Modeling catalytic reaction mechanisms in glycoside hydrolases

Modeling catalysis in carbohydrate-active enzymes is a daunting challenge because of the high flexibility and diversity of both enzymes and carbohydrates. Glycoside hydrolases (GHs) are an illustrative example, where conformational changes and subtle interactions have been shown to be critical for catalysis. GHs have pivotal roles in industry (e.g. biofuel or detergent production) and biomedicine (e.g. targets for cancer and diabetes), and thus, a huge effort is devoted to unveil their molecular mechanisms. Besides experimental techniques, computational methods have served to provide an in-depth understanding of GH mechanisms, capturing complex reaction coordinates and the conformational itineraries that substrates follow during the whole catalytic pathway, providing a framework that ultimately may assist the engineering of these enzymes and the design of new inhibitors.     

Force field comparisons of the heat capacity of carbon nanotubes

The force fields Tersoff, CHARMM, COMPASS, CVFF and PCFF are compared using molecular calculations and simulations of SWNT thermal properties. The heat capacity results from the force fields vary significantly in the low (room) temperature range. The COMPASS force field best reproduces the phonon frequencies calculated from density functional theory and is consistent with the Raman scattering results. The temperature dependent behavior of SWNT heat capacity is investigated using harmonic and quasi-harmonic dynamics theories. The impact of quasi-harmonic analysis is not significant in the low and intermediate temperature range (below 500 K). Thus, force field comparisons based on the harmonic approximation are valid in that temperature range. Above 500 K, heat capacity results based on the Tersoff force field using a quasi-harmonic approximation are further investigated.     

Molecular Dynamics Simulation of Platinum Particles Between Graphite Walls

Abstract

We report preliminary molecular dynamics simulations results for platinum atoms confined between two parallel graphite surfaces. The system shows phase transition characteristics corresponding to a second order transition. Significant structural changes are also observed in the range of temperature studied. We have also investigated the effects of two dfferent Pt-wall interaction potentials: the 9-3 form suggested by Crowell and the 10-4 form originally proposed by Steele. The results show that the two systems have rather different structural characteristics but similar thermodynamic behavior.     

Molecular dynamics (MD) simulations for the prediction of chiral discrimination of N-acetylphenylalanine enantiomers by cyclomaltoheptaose (beta-cyclodextrin, beta-CD) based on the MM-PBSA (molecular mechanics-Poisson-Boltzmann surface area) approach

Molecular dynamics (MD) simulations were performed for the prediction of chiral discrimination of N-acetylphenylalanine enantiomers by cyclomaltoheptaose (beta-cyclodextrin, beta-CD). Binding free energies and various conformational properties were obtained using by the MM-PBSA (molecular mechanics Poisson-Boltzmann/surface area) approach. The calculated relative difference (DeltaDeltabinding) of binding free energy was in fine agreement with the experimentally determined value. The difference of rotameric distributions of guest N-acetylphenylalanine enantiomers complexed with the host, beta-CD, was observed after the conformational analyses, suggesting that the conformational changes of guest captured within host cavity would be a decisive factor for enantiodifferentiation at a molecular level.     

Cyclen substitution with urea-containing dendrimeric branches. Theoretical study considering the concept of collectivity

Equilibrium structures of novel dendrimeric compounds consisting of 1,4,7,10-tetraazacyclododecane (cyclen) mono- to tetra-substituted with four different dendrimeric branches have been studied. It has been shown using molecular dynamics (MD) that, even in the presence of the macrocycle cyclen, the most stable conformations are those with a globular shape due to close contact interactions between poly-functional branches. No collapse of cyclen occurred, making this cavity available for metal complexation. Terminal branches A=NHCOOtBu, B=OSi(Me)2tBu, C=Imidazole and D=CN have different molecular volumes in the decreasing order: B>A>C>D. This conclusion is in accord with the long range interaction energies, showing that the larger the volume the less the steric hindrance. Considering these energy values, the stability of the systems follows exactly the same tendency as observed for the molecular volume. More polar groups like A=NHCOOtBu and D=CN impart extra stability due to long range interactions between atoms separated by exactly three chemical bonds. The negative charge inside the cyclen cavity increases with the volume of the branches. Besides cyclen, urea groups located at the middle of the branches represent another independent point of negative charge for eventual interaction with small molecules. These compounds show a sum of small contributions of the functionalities in a collective fashion.     

