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Chemical systems glycobiology requires experimental and computational tools to make possible big data analytics benefiting genomics and proteomics. The impediment to tool development is that the nature of glycan construction and mutation is not template driven but rests on cooperative glycosyltransferase (GT) catalytic synthesis. What is needed is the collation of kinetics and inhibition data in a standardized form to make possible analytics of glycan and glycoconjugate synthesis, mechanism extraction, and pattern recognition. Currently, kinetics assays in use for GTs are not universal in processing nucleoside phosphate UDP, GDP, and CMP donor-based glycosylation reactions due to limitations in accuracy and large substrate volume requirements. Here we present a universal glycosyltransferase continuous (UGC) assay able to measure the declining concentration of the NADH reporter molecule through fluorescence spectrophotometry and, therefore, determine reaction rate parameters. The development and parametrization of the assay is based on coupling the nucleotide released from GT reactions with pyruvate kinase, via nucleoside diphosphate kinase (NDK) in the case of NDP-based donor reactions. In the case of CMP-based reactions, the coupling is carried out via another kinase, cytidylate kinase in combination with NDK, which phosphorylates CMP to CDP, then CDP to CTP. Following this, we conduct kinetics and inhibition assay studies on the UDP, GDP, and CMP-based glycosylation reactions, specifically C1GAlT1, FUT1, and ST3GAL1, to represent each class of donor, respectively. The accuracy of calculating initial rates using the continuous assay compared to end point (noncontinuous) assays is demonstrated for the three classes of GTs. The previously identified natural product soyasaponin1 inhibitor was used as a model to demonstrate the application of the UGC assay as a standardized inhibition assay for GTs. We show that the dose response of ST3GAL1 to a serial dilution of Soyasaponin1 has time-dependent inhibition. This brings into question previous inhibition findings, arrived at using an end point assay, that have selected a seemingly random time point to measure inhibition. Consequently, using standardized K m values taken from the UGC assay study, ST3GAL1 was shown to be the most responsive enzyme to soyasaponin1 inhibition, followed by FUT1, then C1GALT1 with IC 50 values of 37, 52, and 886 μM respectively., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

Motivation: Target discovery and drug evaluation for diseases with complex mechanisms call for a streamlined chemical systems analysis platform. Currently available tools lack the emphasis on reaction kinetics, access to relevant databases, and algorithms to visualize perturbations on a chemical scale providing quantitative details as well streamlined visual data analytics functionality., Results: CytoCopasi, a Maven-based application for Cytoscape that combines the chemical systems analysis features of COPASI with the visualization and database access tools of Cytoscape and its plugin applications has been developed. The diverse functionality of CytoCopasi through ab initio model construction, model construction via pathway and parameter databases KEGG and BRENDA is presented. The comparative systems biology visualization analysis toolset is illustrated through a drug competence study on the cancerous RAF/MEK/ERK pathway., Availability and Implementation: The COPASI files, simulation data, native libraries, and the manual are available on https://github.com/scientificomputing/CytoCopasi., (© The Author(s) 2023. Published by Oxford University Press.)

Computing the free energies of molecular mechanisms in multidimensional space relies on combinations of geometrically complex reaction coordinates. We show how a graph theory implementation reduces complexity, and illustrate this on the arrangements of hydrogen bonding of a water dimer. The reaction coordinates and forces are computed using graphs that define the dependencies on the atoms in the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) library. The library can be interfaced with classical molecular dynamics as well as quantum molecular dynamics packages. Multidimensional interdependent reaction coordinates are constructed to produce complex free energy hypersurfaces. The reaction coordinates are graphed from atomic and molecular components to define points, distances, vectors, angles, planes and combinations thereof. The resultant free energy surfaces that are a function of the distance, angles, planes, and so on, can represent molecular mechanisms in reduced dimensions from the component atomic Cartesian coordinate degrees of freedom. The FEARCF library can be interfaced with any molecular package. Here, we demonstrate the link to NWChem to compute a hyperdimensional DFT (aug-cc-pVDZ basis set and X3LYP exchange correlation functionals) free energy space of a water dimer. Analysis of the water dimer free energy hypervolume reveals that while the chain and cyclic hydrogen bonding configurations are located in stable minimum energy wells, the bifurcated hydrogen bond configuration is a gateway to instability and dimer dissociation., (© 2022 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC.)

Enzyme reactions are complex to simulate accurately, and none more so than glycoenzymes (glycosyltransferase and glycosidases). A rigorous sampling of the protein frame and the conformationally plural carbohydrate substrate coupled with an unbiased treatment of the electron dynamics is needed to discover the true reaction landscapes. Here, we demonstrate the effectiveness of two computational methods ported in libraries that we have developed. The first is a flat histogram free energy method called FEARCF capable of multidimensional sampling and rapidly converging to a complete coverage of phase space. The second, the Quantum Supercharger Library (QSL), is a method that accelerates the computation of the ab initio electronic wave function as well as the integral derivatives on graphical processing units (GPUs). These QSL accelerated computations form the core components needed for direct quantum dynamics and QM/MM dynamics when coupled with legacy codes such as GAMESS and NWCHEM, making state of the art hyper-parallel electronic computations in chemistry and chemical biology possible. The combination of QSL (acceleration of ab initio QM computation) and FEARCF (multidimensional hyper-parallel reaction dynamics) makes the simulation of ab initio QM/MM reaction dynamics of enzyme catalysis feasible. Enzymes that process carbohydrates pose an added challenge as their pyranose ring substrates span multidimensional conformational space whose sampling is an intimate function of the catalytic mechanism. Here, we use the pairing of FEARCF and QSL to simulate the catalytic effect of the glycoenzyme β- N -acetylglucosamine transferase (OGT). The reaction mechanism is discovered from a variable three bond reaction surface using SCCDFTB. The role of the OGT in distorting the pyranose ring of β- N -acetylglucosamine (GlcNAc) away from the equilibrium 4 C 1 chair conformation toward the E 3 envelope needed for the transition state is discovered from its pucker free energy hypersurfaces (or free energy volume, FEV). A complete GlcNAc ring pucker HF 6-31g FEV is constructed from ab initio QM dynamics in vacuum and ab initio QM/MM dynamics in the OGT catalytic domain. The OGT is shown to clearly lower the pathway toward the transition state E 3 ring conformer as well as stabilize it by 1.63 kcal/mol. Illustrated here is the use of QSL accelerated ab initio QM/MM dynamics that thoroughly explores carbohydrate catalyzed reactions through a FEARCF multidimensional sampling of the interdependence between reaction and conformational space. This demonstrates how experimentally inaccessible molecular and electronic mechanisms that underpin enzyme catalysis can be discovered by directly modeling the dynamics of these complex reactions.

