On the transferability of the SPCAL water model to biomolecular simulation

We investigated the performance of the recently developed SPC/L model for liquid water, as a pure liquid, in binary mixtures with DMSO, and as a solvent model in a peptide folding simulation. Additionally, in order to test the compatibility with the GROMOS biomolecular force field, free energies of hydration of a set of representative compounds were computed. The results are compared to those for the well established SPC water model, which is generally used as a solvent model in conjunction with the GROMOS force field already for more than two decades. It turns out that as a pure liquid and in binary mixtures with DMSO the SPC/L model outperforms SPC, whereas as solvent in combination with the GROMOS force field both models perform equally well

Engineered factor Xa variants retain procoagulant activity independent of direct factor Xa inhibitors

Thrombosis and Hemostasi

Constraint methods for determining pathways and free energy of activated processes

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach

OFraMP: a fragment-based tool to facilitate the parametrization of large molecules

An Online tool for Fragment-based Molecule Parametrization (OFraMP) is described. OFraMP is a web application for assigning atomic interaction parameters to large molecules by matching sub-fragments within the target molecule to equivalent sub-fragments within the Automated Topology Builder (ATB, atb.uq.edu.au) database. OFraMP identifies and compares alternative molecular fragments from the ATB database, which contains over 890,000 pre-parameterized molecules, using a novel hierarchical matching procedure. Atoms are considered within the context of an extended local environment (buffer region) with the degree of similarity between an atom in the target molecule and that in the proposed match controlled by varying the size of the buffer region. Adjacent matching atoms are combined into progressively larger matched sub-structures. The user then selects the most appropriate match. OFraMP also allows users to manually alter interaction parameters and automates the submission of missing substructures to the ATB in order to generate parameters for atoms in environments not represented in the existing database. The utility of OFraMP is illustrated using the anti-cancer agent paclitaxel and a dendrimer used in organic semiconductor devices. Graphical abstract: OFraMP applied to paclitaxel (ATB ID 35922).[Figure not available: see fulltext.

Improving the iterative linear interaction energy approach using automated recognition of configurational transitions.

Recently an iterative method was proposed to enhance the accuracy and efficiency of ligand-protein binding affinity prediction through linear interaction energy (LIE) theory. For ligand binding to flexible Cytochrome P450s (CYPs), this method was shown to decrease the root-mean-square error and standard deviation of error prediction by combining interaction energies of simulations starting from different conformations. Thereby, different parts of protein-ligand conformational space are sampled in parallel simulations. The iterative LIE framework relies on the assumption that separate simulations explore different local parts of phase space, and do not show transitions to other parts of configurational space that are already covered in parallel simulations. In this work, a method is proposed to (automatically) detect such transitions during the simulations that are performed to construct LIE models and to predict binding affinities. Using noise-canceling techniques and splines to fit time series of the raw data for the interaction energies, transitions during simulation between different parts of phase space are identified. Boolean selection criteria are then applied to determine which parts of the interaction energy trajectories are to be used as input for the LIE calculations. Here we show that this filtering approach benefits the predictive quality of our previous CYP 2D6-aryloxypropanolamine LIE model. In addition, an analysis is performed of the gain in computational efficiency that can be obtained from monitoring simulations using the proposed filtering method and by prematurely terminating simulations accordingly. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00894-015-2883-y) contains supplementary material, which is available to authorized users

To Polarize or not to Polarize? Charge-on-Spring versus KBFF models for water and methanol bulk and vapor-liquid interfacial mixtures.

Simulations of water and methanol mixtures using polarizable force fields (FFs) for methanol (COS/M and CPC) and water (COS/G2) were performed and compared to experiment and also to a nonpolarizable methanol (KBFF) model with SPC/E water in an effort to quantify the importance of explicit electronic polarization effects in bulk liquid mixtures and vapor–liquid interfaces. The bulk liquid mixture properties studied included the center of mass radial distribution functions, Kirkwood–Buff integrals (KBIs), volumetric properties, isothermal compressibility, enthalpy of mixing, dielectric constant, and diffusion coefficients. The vapor–liquid interface properties investigated included the relative surface probability distributions, surface tension, excess surface adsorption, preferred surface molecule orientations, and the surface dipole. None of the three FFs tested here was clearly superior for all of the properties examined. All the force fields typically reproduced the correct trends with composition for both the bulk and interfacial system properties; the differences between the force fields were primarily quantitative. The overall results suggest that the polarizable FFs are not, at the present stage of development, inherently better able to reproduce the studied bulk and interfacial propertiesdespite the added degree of explicit transferability that is, by definition, built into the polarizable models. Indeed, the specific parametrization of the FF appears to be just as important as the class of FF

CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations

Because of the large flexibility and malleability of Cytochrome P450 enzymes (CYPs), in silico prediction of CYP binding affinities to drugs and other xenobiotic compounds is a true challenge. In the current work, we use an iterative linear interaction energy (LIE) approach to compute CYP binding affinities from molecular dynamics (MD) simulation. In order to improve sampling of conformational space, we combine results from simulations starting with different relevant protein-ligand geometries. For calculated binding free energies of a set of thiourea compounds binding to the flexible CYP 2D6 isoform, improved correlation with experiment was obtained by combining results ofMDruns starting from distinct protein conformations and ligand-binding orientations. This accuracy was obtained from relatively short MD simulations, which makes our approach computationally attractive for automated calculations of ligand-binding affinities to flexible proteins such as CYPs. © 2013 by the authors; licensee MDPI, Basel, Switzerland

DFT benchmark study for the oxidative addition of CH4 to Pd. Performance of various density functionals

We have evaluated the performance of 24 popular density functionals for describing the potential energy surface (PES) of the archetypal oxidative addition reaction of the methane C-H bond to the palladium atom by comparing the results with our recent ab initio [CCSD(T)] benchmark study of this reaction. The density functionals examined cover the local density approximation (LDA), the generalized gradient approximation (GGA), meta-GGAs as well as hybrid density functional theory. Relativistic effects are accounted for through the zeroth-order regular approximation (ZORA). The basis-set dependence of the density-functional-theory (DFT) results is assessed for the Becke-Lee-Yang-Parr (BLYP) functional using a hierarchical series of Slater-type orbital (STO) basis sets ranging from unpolarized double-ζ (DZ) to quadruply polarized quadruple-ζ quality (QZ4P). Stationary points on the reaction surface have been optimized using various GGA functionals, all of which yield geometries that differ only marginally. Counterpoise-corrected relative energies of stationary points are converged to within a few tenths of a kcal/mol if one uses the doubly polarized triple-ζ (TZ2P) basis set and the basis-set superposition error (BSSE) drops to 0.0 kcal/mol for our largest basis set (QZ4P). Best overall agreement with the ab initio benchmark PES is achieved by functionals of the GGA, meta-GGA, and hybrid-DFT type, with mean absolute errors of 1.3-1.4 kcal/mol and errors in activation energies ranging from +0.8 to -1.4 kcal/mol. Interestingly, the well-known BLYP functional compares very reasonably with an only slightly larger mean absolute error of 2.5 kcal/mol and an underestimation by -1.9 kcal/mol of the overall barrier (i.e., the difference in energy between the TS and the separate reactants). For comparison, with B3LYP we arrive at a mean absolute error of 3.8 kcal/mol and an overestimation of the overall barrier by 4.5 kcal/mol. © 2005 Elsevier B.V. All rights reserved

A Comparison Between QM/MM And QM/QM Based Fitting of Condensed-Phase Atomic Polarizabilities

Recently we reported a combined QM/MM approach to estimate condensed-phase values of atomic polarizabilities for use in (bio)molecular simulation. The setup relies on a MM treatment of the solvent when determining atomic polarizabilities to describe the response of a QM described solute to its external electric field. In this work, we study the effect of using alternative descriptions of the solvent molecules when evaluating atomic polarizabilities of a methanol solute. In a first step, we show that solute polarizabilities are not significantly affected upon substantially increasing the MM dipole moments towards values that are typically reported in literature for water solvent molecules. Subsequently, solute polarization is evaluated in the presence of a QM described solvent (using the frozen-density embedding method). In the latter case, lower oxygen polarizabilities were obtained than when using MM point charges to describe the solvent, due to introduction of Pauli-repulsion effects. This journal is © the Partner Organisations 2014