Steered molecular dynamics simulations of protein-ligand interactions

Molecular recognition and specific protein-ligandinteractions are central to many biochemical processes,such as enzyme catalysis, assembly of organelles, en-ergy transduction, signaling, diverse control functions,and replication, expression and storage of the geneticmaterial[1]. Moreover, protein-ligand interactions pro-vide the mechanism of many drug therapies and un-derstanding of such interactions is thus significant forrational drug design[1,2]. For the experimental studiesof protein-ligan…     

Atomistic molecular dynamics simulations on the interaction of TEMPO-oxidized cellulose nanofibrils in water

Atomistic molecular dynamics simulations were carried out to obtain information on the rheological, aggregation and disintegration properties of carboxylated (TEMPO-oxidized) cellulose nanofibrils with different functionalization levels. The magnitude of the inter-fibril interaction was quantified for parallel nanofibrils using the umbrella sampling method. The obtained potential of mean force was found highly sensitive to the charge configuration for intermediate functionalization levels. This feature was further studied with an electrostatic model for similar charge configurations and system periodicity as in the case of the molecular dynamics simulations. The electrostatic contribution of the charged surfaces varied from repulsive to attractive depending on the distribution of the carboxylate groups and nearby counter-ions, as well as the distance between the fibrils. The simulated deviations from average behavior for single fibrils in both models suggest heterogeneity in their aggregation and disintegration behavior. This was seen in disintegration experiments, where the differences in disintegration energy and in the structural variation qualitatively agreed with the model predictions. As to aggregation behavior, the studied case with parallel fibrils reflects the upper boundary of the repulsive interaction.     

Atomic-scale investigation of the interaction between coniferyl alcohol and laccase for lignin degradation using molecular dynamics simulations and spectroscopy

The interaction between coniferyl alcohol (CA) and laccase (LAC) was investigated using molecular dynamics (MD) simulations and spectral experiments. The mode of interaction between CA and LAC was established by MD simulations. The micro-environmental changes, stability and rigidity of the LAC-CA system were assessed by relevant parameters. These parameters include root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radius of gyration (Rg). The calculated binding free energy (ΔG_binding=??19.99?kcal·mol.^?1), the van der waals (VDW) contribution (ΔG_vdw=?23.99?kcal·mol^?1) and the electrostatic energy (ΔG_ele=?23.09?kcal·mol^?1) of LAC-CA system demonstrated that the interaction of LAC-CA was a spontaneous process and the main interaction forces were van der Waal's and electrostatic forces. The values of ΔG_vdw and ΔG_ele were negative, which demonstrated that VDW interactions and electrostatic interactions were favorable for the binding of CA and LAC. The binding constants, thermodynamic parameters, molecular force types and binding distances confirmed the interaction between CA and LAC and further verified the rationality of the theoretical model by spectral experiments. The MD simulations and experimental approaches provide clues for the discovery of new mediators and useful references for the mechanism of microbial degradation of lignin and industrialization of lignocellulose.     

Observations concerning the treatment of long-range interactions in molecular dynamics simulations

Molecular dynamics simulations of pure water employing two different empirical water models have been used to study the effects of different methods for truncation of long-range interactions in molecular mechanics calculations. As has been observed previously in integral equation studies, “shifting” these interactions on an atom-by-atom basis was found to produce artificial structuring in the water and affect diffusion rates. In cases where some form of short-range truncation must be used, the ST2 switching function applied on a group-by-group basis was found to be the most realistic procedure. If atom-based shifting must be employed, a cutoff distance greater than or equal to 12.0 Å was found to be required to produce realistic results. © 1993 John Wiley & Sons, Inc.     

Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: molecular dynamics simulations

A set of all-atom molecular dynamics simulations have been performed to better understand critical phenomena regarding a Hofmeister series of anions and lipid bilayers. The simulations isolate the effect of anion size and show clear differences in the interactions with the dipolar phoshpatidylcholine headgroup. Cl- anions penetrate into the headgroup region of the bilayer, but the simulations confirm theories which predict that larger anions penetrate more deeply, into a more heterogeneous and hydrophobic molecular region. That anion size leads to such differences in partitioning in the bilayer provides atomic-level support to hypotheses inspired by several experimental studies. The ability of larger anions to bury deep within the bilayer is correlated with a less well-structured hydration shell, shedding of which upon penetration incurs a smaller penalty for the larger anions than for Cl-.     

Characterizing the dynamics and ligand-specific interactions in the human leukocyte elastase through molecular dynamics simulations

The human leukocyte elastase (HLE), a neutrophil serine protease of the chymotrypsin superfamily, is a major therapeutic target for a number of inflammatory diseases, such as chronic obstructive pulmonary disease (COPD). In this work, we present a comparative explicit water molecular dynamics (MD) study on the free and inhibitor-bound HLE. Knowledge of the flexibility and conformational changes induced by this irreversible inhibitor, whether in a prebound stage or covalently bound at the enzyme binding site, encases fundamental biological interest and is particularly relevant to ongoing structure-based drug design studies. Our results suggest that HLE operates by an induced-fit mechanism with direct intervention of a surface loop which is open toward the solvent in the free enzyme and closed while in the presence of the ligand. MM-PBSA free energy calculations furthermore elucidate the energetic contributions to the distinct conformations adopted by this loop. Additionally, a survey of the major contributions to the inhibitor binding free energies was attained. Our findings enforce the need to account for HLE flexibility, whether through the use of MD-generated ensembles of HLE conformations as targets for molecular docking or via sophisticated flexible-docking algorithms. We anticipate that inclusion of the observed HLE dynamic behavior into future drug design methodologies will have a relevant impact in the development of novel, more efficient, inhibitors.     

Parameterization of electrostatic interactions for molecular dynamics simulations of heterocyclic polymers

The paper focuses on the problem of electrostatic interactions in molecular dynamics simulations of thermal properties of heterocyclic polymers. The study focuses on three thermoplastic polyimides synthesized on the basis of 1,3‐bis‐(3′,4‐dicarboxyphenoxy)benzene (dianhydride R) and three diamines: 4,4′‐bis‐(4″‐aminophenoxy) diphenylsulfone (diamine BAPS), 4,4′‐bis‐(4″‐aminophenoxy) biphenyl (diamine BAPB), and 4,4′‐bis‐(4''‐aminophenoxy) diphenyloxide (diamine BAPO). In the molecular dynamics simulations these polyimides were described by the Gromos53a5 force field. To parameterize the electrostatic interactions four methods of calculating the partial atomic charges were chosen: B3LYP/6–31G*(Mulliken), AM1(Mulliken), HF/6–31G*(Mulliken), and HF/6–31G*(ChelpG). As our parameterization is targeted to reproduce thermal properties of the thermoplastic polyimides, the choice of proper partial charges was finalized on a basis of the closest match between computational and experimental data for the thermal expansion coefficients of the polyimides below glass transition temperatures. Our finding clearly show that the best agreement with experimental data is achieved with the Mulliken partial atomic charges calculated by the Hartree‐Fock method with 6–31G* basis set. Furthermore, in addition to the thermal expansion coefficients this set of partial atomic charges predicts an experimentally observed relationship between glass transition temperatures of the three polyimides under study: . A mechanism behind the change in thermal properties upon the change in the chemical structure in considered polyimides may be related to an additional spatial ordering of sulfone groups due to dipole‐dipole interactions. Overall, the modified force‐field is proved to be suitable for accurate prediction of thermal properties of thermoplastic polyimides and can serve as a basis for building up atomistic theoretical models for describing other heterocyclic polymers in bulk. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 912–923     

Effect of cationic polyacrylamides on the interactions between cellulose fibers

The interaction between cellulose fibers in the presence of cationic polyacrylamide (CPAM) was analyzed by rheology as a function of polyelectrolyte concentration, charge density, and molecular weight. CPAM was found to strongly influence the yield stress of cellulose suspensions; low doses of CPAM increased the yield stress, but at higher concentrations the yield stress declined. The charge density of the CPAM was the most significant factor in how yield stress responded to CPAM concentration; this effect was able to be normalized to a master curve by considering only the charged fraction of the polymer. The molecular weight of CPAM samples had some effect at high concentrations, but for lower CPAM doses the yield stress was independent of molecular weight over the range studied. The data suggest that CPAM modifies the interaction between cellulose surfaces via several mechanisms, with electrostatic interactions in the form of charge neutralization and charged patch formation dominating; polymer bridging and steric repulsion also influence the overall balance of forces between interacting cellulose fibers.     

Parameterization of Ca+2-protein interactions for molecular dynamics simulations

Molecular dynamics simulations of Ca+2 ions near protein were performed with three force fields: GROMOS96, OPLS-AA, and CHARMM22. The simulations reveal major, force-field dependent, inconsistencies in the interaction between the Ca+2 ions with the protein. The variations are attributed to the nonbonded parameterizations of the Ca+2-carboxylates interactions. The simulations results were compared to experimental data, using the Ca+2-HCOO- equilibrium as a model. The OPLS-AA force field grossly overestimates the binding affinity of the Ca+2 ions to the carboxylate whereas the GROMOS96 and CHARMM22 force fields underestimate the stability of the complex. Optimization of the Lennard-Jones parameters for the Ca+2-carboxylate interactions were carried out, yielding new parameters which reproduce experimental data.     

Molecular dynamics simulations of the interactions between platinum clusters and carbon platelets

Molecular dynamics simulations have been performed with two reactive force fields to investigate the structure of a Pt100 cluster adsorbed on the three distinct sides of a carbon platelet. A revised Reax force field for the carbon-platinum system is presented. In the simulations, carbon platelet edges both with and without hydrogen termination have been studied. It is found that the initial mismatch between the atomic structure of the platelet egde and the adsorbed face of the Pt100 cluster leads to a desorption of a few platinum atoms from the cluster and the subsequent restructuring of the cluster. Consequently, the average Pt-Pt bond length is enlarged in agreement with experimental results. This change in the bond length is supposed to play an important role in the enhancement of the catalytic activity, which is demonstrated by studying the changes in the bond order of the platinum atoms. We found an overall shift to lower values as well as a loss of the well-defined peak structure in the bond-order distribution.     

Understanding the mechanism of cellulose dissolution in 1-butyl-3-methylimidazolium chloride ionic liquid via quantum chemistry calculations and molecular dynamics simulations

While N,N′-dialkylimidazolium ionic liquids (ILs) have been well-established as effective solvents for dissolution and processing of cellulose, the detailed mechanism at the molecular level still remains unclear. In this work, we present a combined quantum chemistry and molecular dynamics simulation study on how the ILs dissolve cellulose. On the basis of calculations on 1-butyl-3-methylimidazolium chloride, one of the most effective ILs dissolving cellulose, we further studied the molecular behavior of cellulose models (i.e. cellulose oligomers with degrees of polymerization n = 2, 4, and 6) in the IL, including the structural features and hydrogen bonding patterns. The collected data indicate that both chloride anions and imidazolium cations of the IL interact with the oligomer via hydrogen bonds. However, the anions occupy the first coordination shell of the oligomer, and the strength and number of hydrogen bonds and the interaction energy between anions and the oligomer are much larger than those between cations and the oligomer. It is observed that the intramolecular hydrogen bond in the oligomer is broken under the combined effect of anions and cations. The present results emphasize that the chloride anions play a critically important role and the imidazolium cations also present a remarkable contribution in the cellulose dissolution. This point of view is different from previous one that only underlines the importance of the chloride anions in the cellulose dissolution. The present results improve our understanding for the cellulose dissolution in imidazolium chloride ILs.     

Time versus temperature rescaling for coarse grain molecular dynamics simulations

Coarse graining procedures are intended to well reproduce the structure of a material while increasing the simulations efficiency. However, the dynamics usually accelerates with coarse graining and a scaling procedure has to be used for dynamical data calculations. Most often a simple time-scaling coefficient is used for this purpose. However, for low temperature liquids this simple scaling procedure is questionable. Because supercooled liquids in their approach to the glass transition temperature do not follow a simple dynamics. In order to test if this scaling procedure is still pertinent at low temperature, we use molecular dynamics simulations of a coarse grain model of the methylmethacrylate molecule compared to simulations with the All atom model. We compare two different rescaling procedures, a time rescale and a temperature rescale procedure. Using these two procedures we compare the behaviors of the mean square displacements, the incoherent scattering functions, the self and distinct part of the Van Hove correlation functions and the non-Gaussian parameters. Results show that the temperature rescaling procedure reproduces well the All atom dynamical data at low temperatures, while the time rescaling procedure is correct only in the Brownian regime. We also find that the melting and the glass-transition temperatures are relatively well reproduced with the temperature rescaling procedure.     

Properties of inhibitors of methane hydrate formation via molecular dynamics simulations

Within the framework of a proposed two-step mechanism for hydrate inhibition, the energy of binding of four inhibitor molecules (PEO, PVP, PVCap, and VIMA) to a hydrate surface is estimated with molecular dynamic simulations. One key feature of this proposed mechanism is that the binding of an inhibitor molecule to the surface of an ensuing hydrate crystal disrupts growth and therein crystallization. It is found through the molecular dynamic simulations that inhibitor molecules that experimentally exhibit better inhibition strength also have higher free energies of binding, an indirect confirmation of our proposed mechanism. Inhibitors increasing in effectiveness, PEO < PVP < PVCap < VIMA, have increasingly negative (exothermic) binding energies of -0.2 < -20.6 < -37.5 < -45.8 kcal/mol and binding free energies of increasing favorability (+0.4 approximately = +0.5 < -9.4 < -15.1 kcal/mol). Furthermore, the effect of an inhibitor molecule on the local liquid water structure under hydrate-forming conditions was examined and correlated to the experimental effectiveness of the inhibitors. Two molecular characteristics that lead to strongly binding inhibitors were found: (1) a charge distribution on the edge of the inhibitor that mimics the charge separation in the water molecules on the surface of the hydrate and (2) the congruence of the size of the inhibitor with respect to the available space at the hydrate-surface binding site. Equipped with this molecular-level understanding of the process of hydrate inhibition via low-dosage kinetic hydrate inhibitors we can design new, more effective inhibitor molecules.     

Surface physics at the nano-scale via scanning probe microscopy and molecular dynamics simulations

Probe-based scanning microscopes, such as the STM and the AFM, are used to obtain the topographical and electronic structure maps of material surfaces, and to modify their morphologies on nanoscopic scales. They have generated new areas of research in condensed matter physics and materials science. We will review some examples from the fields of experimental nano-mechanics, nano-electronics and nano-magnetism. These now form the basis of the emerging field of Nano-technology. A parallel development has been brought about in the field of Computational Nano-science, using quantum-mechanical techniques and computer-based numerical modelling, such as the Molecular Dynamics (MD) simulation method. We will report on the simulation of nucleation and growth of nano-phase films on supporting substrates. Furthermore, a theoretical modelling of the formation of STM images of metallic clusters on metallic substrates will also be discussed within the non-equilibrium Keldysh Green function method to study the effects of coherent tunnelling through different atomic orbitals in a tip-sample geometry.     

Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials

We present results addressing properties of a polarizable force field for hexane based on the fluctuating charge (FQ) formalism and developed in conjunction with the Chemistry at Harvard Molecular Mechanics (CHARMM) potential function. Properties of bulk neat hexane, its liquid-vapor interface, and its interface with a polarizable water model (TIP4P-FQ) are discussed. The FQ model is compared to a recently modified alkane model, C27r, also based on the CHARMM potential energy function. With respect to bulk properties, both models predict bulk density within 1%; the FQ model predicts the liquid vaporization enthalpy within 2%, while the C27r force field underestimates the property by roughly 20% (and in this sense reflects the quality of the C27r force field across the spectrum of linear and branched alkanes). The FQ hexane model realistically captures the dielectric properties of the bulk in terms of a dielectric constant of 1.94, in excellent agreement with experimental values in the range of 1.9-2.02. This behavior is also in conformity with a recent polarizable alkane model based on Drude oscillators. Furthermore, the bulk dielectric is essentially captured in the infinite frequency, or optical, dielectric contribution. The FQ model is in this respect a more realistic force field for modeling lipid bilayer interiors for which most current state-of-the-art force fields do not accurately capture the dielectric environment. The molecular polarizability of the FQ model is 11.79 A3, in good agreement with the range of experimental and ab initio values. In contrast to FQ models of polar solvents such as alcohols and water, there was no need to scale gas-phase polarizabilities in order to avoid polarization catastrophes in the pure bulk. In terms of the liquid-vapor and liquid-liquid interfaces, the FQ model displays a rich orientational structure of alkane and water in the respective interfacial systems, in general conforming with earlier simulation studies of such interfaces. The FQ force field shows a marked deviation in the interfacial dipole potentials computed from the charge densities averaged over simulation trajectories. At the liquid-vapor interface, the FQ model predicts a potential drop of -178.71 mV in contrast to the C27r estimate of -433.80 mV. For the hexane-water interface, the FQ force field predicts a dipole potential drop of -379.40 mV in contrast to the C27r value of -105.42 mV. Although the surface dipole potential predicted by the FQ model is roughly 3.5 times that predicted by the C27r potential, it is consistent with reported experimental potentials across solvated lipid bilayers in the range of 400-600 mV.     

A noncanonical binding site of linezolid revealed via molecular dynamics simulations

Linezolid, an antibiotic of oxazolidinone family, is a translation inhibitor. The mechanism of its action that consists in preventing the binding of aminoacyl-tRNA to the A-site of the large subunit of a ribosome was embraced on the basis of the X-ray structural analysis of the linezolid complexes with vacant bacterial ribosomes. However, the known structures of the linezolid complexes with bacterial ribosomes poorly explain the linezolid selectivity in suppression of protein biosynthesis, depending on the amino acid sequence of the nascent peptide. In the present study the most probable structure of the linezolid complex with a E. coli ribosome in the A,A/P,P-state that is in line with the results of biochemical studies of linezolid action has been obtained by molecular dynamics simulation methods.     

Effects of humidity and temperature on laser-assisted dip-pen nanolithography array using molecular dynamics simulations

Reactions of As(III) and As(V) with pyrite were investigated using pristine pyrite (produced and reacted in a rigorously anoxic environment with P_O2 < 10⁻⁸ atm) and using surface-oxidized pyrite (produced under anoxic conditions, exposed to air, then stored and reacted under rigorously anoxic conditions). Results with surface-oxidized pyrite were similar to previously reported arsenic-pyrite results. However As(III) adsorbed over a broader pH range on pristine pyrite than on surface-oxidized pyrite, As(V) adsorbed over a narrower pH range on pristine pyrite than on surface-oxidized pyrite, and adsorbed As(V) on pristine pyrite was reduced to As(III) but adsorbed As(V) was not reduced with surface-oxidized pyrite. Reduction of As(V) with pristine pyrite was first-order in total As(V), Fe(II) was released, and sulfur was oxidized. The proposed mechanism for pyrite oxidation by As(V) was similar to the published mechanism for oxidation by O₂ and rates were compared. The results can be used to predict the removals of As(V) and As(III) on pyrite in continuously anoxic environments or on pyrite in intermittently oxic/anoxic environments. Rigorous cleanup and continuous maintenance of strictly anoxic conditions are required if commercial or produced pyrites are to be used as surrogates for pristine pyrite.     

A comparison between parallelization approaches in molecular dynamics simulations on GPUs

We test the relative performances of two different approaches to the computation of forces for molecular dynamics simulations on graphics processing units. A “vertex‐based” approach, where a computing thread is started per particle, is compared to an “edge‐based” approach, where a thread is started per each potentially non‐zero interaction. We find that the former is more efficient for systems with many simple interactions per particle while the latter is more efficient if the system has more complicated interactions or fewer of them. By comparing computation times on more and less recent graphics processing unit technology, we predict that, if the current trend of increasing the number of processing cores—as opposed to their computing power—remains, the “edge‐based” approach will gradually become the most efficient choice in an increasing number of cases. © 2014 Wiley Periodicals, Inc.     

Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations

The intrinsically disordered protein alpha-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of alpha-synuclein consists of a broad distribution of conformers with an ensemble-averaged hydrodynamic radius significantly smaller than that expected for a random coil structure. This partial condensation is driven by interactions between the highly charged C-terminus and a large hydrophobic central region of the protein sequence. We suggest that this structure could inhibit the formation of alpha-synuclein aggregates, which are thought to be the cytotoxic species responsible for neurodegeneration in PD.