Brownian ratchet mechanism of translocation in T7 RNA polymerase facilitated by a post-translocation energy bias arising from the conformational change of the enzyme

T7 RNA polymerase can transcribe DNA to RNA by translocating along the DNA. Structural studies suggest that the pivoting rotation of the O helix in the fingers domain may drive the movement of the O helix C-terminal Tyr639 from pre- to post-translocation positions. In a series of all-atom molecular dynamics simulations, we show that the movement of Tyr639 is not tightly coupled to the rotation of the O helix, and that the two processes are only weakly dependent on each other. We also show that the internal potential of the enzyme itself generates a small difference in free energy (ΔE) between the post- and pre-translocation positions of Tyr639. The calculated value of ΔE is consistent with that obtained from single-molecule experimental data. These findings lend support to a model in which the translocation takes place via a Brownian ratchet mechanism, with the small free energy bias ΔE arising from the conformational change of the enzyme itself.     

Unravelling the mechanism of RNA-polymerase forward motion by using mechanical force

Polymerases form a class of enzymes that act as molecular motors as they move along their nucleic acid substrate during catalysis, incorporating nucleotide triphosphates at the end of the growing chain and consuming chemical energy. A debated issue is how the enzyme converts chemical energy into motion [J. Gelles and R. Landick, Cell 93, 13 (1998)]. In a single molecule assay, we studied how an opposing mechanical force affects the translocation rate of T7 RNA polymerase. Our measurements show that force acts as a competitive inhibitor of nucleotide binding. This result is interpreted in the context of possible models, and with respect to published crystal structures of T7 RNA polymerase. The transcribing complex appears to utilize only a small fraction of the energy of hydrolysis to perform mechanical work, with the remainder being converted to heat.     

Coupled dynamics of RNA folding and nanopore translocation

The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base pairing theoretically, using kinetic Monte Carlo simulations and analytical methods. We find that the transient formation of base pairs that do not occur in the ground state can significantly speed up translocation.     

Density functional study of the phosphate diester hydrolysis of RNA in RNA/DNA hybrid by RNase HI

Ribonuclease HI (RNase HI) catalyses the non-specific hydrolysis of RNA in an RNA/DNA hybrid. This enzyme is found in almost all organisms and involved in replication initiation and DNA topology restoration. A similar fold has been observed in other enzymes such as DNA transposases. In particular, RNases HI has emerged as important therapeutic targets because the enzymatic activity is absolutely required for proliferation of HIV and other retroviruses. The X-ray crystallographic structures of RNase HI revealed that the Mg²⁺ ion is essential for the enzymatic reaction and that Asp and Glu coordinate to the Mg²⁺ ion. There are, however, controversies about the catalytic mechanism of RNase HI, the number of Mg²⁺ ions, the proton transfer pathway, and the protonation states of the active site residues. In the present study, we have explored the hydrolysis of the phosphate diester group of RNA by RNase HI using density functional theory to elucidate how many Mg²⁺ ions are required for the catalysis of RNase HI. Our computation demonstrates that both one- and two-metal models show the stepwise hydrolysis pathway via a pentacovalent intermediate. However, the activation barrier of the two-metal model is lower than that of the one-metal model by 11.7 kcal/mol.     

Nonequilibrium phase transitions associated with DNA replication

Thermodynamics governing the synthesis of DNA and RNA strands under a template is considered analytically and applied to the population dynamics of competing replicators. We find a nonequilibrium phase transition for high values of polymerase fidelity in a single replicator, where the two phases correspond to stationary states with higher elongation velocity and lower error rate than the other. At the critical point, the susceptibility linking velocity to thermodynamic force diverges. The overall behavior closely resembles the liquid-vapor phase transition in equilibrium. For a population of self-replicating macromolecules, Eigen's error catastrophe transition precedes this thermodynamic phase transition during starvation. For a given thermodynamic force, the fitness of replicators increases with increasing polymerase fidelity above a threshold.     

Computational study of the force dependence of phosphoryl transfer during DNA synthesis by a high fidelity polymerase

High fidelity polymerases are efficient catalysts of phosphodiester bond formation during DNA replication or repair. We interpret molecular dynamics simulations of a polymerase bound to its substrate DNA and incoming nucleotide using a quasiharmonic model to study the effect of external forces applied to the bound DNA on the kinetics of phosphoryl transfer. The origin of the force dependence is shown to be an intriguing coupling between slow, delocalized polymerase-DNA modes and fast catalytic site motions. Using noncognate DNA substrates we show that the force dependence is context specific.     