Molecular Modeling of Fullerene Dendrimers

The fullerene skeleton offers the possibility of attaching several dendrimer branches. Thus, starburst-dendrimers are obtained that might lead to self-limiting generation because of very large, sterically overburdened molecular systems. Two approaches for the generation of molecular models of such fullerene dendrimers are presented: Molecular mechanics and molecular dynamics calculations have been performed to explore the geometries and energetics of the compounds. The other approach utilized an empirical 3D structure generator that started from information on only the constitution of the molecules concerned.Electronic Supplementary Material available.     

A database of 32 DNA triplets to study triple helices by molecular mechanics and dynamics

We present here a database of 32 deoxyribonucleotide triplets, that can be used as building blocks of triple helix forming deoxyribonucleotides on a computer. This database is made of all the pairing schemes of the triplets ATT, GCC⁺, ATA and GCG where the third base forms two hydrogen bonds with the purine of the first two Watson-Crick strands. The essential features of the known triple helices were preserved in the resulting structures. A triple helix can be easily built from any combination of these basic triplets. Four homogeneous and alternate triple helices thus obtained were studied by molecular mechanics and dynamics in vacuo. The results are in agreement with known experimental observations for ATT and suggest a possible structure for the GCG triple helix. In order to characterize the geometry of the structures obtained, the definitions of nucleic acid structure parameters (R.E. Dickerson et al., EMBO J. 8 (1989) 1–4) have been extended to triple helical polynucleotides.     

Acyl chain conformations in phospholipid bilayers: a comparative study of docosahexaenoic acid and saturated fatty acids

A variety of experimental methods indicate unique biophysical properties of membranes containing the highly polyunsaturated ω-3 fatty acid, docosahexaenoic acid (DHA). In the following we review the atomically detailed picture of DHA acyl chains structure and dynamics that has emerged from computational studies of this system in our lab. A comprehensive approach, beginning with ab-initio quantum chemical studies of model compounds representing segments of DHA and ending with large scale classical molecular dynamics simulations of DHA-containing bilayers, is described with particular attention paid to contrasting the properties of DHA with those of saturated fatty acids. Connection with experiment is made primarily through comparison with Nuclear Magnetic Resonance (NMR) studies, particularly those that probe details of the chain structure and dynamics. Our computational results suggest that low torsional energy barriers, comparable to kT at physiological conditions, for the rotatable bonds in the DHA chain are the key to the differences observed between polyunsaturated and saturated acyl chains.     

Modeling ganglioside headgroups by conformational analysis and molecular dynamics

The conformations and dynamics of gangliosides GM1, GM2, 6-GM2 and GM4 have been studied by computational means, and the results compared to NMR data. Unconstrained conformational searches were run using the AMBER* force field augmented by MNDO derived parameters for the Neu5Ac anomeric torsion, the GB/SA water solvation model, and the MC/EM alogorithm; extended (10–12[emsp4 ]ns) dynamic simulations in GB/SA water were performed with the MC/SD protocol, and the stored structures were minimized. The overall mobility of the Neu5Ac2,3Gal linkage and the position of its minimum energy conformation have been shown to depend mainly on the presence or the absence of a GalNAc residue at the adjacent position. The best quantitative agreement with the available NOE data was achieved after minimization of the structures stored during the MC/SD dynamic runs. The latter protocol appears to reproduce satisfactorily the available experimental data, and can be used with confidence to build three-dimensional models of ganglioside headgroups.     

蓖麻毒素A链突变体(MRTA)的分子设计

利用同源模建的方法,借助分子力学优化、分子动力学模拟退火设计构建了删除部分氨基酸序列的蓖麻毒素Ａ链突变体（ＭＲＴＡ）。采用泊松—玻尔兹曼方程对比分析了蓖麻毒素Ａ链（ＲＴＡ）与ＭＲＴＡ表观静电势分布,研究ＲＴＡ与ＭＲＴＡ蛋白表面静电性质;通过半经验量子化学ＡＭ１与分子力学结合方法探讨ＲＴＡ与ＭＲＴＡ功能域氨基酸前线分子轨道性质、能级分布,从理论上预测ＭＲＴＡ功能活性     

Computer simulation studies of microcrystalline cellulose Ibeta

Molecular mechanics (MM) simulations have been used to model two small crystals of cellulose Ibeta surrounded by water. These small crystals contained six different extended surfaces: (110), (11 0), two types of (100), and two types of (010). Significant changes took place in the crystal structures. In both crystals there was an expansion of the unit cell, and a change in the gamma angle to almost orthogonal. Both microcrystals developed a right-hand twist of about 1.5 degrees per cellobiose unit, similar to the twisting of beta-sheets in proteins. In addition, in every other layer, made up of the unit cell center chains, a tilt of the sugar rings of 14.8 degrees developed relative to the crystal plane as a result of a transition of the primary alcohol groups in these layers away from the starting TG conformation to GG. In this conformation, these groups made interlayer hydrogen bonds to the origin chains above and below. No change in the primary alcohol conformations or hydrogen-bonding patterns in the origin chain layers was observed. Strong localization of the adjacent water was found for molecules in the first hydration layer of the surfaces, due to both hydrogen bonding to the hydroxyl groups of the sugar molecules and also due to hydrophobic hydration of the extensive regions of nonpolar surface resulting from the axial aliphatic hydrogen atoms of the 'tops' of the glucose monomers. Significant structuring of the water was found to extend far out into the solution. It is hypothesized that the structured layers of water might present a barrier to the approach of cellulase enzymes toward the cellulose surfaces in enzyme-catalyzed hydrolysis, and might inhibit the escape of soluble products, contributing to the slow rates of hydrolysis observed experimentally. Since the water structuring is different for the different surfaces, this might result in slower hydrolysis rates for some surfaces compared to others.     

Cellular interaction through LewisX cluster: theoretical studies

It is well known that cell surface carbohydrates play a role in cell–cell adhesion and communication. LewisX glycosphingolipids form microdomains on cell surfaces. Homotypic and calcium-mediated LewisX–LewisX (LeX-LeX) interactions were proposed to be responsible for the initial steps of cell adhesion, and to mediate embryogenesis and metastasis. Various techniques have been used to investigate such interactions, but little information is available on the geometry and the mechanism of dimerisation. To better understand these interactions, a new molecular model was developed to simulate homotypic interactions in explicit solvent with and without calcium ions. Accurate analysis of both trajectories yielded valuable information about the energetics of LeX-LeX dimerisation. Detailed interpretation of the hydrogen bond network and the presence of calcium ions along the trajectory provide valuable insights into the role of calcium ions in this carbohydrate–carbohydrate interaction. Figure Calcium population density around the LewisX carbohydrate (after the trajectory has been fitted to the primary unit cell). All central dimer coordinates are fitted along the time axis, whereas calcium ion positions are recorded and represented as points. The clouds of points indicate that the ions are not randomly placed around the dimer but take up preferred positions     

Prevalent Mutations of Human Prion Protein: A Molecular Modeling and Molecular Dynamics Study

Abstract

Point mutations in the human prion protein gene, leading to amino acid substitutions in the human prion protein contribute to conversion of PrP^C to PrP^Sc and amyloid formation, resulting in prion diseases such as familial Creutzfeldt-Jakob disease (CJD), Gerstmann-Straussler-Scheinker disease (GSS), and fatal familial insomnia. We have investigated impressions of prevalent mutations including Q217R, D202N, F198S, on the human prion protein and compared the mutant models with wild types. Structural analyses of models were performed with molecular modeling and molecular dynamics simulation methods. According to our results, frequently occurred mutations are observed in conserved and fully conserved sequences of human prion protein and the most fluctuation values occur in the Helix 1 around residues 144–152 and C-terminal end of the Helix 2. Our analysis of results obtained from MD simulation clearly shows that this long-range effect plays an important role in the conformational fluctuations in mutant structures of human prion protein. Results obtained from molecular modeling such as creation or elimination of some hydrogen bonds, increase or decrease of the accessible surface area and molecular surface, loss or accumulation of negative or positive charges on specific positions, and altering the polarity and pKa values, show that amino acid point mutations, though not urgently change the stability of PrP, might have some local impacts on the protein interactions which are required for oligomerization into fibrillar species.     

Rare events out of equilibrium: mobility through the liquid–liquid interface

Transition state theory provides a well established means to compute the rate at which rare events occur; however, this is strictly an equilibrium approach. Here we consider a nonequilibrium problem of this nature in the form of transport through a liquid–liquid interface. When two immiscible liquids are coexisting in equilibrium, there will be a certain amount of mixing between the two phases, resulting in a finite linear mobility across the liquid–liquid interface. We derive an exact relationship between the mobility and the local diffusion in the direction perpendicular to the interface. We compute the mobility using both nonequilibrium molecular dynamics and a variety of linear response type approaches, with accurate agreement being obtained for the best of these. Our analysis makes it clear how the local diffusion is influenced by the inhomogeneities of the interface, even when at a distance from it. This nonlocal character to the mobility has not been appreciated before and results in a strong variation in the local diffusion, which is formally coupled to the variation in the potential of mean force. The nonlocal aspect of the diffusion requires the velocity autocorrelation function to be integrated out to far longer times than is the case for homogeneous liquids, and requires special care with regard to the choice of numerical approach.     

A Free Energy Based Computational Pathway from Chemical Templates to Lead Compounds: A Case Study of COX-2 Inhibitors

Abstract

Automation of lead compound design in silico given the structure of the protein target and a definition of its active site vies for the top of the wish list in any drug discovery programme. We present here an enumeration of steps starting from chemical templates and propose a solution at the state of the art, in the form of a system independent comprehensive computational pathway. This methodology is illustrated with cyclooxygenase-2 (COX-2) as a target. We built candidate molecules including a few Non Steroidal Anti-inflammatory Drugs (NSAIDs) from chemical templates, passed them through empirical filters to assess drug-like properties, optimized their geometries, derived partial atomic charges via quantum calculations, performed Monte Carlo docking, carried out molecular mechanics and developed free energy estimates with Molecular Mechanics Generalized Born Solvent Accessibility (MMGBSA) methodology for each of the candidate molecules. For the case of aspirin, we also conducted molecular dynamics on the enzyme, the drug and the complex with explicit solvent followed by binding free energy analysis. Collectively, the results obtained from the above studies viz. sorting of drugs from non-drugs, semi-quantitative estimates of binding free energies, amply demonstrate the viability of the strategy proposed for lead selection/design for biomolecular targets.     

Modeling the interplay of glycine protonation and multiple histidine binding of copper in the prion protein octarepeat subdomains

The octarepeat region of the prion protein can bind Cu²⁺ ions up to full occupancy (one ion per octarepeat) at neutral pH. While crystallographic data show that the HGGG octarepeat subdomain is the basic binding unit, multiple histidine coordination at lower Cu occupancy has been reported by X-ray absorption spectroscopy, EPR, and potentiometric experiments. In this paper we investigate, with first principles Car–Parrinello simulations, the first step for the formation of the Cu low-level binding mode, where four histidine side chains are coordinated to the same Cu²⁺ ion. This step involves the further binding of a second histidine to an already HGGG domain bonded Cu²⁺ ion. The influence of the pH on the ability of Cu to bind two histidine side chains was taken into account by simulating different protonation states of the amide N atoms of the two glycines lying nearest to the first histidine. Multiple histidine coordination is also seen to occur when glycine deprotonation occurs and the presence of the extra histidine stabilizes the Cu–peptide complex. Though the stabilization effect slightly decreases with the number of deprotonated glycines (reaching a minimum when both N atoms of the two nearest glycines are available as Cu ligands), the system is still capable of binding the second histidine in a 4N tetrahedral (though slightly distorted) coordination, whose energy is very near to that of the crystallographic square-planar 3N1O coordination. This result suggests that at low metal concentration the reorganization energy associated with Cu(II)/Cu(I) reduction is small also at pH ~ 7, when glycines are deprotonated. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

Modeling of Proton Transfer in Polymer Electrolyte Membranes on Different Time and Length Scales

Polymer electrolyte membranes (PEMs) are key component materials in fuel cell technology. Understanding the relationship between the elementary acts of proton transport and the operation of the entire cell on different time and length scales is therefore particularly rewarding. We discuss the results of recent atomistic computer simulations of proton transport in porous PEMs. Different models cover the range from individual local proton hops to diffusion processes with polymer mobility included.     

Spatial Separation of Molecular Conformers and Clusters

Gas-phase molecular physics and physical chemistry experiments commonly use supersonic expansions through pulsed valves for the production of cold molecular beams. However, these beams often contain multiple conformers and clusters, even at low rotational temperatures. We present an experimental methodology that allows the spatial separation of these constituent parts of a molecular beam expansion. Using an electric deflector the beam is separated by its mass-to-dipole moment ratio, analogous to a bender or an electric sector mass spectrometer spatially dispersing charged molecules on the basis of their mass-to-charge ratio. This deflector exploits the Stark effect in an inhomogeneous electric field and allows the separation of individual species of polar neutral molecules and clusters. It furthermore allows the selection of the coldest part of a molecular beam, as low-energy rotational quantum states generally experience the largest deflection. Different structural isomers (conformers) of a species can be separated due to the different arrangement of functional groups, which leads to distinct dipole moments. These are exploited by the electrostatic deflector for the production of a conformationally pure sample from a molecular beam. Similarly, specific cluster stoichiometries can be selected, as the mass and dipole moment of a given cluster depends on the degree of solvation around the parent molecule. This allows experiments on specific cluster sizes and structures, enabling the systematic study of solvation of neutral molecules.