A high-speed numerical potential delivering computational performance comparable with complex coarse-grained analytic potentials makes available models that have greater degrees of physical and chemical accuracy. This opens the possibility of increased accuracy in classical molecular dynamics simulations of anisotropic systems. In this work, we report the development of a high-speed lookup table (LUT) of four-dimensional gridded data, that uses cubic B-spline interpolations to derive off grid values and their associated partial derivatives that are located between the known grid data points. The accuracy of the coarse-grained numerical potential using a LUT from uniaxial Gay-Berne (GB) potential produced array of values is within a 3% and a 5% margin of error respectively for the interpolation of the uniaxial GB potential and its partial derivatives. The numerical potential model and partial derivatives speedup is made competitive with the analytical potential by exploiting graphics processing units on board functionality. The capability of the numerical potential is demonstrated by comparing minimizations of a box of 500 naphthalene molecules. The minimizations using a full atomistic (NAMD/CHARMM force field), a biaxial GB and a numerical potential from a LUT using data from the CHARMM pair potential was done. The numerical potential model is significantly more accurate in its approximation of the atomistic local minimum configuration than is the biaxial GB analytical potential function. This demonstrates that using a numerical potential founded on a direct lookup of the atomistic potential landscape significantly improves coarse grain (CG) modeling of complex molecules, possibly paving the way for accurate anisotropic system CG modeling., (© 2021 Wiley Periodicals LLC.)

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE) is an open-source web platform developed with the aim to provide an environment for the design of reliable methods to conduct reproducible biomolecular simulations. It is built on the well-known Galaxy bioinformatics platform. Through this, BRIDGE hosts computational chemistry tools on public web servers for internet use and provides machine- and operating-system-independent portability using the Docker container platform for local use. This construction improves the accessibility, shareability, and reproducibility of computational methods for molecular simulations. Here we present integrated free energy tools (or apps) to calculate absolute binding free energies (ABFEs) and relative binding free energies (RBFEs), as illustrated through use cases. We present free energy perturbation (FEP) methods contained in various software packages such as GROMACS and YANK that are independent of hardware configuration, software libraries, or operating systems when ported in the Galaxy-BRIDGE Docker container platform. By performing cyclin-dependent kinase 2 (CDK2) FEP calculations on geographically dispersed web servers (in Africa and Europe), we illustrate that large-scale computations can be performed using the exact same codes and methodology by collaborating groups through publicly shared protocols and workflows. The ease of public sharing and independent reproduction of simulations via BRIDGE makes possible an open review of methods and complete simulation protocols. This makes the discovery of inhibitors for drug targets accessible to nonexperts and the computer experiments that are used to arrive at leads verifiable by experts and reviewers. We illustrate this on β-galactoside α-2,3-sialyltransferase I (ST3Gal-I), a breast cancer drug target, where a combination of RBFE and ABFE methods are used to compute the binding free energies of three inhibitors.

When faced with the investigation of the preferential binding of a series of ligands against a known target, the solution is not always evident from single structure analysis. An ensemble of structures generated from computer simulations is valuable; however, visual analysis of the extensive structural data can be overwhelming. Rapid analysis of trajectory data, with tools available in the Galaxy platform, can be used to understand key features and compare differences that inform the preferential ligand structure that favors binding. We illustrate this informatics approach by investigating the in-silico binding of a peptide and glycopeptide epitope of the glycoprotein Mucin 1 (MUC1) binding with the antibody AR20.5. To study the binding, we performed molecular dynamics simulations using OpenMM and then used the Galaxy platform for data analysis. The same analysis tools are applied to each of the simulation trajectories and this process was streamlined by using Galaxy workflows. The conformations of the antigens were analyzed using root-mean-square deviation, end-to-end distance, Ramachandran plots, and hydrogen bonding analysis. Additionally, RMSF and clustering analysis were carried out. These analyses were used to rapidly assess key features of the system, interrogate the dynamic structure of the ligand, and determine the role of glycosylation on the conformational equilibrium. The glycopeptide conformations in solution change relative to the peptide; thus a partially pre-structuring is seen prior to binding. Although the bound conformation of peptide and glycopeptide is similar, the glycopeptide fluctuates less and resides in specific conformers for more extended periods. This structural analysis which gives a high-level view of the features in the system under observation, could be readily applied to other binding problems as part of a general strategy in drug design or mechanistic analysis., (Copyright © 2020, Barnett et al.; licensee Beilstein-Institut.)

Protein-ligand binding prediction is central to the drug-discovery process. This often follows an analysis of genomics data for protein targets and then protei n structure discovery. However, the complexity of performing reproducible protein conformational analysis and ligand binding calculations, using vetted methods and protocols can be a challenge. Here we show how Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE), an open-source web-based compute and analytics platform for computational chemistry developed based on the Galaxy bioinformatics platform, makes protocol sharing seamless following genomics and proteomics. BRIDGE makes available tools and workflows to carry out protein molecular dynamics simulations and accurate free energy computations of protein-ligand binding. We illustrate the dynamics and simulation protocols for predicting protein-ligand binding affinities in silico on the T4 lysozyme system. This protocol is suitable for both novice and experienced practitioners. We show that with BRIDGE, protocols can be shared with collaborators or made publicly available, thus making simulation results and computations independently verifiable and reproducible., Competing Interests: Competing interestsThere are no competing interests., (Copyright © 2020 The Authors; exclusive licensee Bio-protocol LLC.)

ProtoCaller is a Python library distributed through Anaconda which automates relative protein-ligand binding free energy calculations in GROMACS. It links a number of popular specialized tools used to perform protein setup and parametrization, such as PDB2PQR, Modeller, and AmberTools. ProtoCaller supports commonly used AMBER force fields with additional cofactor parameters, and AM1-BCC is used to derive ligand charges. ProtoCaller also comes with an extensive PDB parser, an enhanced maximum common substructure algorithm providing improved ligand-ligand mapping, and a light GROMACS wrapper for running multiple molecular dynamics simulations. ProtoCaller is highly relevant to most researchers in the field of biomolecular simulation, allowing a customizable balance between automation and user intervention.