重新审视桥式吸附甲酸根在铂电极上电催化氧化甲酸过程中的作用 (cited: 2)

基于以前报道的电化学原位ATR-FTIRS数据(Langmuir 22,10399 (2006)和Angewa. Chem. Int. Ed., 50,1159 (2011)),详细讨论了甲酸在铂电极上电催化氧化机理及动力学过程．提出了直接反应路径的动力学模型,即甲酸吸附(同时C-H键活化)作为此反应的决速步骤,此反应路径贡献甲酸氧化反应的大部分电流．该动力学模型可以很好地拟合在无CO毒化影响和浓度在0.1 mol/L以下的红外光谱结果．这种机理预测了甲酸氧化直接途径可能只需要一个Pt原子作为反应位点,甲酸根阻碍活性位点,并非为反应中间物．另外还详细检验了之前其他小组曾提出的甲酸根途径(一级或二级反应)为甲酸氧化直接途径,并指出了引起分歧的原因．     

Quantum state of muon and proton in crystalline silicon

Quantum state and dynamics of muon and proton in crystalline silicon have been studied by solving one‐particle Schrödinger equations for the impurities. The ground state wavefunctions and energies are determined as a function of local distortion of the host Si lattice, where the Si–H interaction we used is that parameterized by Ramírez and Herrero following the results of earlier pseudopotential‐density‐functional calculation. It is shown that quantum zero‐point motion of muon induces an effective potential barrier between the tetrahedral‐symmetry (T) site and the bond‐center (BC) site, which ensures bistability of muonium states observed in experiments. It is also shown that, if we fully consider the quantum effect with the present model potential, the BC site becomes less stable than the T site on the contrary to the experiments and former theoretical calculations.     

Direct proton transfer in a putative L-state intermediate of the bacteriorhodopsin photocycle

In the light-driven proton pump bacteriorhodopsin, photoisomerization of the all-trans retinal chromophore triggers a photocycle whose net effect is the transfer of one proton from the cytoplasmic to the extracellular side of the membrane. The first proton transfer step, from the retinal Schiff base to Asp85, occurs between the L and M intermediate states. Details of the geometry of the retinal binding region are important for the pathway followed by the proton. Here we report some preliminary results on combined Quantum Mechanical/Molecular Mechanical reaction path calculations for retinal deprotonation and discuss the hydrogen-bonding pattern in the active site.     

Size selected growth of nanodots: effects of growth kinetics and energetics on the formation of stationary size distributions

The size selection of nanodots during the growth is studied by using a reaction kinetic model, where reaction rates depend on the dot size. The characteristic feature of the reaction rates is the energetics, where the free energy of dots has a minimum at the certain dot size. The model equations are solved by using a particle coalescence simulation method. We find phenomenologically three distinct stages of growth. First, during the initial deposition stage, distributions with high density of small dots occur. Second, there is an intermediate and short-lived stationary state, which is controlled by kinetics of growth. Third, a long-lived stationary state is obtained, with nearly Gaussian size distributions, mostly determined by the energetics of the growth but also significantly affected by the kinetics. In the final stage, size selection and narrowing of the distributions occur. It is also shown that in the final stage of growth the Fokker-Planck type continuum model describes well the evolution of the distributions and the size selection.     

Theoretical study of the mechanism of cycloaddition reaction between dichloromethylene silylene and formaldehyde

The mechanism of cycloaddition reaction between singlet dichloromethylene silylene and formaldehyde has been investigated using a MP2/6-31G* method, including geometry optimization and vibrational analysis for the stationary points on the potential energy surface. The energies of different conformations are calculated by CCSD(T)//MP2/6-31G* method. From the potential energy profile, it can be predicted that the cycloaddition reaction between singlet dichloromethylene silylene and formaldehyde has three competitive dominant reaction channels: (1) the two reactants first form a highly strained three-membered ring intermediate INT1c, which then isomerizes to an active four-membered ring product P1 via a transition state TS1c by ring-increasing reaction; Subsequently, P1 further reacts with formaldehyde to form the more stable silapolycyclic product P2; (2) the two reactants first form a four-membered ring intermediate INT1b by the [2?+?2] cycloaddition reaction, which then isomerizes to the four-membered ring product P3.1 via a transition state TS3.1, resulting from the chlorine transfer reaction; (3) INT1b further reacts with formaldehyde to form a silapolycyclic intermediate INT4, which then isomerizes to a silapolycyclic product P₄ via a transition state TS4.     

Implementation Scheme of Two-Photon Post-Quantum Correlations

The pre-and post-selection processes of the "two-state vector formalism" lead to a fair sampling loophole in Bell test, so it can be used to simulate post-quantum correlations. In this paper, we propose a physical implementation of such a correlation with the help of quantum non-demolition measurement, which is realized via the cross-Kerr nonlinear interaction between the signal photon and a probe coherent beam. The indirect measurement on the polarization state of photon is realized by the direct measurement on the phase shift of the probe coherent beam, which enhances the detection efficiency greatly and leaves the signal photon unabsorbed. The maximal violation of the CHSH inequality 4 can be achieved by pre-and post-selecting maximally entangled states. The reason why we can get the post-quantum correlation is that the selection of the results after measurement opens fair-sampling loophole. The fair-sampling loophole opened here is different from the one usually used in the currently existing simulation schemes for post-quantum correlations,which are simulated by selecting the states to be measured or enlarging the Hilbert space. So, our results present an alternative way to mimic post-quantum correlations.