Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields

Summary A methodology aimed at improving the accuracy of current docking–scoring procedures is proposed, and validated through detailed tests of its performance in predicting the activity of HIV-1 protease inhibitors. This methodology is based on molecular dynamics simulations using a force field whose effective charges are refined by means of a novel procedure that relies on quantum-mechanical calculations and preserves the internal consistency of the parameterization scheme.     

Development of the force field parameters for phosphoimidazole and phosphohistidine

Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule--a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent.     

Real bounds, ergodicity and negative Schwarzian for multimodal maps

We consider smooth multimodal maps which have finitely many non-flat critical points. We prove the existence of real bounds. From this we obtain a new proof for the non-existence of wandering intervals, derive extremely useful improved Koebe principles, show that high iterates have `negative Schwarzian derivative' and give results on ergodic properties of the map. One of the main complications in the proofs is that we allow to have inflection points.

     

A Cosmological Model of Holographic Brane Gravity

A cosmological scenario with two branes (A and B) moving in a 5-dimensional bulk is considered. As in the case of ecpyrotic and born-again braneworld models it is possible that the branes collide. The energy-momentum tensor is taken to describe a perfect barotropic fluid on the A-brane and a phenomenological time-dependent cosmological constant on the B-brane. The A-brane is identified with our Universe and its cosmological evolution in the approximation of a homogeneous and isotropic brane is analysed. The dynamics of the radion (a scalar field on the brane) contains information about the proper distance between the branes. It is demonstrated that the deSitter type solutions are obtained for late time evolution of the braneworld and accelerative behaviour is anticipated at the present time.     

On a Theorem of Høegh-Krohn

A theorem proved by R. Høegh-Krohn in Comm. Math. Phys. 38(1974), 195–224, which yields a possibility to define states of systems of quantum particles by their values on the products , where \mathfraka _t , t are time automorphisms and F _j are multiplication operators, is generalized and extended. In particular, it is shown that the algebras generated by such products with F _j taken from the families of multiplication operators satisfying certain conditions are dense in the algebras of observables in the -weak topology, in which normal states are continuous. This result was obtained for the systems with two types of kinetic energy: the usual one expressed by means of the Laplacian; the relativistic kinetic energy defined by a pseudo-differential operator.     

Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics

The present study describes an extensive conformational search of substance P using two different computational methods. On the one hand, the peptide was studied using the iterative simulated annealing, and on the other, molecular dynamics simulations at 300 and 400 K. With the former method, the peptide was studied in vacuo with a dielectric constant of 80, whereas using the latter study the peptide was studied in a box of TIP3P water molecules. Analysis of the results obtained using both methodologies was carried out using an in-house methodology using a cluster analysis method based on information theory. Comparison of the two sampling methodologies and the different environment used in the calculations is also analyzed. Finally, the conformational motifs that are characteristic of substance P in a hydrophilic environment are presented and compared with the experimental results available in the literature.     

35MeV/u36Ar+124Sn反应中类弹产物的同位素分布特性

测量了35MeV/u³⁶Ar+¹²⁴Sn反应中5.3°处类弹产物的同位素分布,观察到随着出射动能的增加,产物的平均中质比逐渐减小而接近弹核的平均中质比.同位旋相关的量子分子动力学计算表明,随着反应时间的增加,类弹产物的平均出射动能逐渐减小而平均N/Z值则逐渐增大.另外,碰撞参数也影响类弹产物的同位素组成:随着碰撞参数的减小,类弹产物的平均N/Z值减小.     

The Percolation Transition for the Zero-Temperature Stochastic Ising Model on the Hexagonal Lattice

On the planar hexagonal lattice , we analyze the Markov process whose state (t), in , updates each site v asynchronously in continuous time t0, so that _v (t) agrees with a majority of its (three) neighbors. The initial _v (0)'s are i.i.d. with P[ _v (0)=+1]=p[0,1]. We study, both rigorously and by Monte Carlo simulation, the existence and nature of the percolation transition as t and p1/2. Denoting by ⁺(t,p) the expected size of the plus cluster containing the origin, we (1) prove that ⁺(,1/2)= and (2) study numerically critical exponents associated with the divergence of ⁺(,p) as p1/2. A detailed finite-size scaling analysis suggests that the exponents and of this t= (dependent) percolation model have the same values, 4/3 and 43/18, as standard two-dimensional independent percolation. We also present numerical evidence that the rate at which (t)() as t is exponential.     

Probing the Conformational Stability of Two Different Copper Proteins: A Dynamic Fluorescence Study on Azurin and Ascorbate Oxidase

Tryptophan fluorescence is extremely useful to monitor structural conformational transitions in proteins. Denaturant-induced unfolding of azurin and ascorbate oxidase has been studied by dynamic fluorescence measurements in the frequency domain and the results have been interpreted in terms of continuous distribution of lifetimes. The data add new information on the unfolding mechanism that was previously analyzed by steady-state emission spectroscopy. In particular, the existence of multiple, parallel unfolding pathways may be envisaged and correlated, in both cases, to the two protein structures. The effect of metal depletion has been also characterized by fluorescence lifetime measurements. In the case of azurin, a monomeric protein, the data demonstrate that copper removal yields a totally different unfolding pathways with respect to the holo protein, indicating that metal ion plays a fundamental structural role in the wild type, native protein. In the case of ascorbate oxidase a dimer of 140 kDa, only minor effects have been detected by copper removal. However, the analysis of the fluorescence decay in presence of different amounts of guanidinium hydrochloride gives new important insights on the unfolding intermediates. In particular the data support the hypothesis of a partial exposure of an outer layer of dimer at intermediate denaturant concentration. This ability of dynamic fluorescence to pinpoint the presence of structural micro-heterogeneity in the unfolding pathways of proteins demonstrates the greater power of this technique compared to the most commonly used steady-state measurements.     

Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

By using distributed computing techniques and a supercluster of more than 20,000 processors we simulated folding of a 20-residue Trp Cage miniprotein in atomistic detail with implicit GB/SA solvent at a variety of solvent viscosities (gamma). This allowed us to analyze the dependence of folding rates on viscosity. In particular, we focused on the low-viscosity regime (values below the viscosity of water). In accordance with Kramers' theory, we observe approximately linear dependence of the folding rate on 1/gamma for values from 1-10(-1)x that of water viscosity. However, for the regime between 10(-4)-10(-1)x that of water viscosity we observe power-law dependence of the form k approximately gamma(-1/5). These results suggest that estimating folding rates from molecular simulations run at low viscosity under the assumption of linear dependence of rate on inverse viscosity may lead to erroneous results.