Motivation: The pathway from genomics through proteomics and onto a molecular description of biochemical processes makes the discovery of drugs and biomaterials possible. A research framework common to genomics and proteomics is needed to conduct biomolecular simulations that will connect biological data to the dynamic molecular mechanisms of enzymes and proteins. Novice biomolecular modelers are faced with the daunting task of complex setups and a myriad of possible choices preventing their use of molecular simulations and their ability to conduct reliable and reproducible computations that can be shared with collaborators and verified for procedural accuracy., Results: We present the foundations of Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE) developed on the Galaxy platform that makes possible fundamental molecular dynamics of proteins through workflows and pipelines via commonly used packages, such as NAMD, GROMACS and CHARMM. BRIDGE can be used to set up and simulate biological macromolecules, perform conformational analysis from trajectory data and conduct data analytics of large scale protein motions using statistical rigor. We illustrate the basic BRIDGE simulation and analytics capabilities on a previously reported CBH1 protein simulation., Availability and Implementation: Publicly available at https://github.com/scientificomputing/BRIDGE and https://usegalaxy.eu., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

In this report, we address the question of combining nonlinearities of neurons into networks for modeling increasingly varying and progressively more complex functions. A fundamental approach is the use of higher-level representations devised by restricted Boltzmann machines and (denoising) autoencoders. We present the Denoising Autoencoder Self-Organizing Map (DASOM) that integrates the latter into a hierarchically organized hybrid model where the front-end component is a grid of topologically ordered neurons. The approach is to interpose a layer of hidden representations between the input space and the neural lattice of the self-organizing map. In so doing the parameters are adjusted by the proposed unsupervised learning algorithm. The model therefore maintains the clustering properties of its predecessor, whereas by extending and enhancing its visualization capacity enables an inclusion and an analysis of the intermediate representation space. A comprehensive series of experiments comprising optical recognition of text and images, and cancer type clustering and categorization is used to demonstrate DASOM's efficiency, performance and projection capabilities., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The SCC-DFTB/MIO/CHARMM free energy surface for a glycosyltransferase, TcTS, is benchmarked against a DFT/MM reaction trajectory using the same CHARMM MM force field ported to the NWChem package. The popular B3LYP functional, against which the MIO parameter set was parameterized is used to optimize TS structures and run DFT reaction dynamics. A novel approach was used to generate reaction forces from a SCC-DFTB/MIO/CHARMM reaction surface to drive B3LYP/6-31G/MM and B3LYP/6-31G(d)/MM reaction trajectories. Although TS structures compare favorably, differences stemming primarily from a minimal basis set approximation prevented a successful 6-31G(d) FEARCF reaction dynamics trajectory. None the less, the dynamic evolution of the B3LYP/6-31G/MM-computed electron density provided an opportunity to perform NBO analysis along the reaction trajectory. Here, we illustrate that a successful ab initio reaction trajectory is computationally accessible when the underlying potential energy function of the semi-empirical method used to produce driving forces is sufficiently close to the ab initio potential. © 2017 Wiley Periodicals, Inc., (© 2017 Wiley Periodicals, Inc.)

Mammalian sialyltransferases play a role in the metastasis of various cancers in humans. Inhibitors of these enzymes will in principle be able to directly inhibit aberrant sialylation in cancer. Inhibitors of ST3Gal-I resembling the donor component of S N 1 Transition State structures were previously evaluated as part of a kinetics study. Here, using classical dynamics simulations and free energy perturbation calculations, we rationalize the performance of three of these donor analogue ST3Gal-I enzyme inhibitors. We find to inhibit the mammalian ST3Gal-I enzyme a donor analogue requires configurationally limited functionality. This is mediated by the binding of the inhibitor to the enzyme. The inhibitor's ability to interact with Y194 and T272 through a charged group such as a carboxylate is especially important. Furthermore, a conformational rigid form approximating the donor substrate is central. Here this is achieved by an intramolecular hydrogen bond formed between the carboxylate group and one of the ribose hydroxyl groups of the cytidine monophosphate (CMP) leaving group. This intramolecular interaction results in the donor substrate conformer complimenting the form of the catalytic binding site. Finally the carboxylate charge is essential for electrostatic pairing with the binding site. Substituting this group for an alcohol or amide results in severe weakening of the ligand binding. The carboxylate thus proves an to be an irreplaceable functional group and an essential pharmacophore., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Motivation: Complex carbohydrates play a central role in cellular communication and in disease development. O- and N-glycans, which are post-translationally attached to proteins and lipids, are sugar chains that are rooted, tree structures. Independent efforts to develop computational tools for analyzing complex carbohydrate structures have been designed to exploit specific databases requiring unique formatting and limited transferability. Attempts have been made at integrating these resources, yet it remains difficult to communicate and share data across several online resources. A disadvantage of the lack of coordination between development efforts is the inability of the user community to create reproducible analyses (workflows). The latter results in the more serious unreliability of glycomics metadata., Results: In this paper, we realize the significance of connecting multiple online glycan resources that can be used to design reproducible experiments for obtaining, generating and analyzing cell glycomes. To address this, a suite of tools and utilities, have been integrated into the analytic functionality of the Galaxy bioinformatics platform to provide a Glycome Analytics Platform (GAP).Using this platform, users can design in silico workflows to manipulate various formats of glycan sequences and analyze glycomes through access to web data and services. We illustrate the central functionality and features of the GAP by way of example; we analyze and compare the features of the N-glycan glycome of monocytic cells sourced from two separate data depositions.This paper highlights the use of reproducible research methods for glycomics analysis and the GAP presents an opportunity for integrating tools in glycobioinformatics., Availability and Implementation: This software is open-source and available online at https://bitbucket.org/scientificomputing/glycome-analytics-platform, Contacts: chris.barnett@uct.ac.za or kevin.naidoo@uct.ac.za, Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Aberrant glycosylation in tumours stem from altered glycosyltransferase (GT) gene expression but can the expression profiles of these signature genes be used to classify cancer types and lead to cancer subtype discovery? The differential structural changes to cellular glycan structures are predominantly regulated by the expression patterns of GT genes and are a hallmark of neoplastic cell metamorphoses. We found that the expression of 210 GT genes taken from 1893 cancer patient samples in The Cancer Genome Atlas (TCGA) microarray data are able to classify six cancers; breast, ovarian, glioblastoma, kidney, colon and lung. The GT gene expression profiles are used to develop cancer classifiers and propose subtypes. The subclassification of breast cancer solid tumour samples illustrates the discovery of subgroups from GT genes that match well against basal-like and HER2-enriched subtypes and correlates to clinical, mutation and survival data. This cancer type glycosyltransferase gene signature finding provides foundational evidence for the centrality of glycosylation in cancer.

The interaction of chloroquine (CQ) and the μ-oxo dimer of iron(III) protoporphyrin IX (ferriheme) in aqueous solution was modeled using molecular dynamics (MD) simulations. Two models of the CQ-(μ-oxo ferriheme) complex were investigated, one involving CQ π-stacked with an unligated porphyrin face of μ-oxo ferriheme and the other in which CQ was docked between the two porphyrin rings. The feasibility of both models was tested by fitting computed structures to the experimental extended X-ray absorption fine structure (EXAFS) spectrum of the CQ-(μ-oxo ferriheme) complex in frozen aqueous solution. The docked model produced better agreement with experimental data, suggesting that this is the more likely structure in aqueous solution. The EXAFS fit indicated a longer than expected Fe-O bond of 1.87Å, accounting for the higher than expected magnetic moment of the complex. As a consequence, the asymmetric Fe-O-Fe stretch shifts much lower in frequency and was identified in the precipitated solid at 744cm(-1) with the aid of the O(18) isomer shift. Three important CQ-ferriheme interactions were identified in the docked structure. These were a hydrogen bond between the oxide bridge of μ-oxo ferriheme and the protonated quinolinium nitrogen atom of CQ; π-stacking between the quinoline ring of CQ and the porphyrin rings; and a close contact between the 7-chloro substituent of CQ and the porphyrin methyl hydrogen atoms. These interactions can be used to rationalize previously observed structure-activity relationships for quinoline-ferriheme association., (Copyright © 2015 Elsevier Inc. All rights reserved.)

We present here a set of algorithms that completely rewrites the Hartree-Fock (HF) computations common to many legacy electronic structure packages (such as GAMESS-US, GAMESS-UK, and NWChem) into a massively parallel compute scheme that takes advantage of hardware accelerators such as Graphical Processing Units (GPUs). The HF compute algorithm is core to a library of routines that we name the Quantum Supercharger Library (QSL). We briefly evaluate the QSL's performance and report that it accelerates a HF 6-31G Self-Consistent Field (SCF) computation by up to 20 times for medium sized molecules (such as a buckyball) when compared with mature Central Processing Unit algorithms available in the legacy codes in regular use by researchers. It achieves this acceleration by massive parallelization of the one- and two-electron integrals and optimization of the SCF and Direct Inversion in the Iterative Subspace routines through the use of GPU linear algebra libraries. © 2015 Wiley Periodicals, Inc., (© 2015 Wiley Periodicals, Inc.)

This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two-electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree-Fock ab initio gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS-UK, which uses the efficient Schlegel method for s- and l-orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose in vacuo and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6-31G basis set. The QSL can perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc., (© 2015 Wiley Periodicals, Inc.)

Enzymatically catalyzed reactions pass from reactants to products via transition states that are short-lived and potentially characterized from free-energy reaction surfaces. We compute the reaction surface for Trypanosoma cruzi trans-sialidase using the Free Energy from Adaptive Reaction Coordinate Forces method. The reaction coordinates are the bonds between the sialic acid and the leaving group (TYR342) and the sialic acid and the nucpleophile (ASP59). We are able to track progress of the reaction trajectories up to (incomplete), about (recrossed), and across (crossed) the col that divides the reactant (covalent intermediate) and product (Michaelis complex) surfaces. More than 40 transition state configurations were isolated from these trajectories, and the sialic acid substrate conformations were analyzed as well as the substrate interactions with the nucleophile and catalytic acid/base. A successful barrier crossing requires that the substrate passes through a family of E5, (4)H5, and (6)H5 pucker conformations. These puckers interact slightly differently with the enzyme. The E5 and (4)H5 conformations have a high-frequency hydrogen bonding with Asp96, while (6)H5 puckers show increased hydrogen bonding between sialic acid O-8-Glu230. Our analysis of Trypanosoma cruzi trans-sialidase configurations that populate the col separating the reactant from product surfaces brings new evidence to the prevailing premise that there are several pathways from reactant to product passing through the saddle and successful product formation is not restricted to the minimum energy path and transition state.

The herpes simplex virus uracil-DNA glycosylase (hsvUNG) enzyme is responsible for the reactivation of the virus from latency and efficient viral replication in nerve tissue. The lack of uracil-DNA glycosylase enzyme in human neurons and the continuous deamination of cytosine create an environment where the presence of viral uracil-DNA glycosylase is a necessity for the proliferation of the virus. A series of 6-(4-alkylanilino)-uracil inhibitors has been developed that selectively and strongly binds to the hsvUNG enzyme while weakly binding to human uracil-DNA glycosylase (hUNG). Here, by using a combination of sequence and structural comparisons between the two enzymes along with free energy of binding computations and principal component analysis of the ligands, we investigate and rationalize the inhibitory effect of the 6-(4-alkylanilino)-uracil series as a function of alkyl chain length on the hsvUNG. The results of these computations corroborate the experimental finding that the inhibitor with an octyl aliphatic chain selectively binds hsvUNG best. More importantly we find that 6-(4-octylanilino)-uracil's selective inhibition of hsvUNG over hUNG is due to the combination of the solution preconfigured bent conformation of that specific chain length and the position of HIS92 (absent in hUNG) just outside hsvUNG's hydrophobic gorge lying adjacent to its uracil binding pocket. The similarities between the uracil binding pockets in hsvUNG and hUNG obfuscate an understanding of the preferential inhibition of the virus enzyme. However, the differences in the enzymes' shallow hydrophobic grooves adjacent to the binding pockets, such as the gorge we identify here, rationalizes 6-(4-alkylanilino)-uracil with an octyl chain length as an excellent pharmacophore template for hsvUNG inhibitor design.

CHARMM force field parameters have been developed to model nonprotein bound five-coordinate ferriheme (ferriprotoporphyrin IX) species in aqueous solution. Structures and solvation were determined from molecular dynamics (MD) simulations at 298 K of monomeric [HO-ferriheme](2-), [H2O-ferriheme](-), and [H2O-ferriheme](0); π-π dimeric [(HO-ferriheme)2](4-), [(H2O-ferriheme)(HO-ferriheme)](3-), [(H2O-ferriheme)2](2-), and [(H2O-ferriheme)2](0); and μ-oxo dimeric [μ-(ferriheme)2O](4-). Solvation of monomeric species predominated around the axial ligand, meso-hydrogen atoms of the porphyrin ring (Hmeso), and the unligated face. Existence of π-π ferriheme dimers in aqueous solution was supported by MD calculations where such dimers remained associated over the course of the simulation. Porphyrin rings were essentially coplanar. In these dimers major and minor solvation was observed around the axial ligand and Hmeso positions, respectively. In μ-oxo ferriheme, strong solvation of the unligated face and bridging oxide ligand was observed. The solution structure of the μ-oxo dimer was investigated using extended X-ray absorption fine structure (EXAFS) spectroscopy. The EXAFS spectrum obtained from frozen solution was markedly different from that recorded on dried μ-oxo ferriheme solid. Inclusion of five solvent molecules obtained from spatial distribution functions in the structure generated from MD simulation was required to produce acceptable fits to the EXAFS spectra of the dimer in solution, while the solid was suitably fitted using the crystal structure of μ-oxo ferriheme dimethyl ester which included no solvent molecules.

The newly parametrized AM1/d-CB1 is evaluated for its performance in modeling monosaccharide structure, carbohydrate ring pucker, amino acid proton transfer, DNA base pair interactions, carbohydrate-aromatic π interactions, and phosphates that are prominent in glycosyltransferases. The accuracy of the method in these computations is compared to a comprehensive range of NDDO methods commonly used to study glycan structure and reactivity in chemical biology. AM1/d-CB1 shows significant improvement over existing NDDO type methods in the computation of five and six membered carbohydrate ring pucker free energy surfaces. Moreover, the computation of carbohydrate amino acid interactions commonly present in catalytic domains and binding sites are improved over existing NDDO methods. AM1/d-CB1 shows slight improvement for carbohydrate-aromatic π interactions compared to a commonly used NDDO method (AM1). The method is applied to a glycosyltransferase reaction, where it is the only NDDO method able to achieve an optimized reaction profile. Moreover, a comparison of the geometry optimized computations of the reaction scheme give a transition state energy barrier that best compares with DFT (MPW1K). Overall, AM1/d-CB1 is shown to significantly improve on existing NDDO methods in modeling chemical glycobiological events.

We investigated link atom approaches for treating the polar C-O bond with particular reference to the glycosidic bond found in complex carbohydrates. We show that cutting this bond after the oxygen in the QM region and saturating the QM system with a hydrogen link atom leads to greater conformational and configurational accuracy at the boundary compared with cutting the bond before oxygen and saturating the QM system with a halogen link atom to represent the oxygen. Furthermore, we find that balancing the MM atom charges and redistributing the boundary atom charges at the QM/MM boundary minimizes the effect of the link atom, both energetically and structurally. This is illustrated via a series of calculations on a set of carbohydrate and carbohydrate-like model compounds. Finally, we confirm the validity of our model by performing molecular dynamics simulations for a typical disaccharide model compound in water. Our postsimulation conformational and configurational analyses show that the oxygen-to-water hydrogen pair distribution functions and the Φ,Ψ distributions at the glycosidic boundary between the quantum and classical regions compare favorably with results obtained from complete QM and complete MM treatments of the saccharide.

A semiempirical method based on the AM1/d Hamiltonian is introduced to model chemical glycobiological systems. We included in the parameter training set glycans and the chemical environment often found about them in glycoenzymes. Starting with RM1 and AM1/d-PhoT models we optimized H, C, N, O, and P atomic parameters targeting the best performing molecular properties that contribute to enzyme catalyzed glycan reaction mechanisms. The training set comprising glycans, amino acids, phosphates and small organic model systems was used to derive parameters that reproduce experimental data or high-level density functional results for carbohydrate, phosphate and amino acid heats of formation, amino acid proton affinities, amino acid and monosaccharide dipole moments, amino acid ionization potentials, water-phosphate interaction energies, and carbohydrate ring pucker relaxation times. The result is the AM1/d-Chemical Biology 1 or AM1/d-CB1 model that is considerably more accurate than existing NDDO methods modeling carbohydrates and the amino acids often present in the catalytic domains of glycoenzymes as well as the binding sites of lectins. Moreover, AM1/d-CB1 computed proton affinities, dipole moments, ionization potentials and heats of formation for transition state puckered carbohydrate ring conformations, observed along glycoenzyme catalyzed reaction paths, are close to values computed using DFT M06-2X. AM1/d-CB1 provides a platform from which to accurately model reactions important in chemical glycobiology.

Purine nucleoside phosphorylase is a transferase that catalyzes the addition of phosphate and removal of a purine base from guanosine and similar nucleosides. Here the interplay between sugar puckering conformation, the enzyme, and the perceived course of the reaction is examined using QM/MM FEARCF dynamics simulations. The enzyme biases the guanosine sugar ring toward a flattened (4)E conformer as a step that is critical to the success of the phosphorylation reaction. The C4' endo conformer allows the nonbonded ring oxygen orbital to align and donate electrons into the antibonding glycosidic bond orbital, thus weakening the bond. This conformational preference is due to sustained and directed noncovalent interactions anchored by the phosphate nucleophile's hydrogen bonds to the sugar C2' and C3' hydroxyls. In so doing, PNP alters the solution sugar ring pucker preferences as part of its catalytic reaction barrier lowering function.

Cyclic conformational coordinates are essential for the distinction of molecular ring conformers as the use of Cremer-Pople coordinates have illustrated for five- and six-membered rings. Here, by tessellating medium rings into triangular planes and using the relative angles made between triangular planes we are able to assign macrocyclic pucker conformations into canonical pucker conformers such as chairs, boats, etc. We show that the definition is straightforward compared with other methods popularly used for small rings and that it is computationally simple to implement for complex macrocyclic rings. These cyclic conformational coordinates directly couple to the motion of individual nodes of a ring. Therefore, they are useful for correlating the physical properties of macrocycles with their ring pucker and measuring the dynamic ring conformational behavior. We illustrate the triangular tessellation, assignment, and pucker analysis on 7- and 8-membered rings. Sets of canonical states are given for cycloheptane and cyclooctane that have been previously experimentally analysed.

Here we show that a series of inhibitors, constructed from plumbagin conjugated to a phenyl thioglucoside via an alkyl chain of variable length, are bound in solution-favoured ligand conformations to a mycothiol biosynthetic enzyme MshB, a GlcNAc-Ins deacetylase. The kinetic studies of this ligand series show that MshB is more strongly inhibited as a function of increasing alkyl chain length. While docking studies yielded highest ranked conformations in which the ligands extended along the catalytic site, these conformations produced free energy values prone to large errors and which were inconsistent with experimental kinetic measurements. Solution-favoured conformations of the inhibitors feature a preference for intramolecular aromatic association that results in curled conformations. Free energy perturbation calculations of MshB bound to the inhibitors in the preconfigured solution-favoured curled conformations gave the same binding pattern observed in the kinetic experiments. On investigation of these conformations lodged in the catalytic domain, we found that the selective feature determining their relative binding strength was the result of an optimisation of the dispersion interactions between the ligand aromatic groups phenyl and plumbagin, and the enzyme aromatic groups His144 and Tyr142 respectively. These results show that rather than deform the preferred folded ligand solution conformation, such that the hydrophobic C-2 acyl chain is linearly projected into a buried hydrophobic rich binding cavity adjacent to the active site, MshB binds preconfigured solution inhibitor curled conformations with a preference for aromatic association., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Speciation of ferriprotoporphyrin IX, Fe(III)PPIX, in aqueous solution is complex. Despite the use of its characteristic spectroscopic features for identification, the theoretical basis of the unique UV-visible absorbance spectrum of μ-[Fe(III)PPIX](2)O has not been explored. To investigate this and to establish a structural and spectroscopic model for Fe(III)PPIX species, density functional theory (DFT) calculations were undertaken for H(2)O-Fe(III)PPIX and μ-[Fe(III)PPIX](2)O. The models agreed with related Fe(III)porphyrin crystal structures and reproduced vibrational spectra well. The UV-visible absorbance spectra of H(2)O-Fe(III)PPIX and μ-[Fe(III)PPIX](2)O were calculated using time-dependent DFT and reproduced major features of the experimental spectra of both. Transitions contributing to calculated excitations have been identified. The features of the electronic spectrum calculated for μ-[Fe(III)PPIX](2)O were attributed to delocalization of electron density between the two porphyrin rings of the dimer, the weaker ligand field of the axial ligand, and antiferromagnetic coupling of the Fe(III) centers. Room temperature magnetic circular dichroism (MCD) spectra have been recorded and are shown to be useful in distinguishing between these two Fe(III)PPIX species. Bands underlying major spectroscopic features were identified through simultaneous deconvolution of UV-visible and MCD spectra. Computed UV-visible spectra were compared to deconvoluted spectra. Interpretation of the prominent bands of H(2)O-Fe(III)PPIX largely conforms to previous literature. Owing to the weak paramagnetism of μ-[Fe(III)PPIX](2)O at room temperature and the larger number of underlying excitations, interpretation of its experimental UV-visible spectrum was necessarily tentative. Nonetheless, comparison with the calculated spectra of antiferromagnetically coupled and paramagnetic forms of the μ-oxo dimer of Fe(III)porphine suggested that the composition of the Soret band involves a mixture of π→π* and π→d(π) charge transfer transitions. The Q-band and charge transfer bands appear to amalgamate into a mixed low energy envelope consisting of excitations with heavily admixed π→π* and charge transfer transitions.

MshB is the N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-D-glucopyranoside (GlcNAc-Ins) deacetylase active as one of the enzymes involved in the biosynthesis of mycothiol (MSH), a protective low molecular weight thiol present only in Mycobacterium tuberculosis and other actinomycetes. In this study, structural analogues of GlcNAc-Ins in which the inosityl moiety is replaced by a chromophore were synthesized and evaluated as alternate substrates of MshB, with the goal of identifying a compound that would be useful in high-throughput assays of the enzyme. In an unexpected and surprising finding one of the GlcNAc-Ins analogues is shown to undergo a Smiles rearrangement upon MshB-mediated deacetylation, uncovering a free thiol group. We demonstrate that this chemistry can be exploited for the development of the first continuous assay of MshB activity based on the detection of thiol formation by DTNB (Ellman's reagent); such an assay should be ideally suited for the identification of MshB inhibitors by means of high-throughput screens in microplates.

Free energy is a central measure in statistical mechanics and the means by which other thermodynamic properties of a system may be accessed. Using an efficient numerical method referred to as the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) method it is shown that multidimensional free energy volumes (FEVs) are computable and that they are critical to the understanding of reactions, conformational analysis and molecular association. Specifically the FEV of the hydrolysis reaction catalysed by a cellobiohydrolase I is shown to reveal molecular details of the reaction mechanism. The reaction is understood from a combination of the two dimensional reaction free energy surface, W(ξ(1), ξ(2)) and the three dimensional glucopyranose ring pucker FEV, W(ξ(1), ξ(2), ξ(3)). These studies provide for the first time details of the evolution of the oxocarbenium ion, which is a key to characterizing transition state structures seen in carbohydrate chemistry. A long-standing challenge has been the unambiguous assignment of the relative orientation of molecular pairs in solution. Here we describe how the molecular association of the benzene dimer in water and their relative orientational attraction are found from four dimensional, FEVs W(ξ(1), ξ(2), ξ(3), ξ(4)).

In this study of the thermodynamics of benzene association in water, we show that although the potential energy and enthalpy play an important role in the association of benzene dimers, they do not determine the relative orientation of these molecules on close contact in solution. We observe a large variation in the configurations that contribute to the vacuum (i.e., solvent-free) minimum free energy wells of the benzene contact pair. In water, fewer and smaller minimum free energy wells are observed. On examination, we find that fewer close contact configurations of benzene dimers populate these wells and that they are more energetically distinct from each other (compared with the vacuum case). The edge-over-edge configuration is most likely in solution and appears to evolve from the entropically favored side-by-side solvent shared configuration. Therefore, the relative orientation of the benzene molecules (i.e., parallel displaced, T-shaped, etc.) on association is a result of maximizing the contribution of the benzene-benzene entropy of association, to the solution free energy.

Glycosylation of cellobiose hydrolase I (CBHI), is a key step in the processing and degradation of cellulose. Here the pathways and barriers of the reaction are explored using the free energy from adaptive reaction coordinate forces (FEARCF) reaction dynamics method coupled with SCC-DFTB/MM. In many respects CBHI follows the expected general GH7 family mechanism that involves the Glu-X-Asp-X-X-Glu motif. However, critical electronic and conformational details, previously not known, were discovered through our computations. The central feature that ensures the success of the glycosylation reaction are the Glu212 nucleophile's hydrogen bond to the hydroxyl on C2, of the glucose in the -1 position of the cellulosic strand. This Glu212 function restricts the C2 hydroxyl in such a way as to favor the formation of the (4)E ring pucker of the -1 position glucose. A frontier molecular orbital analysis of the structures along the reaction surface proves the existence of an oxocarbenium ion, which has both transition state and intermediate character. The transition state structure is able to descend down the glycosylation pathway through the critical combination of Asp214 (HOMO), ring oxygen (LUMO), and Glu212 (HOMO), anomeric carbon (LUMO) interactions. Using the fully converged FEARCF SCC-DFTB/MM reaction surface, we find a barrier of 17.48 kcal/mol separating bound cellulose chain from the glycosylated CBHI. Taking recrossing into account gives k(cat) = 0.415 s(-1) for cellobiohydrolase glycosylation., (© 2011 American Chemical Society)

The conformations of several β1→β1' diglycosyl disulfides were investigated by NMR and computational methods. Experimental data, such as NOEs, proton-proton and proton-carbon-13 coupling constants, measured for solutions in DMSO, are in good agreement with values obtained by MD simulations in explicit DMSO. The disulfide torsion angles (C1-S-S-C1') preferentially sample values close to either +90° or -90° (+g or -g) and appear as the main metric that determines the conformational behavior of these glycomimetics. There is more conformational freedom around the C1-S and C1'-S' bonds (Φ and Ω torsions, respectively) and population cluster analysis allowed to identify up to four allowed conformational regions for each of the +g or -g forms. Population analysis of the hydroxylic group rotamers, based on proton-proton and proton-carbon-13 couplings as well as on calculated hydrogen bonding statistics, did not reveal any significant intramolecular hydrogen bonds in DMSO solution., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

The approach used to calculate the two-electron integral by many electronic structure packages including generalized atomic and molecular electronic structure system-UK has been designed for CPU-based compute units. We redesigned the two-electron compute algorithm for acceleration on a graphical processing unit (GPU). We report the acceleration strategy and illustrate it on the (ss|ss) type integrals. This strategy is general for Fortran-based codes and uses the Accelerator compiler from Portland Group International and GPU-based accelerators from Nvidia. The evaluation of (ss|ss) type integrals within calculations using Hartree Fock ab initio methods and density functional theory are accelerated by single and quad GPU hardware systems by factors of 43 and 153, respectively. The overall speedup for a single self consistent field cycle is at least a factor of eight times faster on a single GPU compared with that of a single CPU., (Copyright © 2011 Wiley Periodicals, Inc.)

We conducted an ultrasonic study of the hydration number for hexacyclic systems. We find from these experiments that cyclohexane-based molecules such as cyclohexanol and myo-inositol show a very small increase in hydration number despite the large difference in the number of hydroxyl groups present in each of the molecules. There is however a dramatic increase in hydration number when shifting from molecules with a cyclohexane frame to molecules with a cyclopyranose frame particularly glucose. An analysis of classical and quantum molecular dynamics simulation trajectories reveal that the hydration number is strongly linked to the conformational flexibility within the molecule. Cyclopyranose is a more rigid ring system compared with cyclohexane and so its ring fluctuates in a smaller range and frequency. The effect of the ring rigidity is that the hydroxyls tethered to the cyclopyranose ring undergo less positional diffusion compared with those attached to the cyclohexane ring. This allows for long time intermolecular hydrogen bonds between the hydroxyls bonded to cyclopyranose rings and the surrounding waters, which leads to an increase in the hydration numbers of carbohydrates compared with those of hydroxylated cyclohexanes., (© 2011 American Chemical Society)

We investigate the hydration structure and water/ion dynamics about complex anions using a revised platinum group metal chloro-anion force field. Nanosecond atomistic molecular dynamics simulations were performed for the platinum group metal chloro-anion complexes. This investigation makes the first attempt at describing diffusion trends of polyatomic complex anions with counterions such as these using both hydrodynamic and dielectric friction properties of the anion solution. The transition metal anion complex diffusion rates are shown to be correlated to their first solvent shell radial distribution function peaks, their mean water residence times, and their solvation volumes as calculated by Voronoi tessellation of the simulation cell. The general trend is for slower diffusion rates to result from larger hydration shell volumes. This diffusion rate trend calculated from Stokes' law is best described using the solventberg approach with well-chosen effective solvated radii. However, to improve the diffusion constant estimates when they are compared with those calculated from computer simulations, the dielectric friction is required.

The puckered conformations of furanose and pyranose carbohydrate rings are central to analyzing the action of enzymes on carbohydrates. Enzyme reaction mechanisms are generally inaccessible to experiments and so have become the focus of QM(semiempirical)/MM simulations. We show that the complete free energy of puckering is required to evaluate the accuracy of semiempirical methods used to study reactions involving carbohydrates. Interestingly, we find that reducing the free energy space to lower dimensions results in near meaningless minimum energy pathways. We analyze the furanose and pyranose free energy pucker surfaces and volumes using AM1, PM3, PM3CARB-1, and SCC-DFTB. A comparison with DFT optimized structures and a HF free energy surface reveals that SCC-DFTB provides the best semiempirical description of five- and six-membered carbohydrate ring deformation.

Understanding carbohydrate ring pucker is critical to rational design in materials and pharmaceuticals. Recently we have generalized our adaptive reaction coordinate force biasing method to perform calculations on multidimensional reaction coordinates. We termed this the Free Energies from Adaptive Reaction Coordinate Forces (FEARCF) method. Using FEARCF in SCC-DFTB QM/MM non-Boltzmann simulations, we are able to calculate multidimensional ring pucker free energies of conformation. Here we apply this to the six-membered glucopyranose ring located in an eight-membered β 1-4 linked octaose oligosaccharide (cellooctaose). The cellooctaose was built following the conformation of the saccharides bound to cellobiohydrolase I (CBHI) of Trichoderma reesei as reported in the 7CEL crystal structure obtained from the PDB. We calculate the free energy of ring puckering of the glucopyranose ring at the -1 position in vacuum, in water, and bound to the protein. We find that the protein induces (4)E and (4)H(3) conformations that are much more stable than the usually preferred (4)C(1) conformer. Furthermore, for the (4)H(3) conformation in the catalytic binding domain, there is significant electronic rearrangement that drives the structure toward the transition state of the glycosylation reaction.

The calculation of association constants from computer simulations has historically been complicated because of difficulties in validating metal ion force fields for solution simulations. Here we develop a method that produces a force field for divalent metal ions in metal sulfate solutions (i.e., Mg(2+)SO(4)(2-), Ca(2+)SO(4)(2-), Mn(2+)SO(4)(2-), Fe(2+)SO(4)(2-), Co(2+)SO(4)(2-), Ni(2+)SO(4)(2-), Cu(2+)SO(4)(2-), and Zn(2+)SO(4)(2-)). Using free energy of perturbation calculations, we are able to calibrate the potential of mean force W(r) for these metal sulfate solutions. The calibrated free energy profiles then allow us to produce association constants for contact, solvent-shared, and solvent-separated ion pairs that are in excellent agreement with available ultrasonic and dielectric spectroscopic data. This metal solution force field is accurate for the calculation of relative free energies from physical and biophysical computer simulations.

Circular dichroism analysis and proton NMR experiments revealed that solutions of 3-O-(2-methylnaphthyl)-beta-cyclodextrin form different dimer configurations. The exact nature of the dimer configurations were postulated to be of three types in which these capped cyclodextrins (CDs) are orientated in head-to-head and head-to-tail arrangements. Here we show from detailed computer simulations and free-energy calculations on the configurations that the head-to-head configuration in which the naphthyl groups are mutually inserted into each other's CD cavities is the most favoured configuration. This configuration optimises the hydrophobic association of the naphthyl aromatic groups and the ring cavities as well as forming the most inter-CD hydrogen bonds of the three configurations.

We previously used an adaptive reaction coordinate force biasing method for calculating the free energy of conformation (Naidoo and Brady, J Am Chem Soc 1999, 121, 2244) and chemical reactions (Rajamani et al., J Comput Chem 2003, 24, 1775) amongst others. Here, we describe a generalized version able to produce free energies in multiple dimensions, descriptively named the free energies from adaptive reaction coordinate forces method. To illustrate it, we describe how we calculate a multidimensional intermolecular orientational free energy, which can be used to investigate complex systems such as protein conformation and liquids. This multidimensional intermolecular free energy W(r, theta(1), theta(2), phi) provides a measure of orientationally dependent interactions that are appropriate for applications in systems that inherently have molecular anisotropic features. It is a highly informative free energy volume, which can be used to parameterize key terms such as the Gay-Berne intermolecular potential in coarse grain simulations. To demonstrate the value of the information gained from the W(r, theta(1), theta(2), phi) hypersurfaces we calculated them for TIP3P, TIP4P, and TIP5P dimer water models in vacuum. A comparison with a commonly used one-dimensional distance free energy profile is made to illustrate the significant increase in configurational information. The W(r) plots show little difference between the three models while the W(r, theta(1), theta(2), phi) hypersurfaces reveal the underlying energetic reasons why these potentials reproduce tetrahedrality in the condensed phase so differently from each., (Copyright 2009 Wiley Periodicals, Inc.)

Several novel thiourea derivatives of the NNRTI HI-236 substituted at the C-2 oxygen of the phenyl ring have been synthesized and evaluated for their inhibitory activity against HIV-1 (IIIB) replication in MT-2 cell cultures. The compounds were synthesized in order to fine-tune the activity of HI-236 as well as to gain insight into spatial characteristics in the pocket pertaining to the positional choice of tether in the design of [NRTI]-tether-[HI-236] bifunctional inhibitors. Two of the thiourea derivatives bearing a butynyl (6c) or hydroxyethyl tether (6n) were endowed with improved anti-HIV activity compared to HI-236. NNRTI activity was confirmed by a cell-free RT assay on six of the derivatives in which 6c returned an IC(50) of 3.8 nM compared to 28 nM for HI-236, establishing it as an improved lead for HI-236. The structure-activity profile is discussed in terms of potential interactions in the NNRTI pocket as suggested by a docking model using AutoDock, which have a bearing on the bifunctional drug design.

Although the conformational preferences in glucose and galactose have been studied since the early 1970s, only recently have the glucose and galactose hydroxymethyl populations been resolved by combining (3)J(HH) and (2)J(HH) NMR coupling data using a modified Karplus equation. A preference for gauche conformations is observed in monosaccharides, but the reasons for this are not understood. We calculated the free energy of rotation profiles for glucose and galactose primary alcohols using a semiempirical description of the monosaccharides in QM/MM simulations. From this we observed excellent agreement between our simulated population distributions for glucose gg/gt/tg = 35:57:3 and galactose gg/gt/tg = 4:86:7 with those measured from NMR. A stereoelectronic analysis of the minimum energy conformations using natural bond orbitals provides a clear description of the stabilizing contribution to the gauche conformers stemming from the C-H bonding and the C-O antibonding orbital interactions, specifically sigma(C6-H) --> sigma*(C5-O5) and sigma(C5-H) --> sigma*(C6-O6). Analysis of the solution trajectories reveals that persistent intramolecular hydrogen bonds and intermolecular bridging hydrogen bonds formed by water molecules between the ring oxygen and the hydroxymethyl group further stabilizes the gt conformation making it the preferred rotamer in both hydrated glucose and galactose. The hydroxymethyl quantum mechanics/molecular mechanics molecular dynamics trajectories and derived rotational free energies for these monosaccharides in water solutions explain that the experimental observations are due to a combination of competing stereoelectronic (gauche), electronic (intramolecular hydrogen bonding), and electrostatic (solvent-saccharide hydrogen bonding) factors.

We investigate, using molecular dynamics (MD) computer simulations, the conformational behavior of alpha-, beta-, and gamma-cyclodextrins (CDs). Our analysis of a 30 ns trajectory of CD solution dynamics reveals the underlying conformational behaviours of the CDs that explain their relative flexibility. The distributions of the torsion angles related to the glycosidic linkages, P(phi,psi) were calculated for the three CDs. Most noticeable is the limited range in phi torsion rotations compared with psi rotations for all the CDs. This difference between the three CDs is amplified in the motion and dynamics of their glucose monomers when we monitor their orientational and librational positions relative to the macrocyclic mean plane. The relaxation times of the monomers to their equilibrium orientations follow the pattern gamma-CD > alpha-CD > beta-CD. The root-mean-square deviations of the motion of the monomer centers of mass from the mean macrocyclic planes exhibit the same trend.

Several blood-feeding organisms, including the malaria parasite detoxify haem released from host haemoglobin by conversion to the insoluble crystalline ferriprotoporphyrin IX dimer known as haemozoin. To date the mechanism of haemozoin formation has remained unknown, although lipids or proteins have been suggested to catalyse its formation. We have found that beta-haematin (synthetic haemozoin) forms rapidly under physiologically realistic conditions near octanol/water, pentanol/water and lipid/water interfaces. Molecular dynamics simulations show that a precursor of the haemozoin dimer forms spontaneously in the absence of the competing hydrogen bonds of water, demonstrating that this substance probably self-assembles near a lipid/water interface in vivo.

We present a potential of mean force surface for rotation about phi and psi dihedral angles of the alpha(1 --> 4)-glycosidic linkage in the maltose disaccharide (4-O-alpha-d-glucopyranosyl-d-glucopyranose) in aqueous solution. Comparison of the vacuum and solution free energy surfaces for maltose shows the principal effects of water to be an increase in the rotational freedom of the alpha(1 --> 4) linkage brought about by lowering the energy barrier for syn to anti conformational changes as well as expansion of the range of low-energy phi,psi conformations. This free energy analysis thus provides a thermodynamic and conformational rationale for the effects of water on alpha(1 --> 4)-linked polysaccharides and carbohydrate glasses.

We present calculated potential of mean force surfaces for rotation about phi, psi dihedral angles of the alpha(1<-->1)alpha-glycosidic linkage in the disaccharide trehalose (alpha-D-Glc-(1<-->1)-alpha-D-Glc) in both vacuum and aqueous solution. The effects of aqueous solvation upon the alpha(1<-->1)alpha-glycosidic linkage are investigated through comparison of the vacuum and aqueous solution free-energy surfaces. These surfaces reveal that trehalose is restricted to a single minimum-energy conformation in both vacuum and solution. The exceptional rigidity of this disaccharide in solution may provide a molecular rationale for the antidesiccant properties of trehalose glasses.

The primary mechanism for relieving tensile strain in alpha-linked polysaccharides (e.g., [alpha-d-Glc-(1-->4)alpha-d-Glc]n) is achieved by complex rotations of the glycosidic linkages. This is shown through computer simulations of atomic force microscopy stretching experiments in combination with free energy calculations of the unfolding pattern for amylose. The experimental force-extension curve is reproduced and analyzed to reveal that the chair-to-boat conversions play a smaller role than previously proposed.