is employed which includes the fluctuations of the parameters in the Hamiltonian within the vibrational adiabatic approximation. This means that the time-dependent vibrational frequencies along a molecular dynamics trajectory are obtained via a partial geometry optimization of the solute with fixed solvent and a subsequent normal mode calculation. Adopting the amide I mode of N-methylacetamide in heavy water as a test problem, it is shown that the inclusion of dynamic fluctuations may significantly change the vibrational energy relaxation. In particular, it is found that relaxation occurs in two phases, because for short times (approximately < 200 fs) the spectral density appears continuous due to the frequency-time uncertainty relation, while at longer times the discrete nature of the bath becomes apparent. Considering the excellent agreement between theory and experiment, it is speculated if this behavior can explain the experimentally obtained biphasic relaxation the amide I mode of N-methylacetamide.

Quantum and classical vibrational relaxation dynamics of N-methylacetamide on ab initio potential energy surfaces†

Employing extensive quantum-chemical calculations at the DFT/B3LYP and MP2 level, quartic force fields of isolated N-methylacetamide are constructed. Taking into account 24 vibrational degrees of freedom, the model is employed to perform numerically exact vibrational configuration interaction calculations of the vibrational energy relaxation of the amide I mode. It is found that the energy transfer pathways may sensitively depend on details of the theoretical description. Moreover, the exact reference calculations were used to study the applicability and accuracy of (i) the quasiclassical trajectory method, (ii) time-dependent second-order perturbation theory, and (iii) the instantaneous normal mode description of frequency fluctuations. Based on the results, several strategies to describe vibrational energy relaxation in biomolecular systems are discussed.

Saturation of the production of quantum entanglement between weakly coupled mapping systems in a strongly chaotic region.

The production of quantum entanglement between weakly coupled mapping systems, whose classical counterparts are both strongly chaotic, is investigated. In the weak-coupling regime, it is shown that time-correlation functions of the unperturbed systems determine the entanglement production. In particular, we elucidate that the increment of the nonlinear parameter of coupled kicked tops does not accelerate the entanglement production in the strongly chaotic region. An approach to the dynamical inhibition of entanglement is suggested.

Spontaneous Polarization of Deuterated Dicalcium Strontium Propionate, Ca2Sr(C2D5CO2)6

The temperature dependence of the spontaneous polarization P S ( T ) of the deuterated dicalcium strontium propionate (DDSP) has been observed in a temperature range from room temperature to 240 K by the Sawyer-Towar method under a 60 Hz a.c. field. Near the ferroelectric transition point T C D , P S ( T ) is well-described by the relation P S ( T )∼( T C D - T ) 0.42 . The nondeuterated compound (DSP) also shows a similar dependence on temperature P S ( T )∼( T C H - T ) 0.40 , where T C H is the transition temperature of DSP. The distinct effect of deuteration is found on the magnitude of P S ; the ratio of P S of DDSP to that of DSP is about 0.7 at every temperature in the range considered here. A structural isotope effect is suggested to take place in the deuterated propionic molecules and/or in the network formed by metallic cations.

Different inhibitory potency of febuxostat towards mammalian and bacterial xanthine oxidoreductases: insight from molecular dynamics

Febuxostat, a drug recently approved in the US, European Union and Japan for treatment of gout, inhibits xanthine oxidoreductase (XOR)-mediated generation of uric acid during purine catabolism. It inhibits bovine milk XOR with a Ki in the picomolar-order, but we found that it is a much weaker inhibitor of Rhodobacter capsulatus XOR, even though the substrate-binding pockets of mammalian and bacterial XOR are well-conserved as regards to catalytically important residues and three-dimensional structure, and both permit the inhibitor to be accommodated in the active site, as indicated by computational docking studies. To clarify the reason for the difference of inhibitory potency towards the two XORs, we performed molecular dynamics simulations. The results indicate that differences in mobility of hydrophobic residues that do not directly interact with the substrate account for the difference in inhibitory potency.

Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review

Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein–ligand, protein–protein, and protein–DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration.