Molecular Dynamics of HIV1-Integrase in Complex with 93del - A Structural Perspective on the Mechanism of Inhibition

HIV1 integrase is an important target for the antiviral therapy. Guanine-rich quadruplex, such as 93del, have been shown to be potent inhibitors of this enzyme and thus representing a new class of antiviral agents. Although X-ray and NMR structures of HIV1 integrase and 93del have been reported, there is no structural information of the complex and the mechanism of inhibition still remains unexplored. A number of computational methods including automated protein-DNA docking and molecular dynamics simulation in explicit solvent were used to model the binding of 93del to HIV1 integrase. Analysis of the dynamic behaviour of the complex using principal components analysis and elastic network modelling techniques allow us to understand how the binding of 93del aptamer and its interactions with key residues affect the intrinsic motions of the catalytic loops by stabilising them in catalytically inactive conformations. Such insights into the structural mechanism of inhibition can aid in improving the design of anti-HIV aptamers.

Conformational Dynamics of the Human Propeller Telomeric DNA Quadruplex on a Microsecond Time Scale

The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. While G-quartet stems have been well characterised, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 µs. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A:A base pair, triad, pentad and hexad. The results present a threshold in quadruplex simulations, with regards to understanding the flexible nature of the sugar-phosphate backbone in formation of unusual architecture within the topology. Furthermore, this study stresses the importance of simulation time in sampling conformational space for this topology.

A self-learning algorithm for biased molecular dynamics

A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias potential in terms of a patchwork of one-dimensional, locally valid collective coordinates. These collective coordinates are obtained from trajectory analyses so that they adapt to any new features encountered during the simulation. We show how this methodology can be used to enhance sampling in real chemical systems citing examples both from the physics of clusters and from the biological sciences.

A Molecular Dynamics Study of the Early Stages of Calcium Carbonate Growth

The precipitation of calcium carbonate in water has been examined using a combination of molecular dynamics and umbrella sampling. During 20 ns molecular dynamics trajectories at elevated calcium carbonate concentrations, amorphous particles are observed to form and appear to be composed of misaligned domains of vaterite and aragonite. The addition of further calcium ions to these clusters is found to be energetically favorable and virtually barrierless. By contrast, there is a large barrier to the addition of calcium to small calcite crystals. Thus, even though calcite nanocrystals are stable in solution, at high supersaturations, particles of amorphous material form because this material grows much faster than ordered calcite nanocrystals.

Comparison of dynamics of wildtype and V94M human UDP-galactose 4-epimerase-A computational perspective on severe epimerase-deficiency galactosemia

UDP-galactose 4'-epimerase (GALE) catalyzes the interconversion of UDP-galactose and UDP-glucose, an important step in galactose catabolism. Type III galactosemia, an inherited metabolic disease, is associated with mutations in human GALE. The V94M mutation has been associated with a very severe form of type III galactosemia. While a variety of structural and biochemical studies have been reported that elucidate differences between the wildtype and this mutant form of human GALE, little is known about the dynamics of the protein and how mutations influence structure and function. We performed molecular dynamics simulations on the wildtype and V94M enzyme in different states of substrate and cofactor binding. In the mutant, the average distance between the substrate and both a key catalytic residue (Tyr157) and the enzyme-bound NAD(+) cofactor and the active site dynamics are altered making substrate binding slightly less stable. However, overall stability or dynamics of the protein is not altered. This is consistent with experimental findings that the impact is largely on the turnover number (kcat), with less substantial effects on Km. Active site fluctuations were found to be correlated in enzyme with substrate bound to just one of the subunits in the homodimer suggesting inter-subunit communication. Greater active site loop mobility in human GALE compared to the equivalent loop in Escherichia coli GALE explains why the former can catalyze the interconversion of UDP-N-acetylgalactosamine and UDP-N-acetylglucosamine while the bacterial enzyme cannot. This work illuminates molecular mechanisms of disease and may inform the design of small molecule therapies for type III galactosemia.

Molecular dynamics simulation of nanoindentation of Fe3C and tetrahedral Fe4C

Study of nanomechanical response of iron carbides is important because presence of iron carbides greatly influences the performance and longevity of steel components. This work contributes to the literature by exploring nanoindentation of nanocrystalline Fe3C and tetrahedral-Fe4C using molecular dynamics simulation. The chemical interactions of iron and carbon were described through an analytical bond order inter-atomic potential (ABOP) energy function. The indentations were performed at an indentation speed of 50 m/sec and a repeat trial was performed at 5 m/sec. Load-displacement (P-h) curve for both these carbides showed residual indentation depth and maximum indentation depth (hf/hmax) ratio to be higher than 0.7 i.e. a circumstance where Oliver and Pharr method was not appropriate to be applied to evaluate the material properties. Alternate evaluation revealed Fe3C to be much harder than Fe4C. Gibbs free energy of formation and radial distribution function, coupled with state of the average local temperature and von Mises stresses indicate the formation of a new phase of iron-carbide. Formation of this newer phase was found to be due to deviatoric strain rather than the high temperature induced in the substrate during nanoindentation

Robust nonadiabatic molecular dynamics for metals and insulators

We present a new formulation of the correlated electron-ion dynamics (CEID) scheme, which systematically improves Ehrenfest dynamics by including quantum fluctuations around the mean-field atomic trajectories. We show that the method can simulate models of nonadiabatic electronic transitions and test it against exact integration of the time-dependent Schrodinger equation. Unlike previous formulations of CEID, the accuracy of this scheme depends on a single tunable parameter which sets the level of atomic fluctuations included. The convergence to the exact dynamics by increasing the tunable parameter is demonstrated for a model two level system. This algorithm provides a smooth description of the nonadiabatic electronic transitions which satisfies the kinematic constraints (energy and momentum conservation) and preserves quantum coherence. The applicability of this algorithm to more complex atomic systems is discussed.

Influence of temperature on the anisotropic cutting behaviour of single crystal silicon: A molecular dynamics simulation investigation

Using molecular dynamics (MD) simulation, this paper investigates anisotropic cutting behaviour of single crystal silicon in vacuum under a wide range of substrate temperatures (300 K, 500 K, 750 K, 850 K, 1173 K and 1500 K). Specific cutting energy, force ratio, stress in the cutting zone and cutting temperature were the indicators used to quantify the differences in the cutting behaviour of silicon. A key observation was that the specific cutting energy required to cut the (111) surface of silicon and the von Mises stress to yield the silicon reduces by 25% and 32%, respectively, at 1173 K compared to what is required at 300 K. The room temperature cutting anisotropy in the von Mises stress and the room temperature cutting anisotropy in the specific cutting energy (work done by the tool in removing unit volume of material) were obtained as 12% and 16% respectively. It was observed that this changes to 20% and 40%, respectively, when cutting was performed at 1500 K, signifying a very strong correlation between the anisotropy observed during cutting and the machining temperature. Furthermore, using the atomic strain criterion, the width of primary shear zone was found to vary with the orientation of workpiece surface and temperature i.e. it remains narrower while cutting the (111) surface of silicon or at higher machining temperatures. A major anecdote of the study based on the potential function employed in the study is that, irrespective of the cutting plane or the cutting temperature, the state of the cutting edge of the diamond tool did not show direct diamond to graphitic phase transformation.

Molecular dynamics simulation investigation on the plastic flow behaviour of silicon during nanometric cutting

Molecular dynamics (MD) simulation was carried out to acquire an in-depth understanding of the flow behaviour of single crystal silicon during nanometric cutting on three principal crystallographic planes and at different cutting temperatures. The key findings were that (i) the substrate material underneath the cutting tool was observed for the first time to experience a rotational flow akin to fluids at all the tested temperatures up to 1200 K. (ii) The degree of flow in terms of vorticity was found higher on the (1 1 1) crystal plane signifying better machinability on this orientation in accord with the current pool of knowledge (iii) an increase in the machining temperature reduces the springback effect and thereby the elastic recovery and (iv) the cutting orientation and the cutting temperature showed significant dependence on the location of the stagnation region in the cutting zone of the substrate.

A disappearing act performed by magnesium: the nucleotide exchange mechanism of Ran GTPase by Quantum mechanics/Molecular mechanics studies

The Ran GTPase protein is a guanine nucleotide-binding protein (GNBP) with an acknowledged profile in cancer onset, progression and metastases. The complex mechanism adopted by GNBPs in exchanging GDP for GTP is an intriguing process and crucial for Ran viability. The successful completion of the process is a fundamental aspect of propagating downstream signalling events. QM/MM molecular dynamics simulations were employed in this study to provide a deeper mechanistic understanding of the initiation of nucleotide exchange in Ran. Results indicate significant disruption of the metal-binding site upon interaction with RCC1 (the Ran guanine nucleotide exchange factor), overall culminating in the prominent shift of the divalent magnesium ion. The observed ion drifting is reasoned to occur as a consequence of the complex formation between Ran and RCC1 and is postulated to be a critical factor in the exchange process adopted by Ran. This is the first report to observe and detail such intricate dynamics for a protein in Ras superfamily.

Equilibrium polymerization of cyclic carbonate oligomers

A model of the polymerization of ring oligomers of bisphenol A polycarbonate (BPA-PC) is used to investigate the influence of dimensionality (2D or 3D), density and temperature on the size distribution of the polymer chains. The polymerization step is catalyzed by a single active particle, conserves the number and type of the chemical bonds, and occurs without a significant gain in either potential energy or configurational entropy. Monte Carlo and molecular dynamics simulations show that polymerization of cyclic oligomers occurs readily at high density and is driven by the entropy associated with the distribution of interparticle bonds. Polymerization competes at lower densities with long range diffusion, which favors small molecular species, and is prevented if the system is sufficiently dilute. Polymerization occurs in 2D via a weakly first order transition as a function of density and is characterized by low hysteresis and large fluctuations in the size of polymer chains. Polymerization occurs more readily in 3D than in 2D, and is favored by increasing temperature, as expected for an entropy-driven process. (C) 2001 American Institute of Physics.

Concertedness and solvent effects in multiple proton transfer reactions: The formic acid dimer in solution

The issue of multiple proton transfer (PT) reactions in solution is addressed by performing molecular dynamics simulations for a formic acid dimer embedded in a water cluster. The reactant species is treated quantum mechanically, within a density functional approach, while the solvent is represented by a classical model. By constraining different distances within the dimer we analyze the PT process in a variety of situations representative of more complex environments. Free energy profiles are presented, and analyzed in terms of typical solvated configurations extracted from the simulations. A decrease in the PT barrier height upon solvation is rationalized in terms of a transition state which is more polarized than the stable states. The dynamics of the double PT process is studied in a low-barrier case and correlated with solvent polarization fluctuations. Cooperative effects in the motion of the two protons are observed in two different situations: when the solvent polarization does not favor the transfer of one of the two protons and when the motion of the two protons is not synchronized. This body of observations is correlated with local structural and dynamical properties of the solvent in the vicinity of the reactant. (C) 2000 American Institute of Physics. [S0021-9606(00)51121-0].

Simulation of the surface structure of butylmethylimidazolium ionic liquids

Molecular dynamics simulations of the liquid/vacuum surfaces of the room temperature ionic liquids [bmim][PF6], [bmim][BF4] and [bmim][Cl] have been carried out at various temperatures. The surfaces are structured with a top monolayer containing oriented cations and anions. The butyl side chains tend to face the vacuum and the methyl side chains the liquid. However, as the butyl chains are not densely packed, both anions and rings are visible from the vacuum phase. The effects of temperature and the anion on the degree of cation orientation is small, but the potential drop from the vacuum to the interior of the liquid is greater for liquids with smaller anions. We compare the simulation results with a range of experimental observations and suggest that neutron reflection from samples with protiated butyl groups would be a sensitive probe of the structure.

Polarization Relaxation in an Ionic Liquid Confined between Electrified Walls

The response of a room temperature molten salt to an external electric field when it is confined to a nanoslit is studied by molecular dynamics simulations. The fluid is confined between two parallel and oppositely charged walls, emulating two electrified solid-liquid interfaces. Attention is focused on structural, electrostatic, and dynamical properties, which are compared with those of the nonpolarized fluid. It is found that the relaxation of the electrostatic potential, after switching the electric field off, occurs in two stages. A first, subpicosecond process accounts for 80% of the decay and is followed by a second subdiffusive process with a time constant of 8 ps. Diffusion is not involved in the relaxation, which is mostly driven by small anion translations. The relaxation of the polarization in the confined system is discussed in terms of the spectrum of charge density fluctuations in the bulk.