GLYCAM06: A generalizable biomolecular force field. Carbohydrates

Kirschner, Karl N.; Yongye, Austin B.; Tschampel, Sarah M.; González-Outeiriño, Jorge; Daniels, Charlisa R.; Foley, B. Lachele; Woods, Robert J.

doi:10.1002/jcc.20820

Cited by 1,872 publications

(1,877 citation statements)

References 148 publications

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“…Note that the MD force field used chose to average properties of α-and β-glucose anomers to provide general, widely applicable parameters. 63 Consequently, we do not expect the MD simulations completed here to capture fine-grained differences between the behaviors of the anomers. However, the MD system provides valuable information about the interaction of the glucose molecules and the solvent environment.…”

Section: ■ Experimental Methodsmentioning

confidence: 86%

Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment

Mayes

Tian

Nolte³

et al. 2013

J. Phys. Chem. B

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In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on B-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of Î±-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na + suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na + interacts similarly with a-and B-glucose. ABSTRACT: In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on β-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na + suggests that computational studies of g...

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Section: ■ Experimental Methodsmentioning

confidence: 86%

Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment

Mayes

Tian

Nolte³

et al. 2013

J. Phys. Chem. B

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“…27,28 Cellulose was modelled using the GLYCAM06h force field. 29 Scaling factors for 1-4 electrostatic and van der Waals interactions were both taken as unity for cellulose; and the AMBER defaults of 1.2 and 2.0 respectively for graphene. We note that in previous work examining carbohydratearomatic complexes containing CH- and OH- interactions, we found that the GLYCAM06 force field yielded interaction energies within 1 kcal/mol of complete basis set CCSD(T) values.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Molecular Dynamics of Cellulose Amphiphilicity at the Graphene–Water Interface

2015

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Molecular dynamics (MD) simulations have been applied to study the interactions between hydrophobic and hydrophilic faces of ordered cellulose chains and a single layer of graphene in explicit aqueous solvent. The hydrophobic cellulose face is predicted to form a stable complex with graphene. This interface remains solvent-excluded over the course of simulations; the cellulose chains contacting graphene in general preserve intra-and inter-chain hydrogen bonds and a tg orientation of hydroxymethyl groups. Greater flexibility is observed in the more solvent-exposed cellulose chains of the complex. By contrast, the hydrophilic face of cellulose exhibits progressive rearrangement over the course of MD simulations, as it seeks to present its hydrophobic face, with disrupted intra-and interchain hydrogen bonding; residue twisting to form CH- interactions with graphene; and partial permeation of water. This transition is also accompanied by a more favorable cellulose-graphene adhesion energy as predicted at the PM6-DH2 level of theory. The stability of the cellulose-graphene hydrophobic interface in water exemplifies the amphiphilicity of cellulose and provides insight into favored interactions within graphene-cellulose materials. Furthermore, partial permeation of water between exterior cellulose chains may indicate potential in addressing cellulose recalcitrance.3

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“…Development of accurate force fields describing the inherently complex properties of carbohydrates is a nontrivial task. There have been extensive re-parameterization of the general purpose force fields used in CHARMM Hatcher et al 2009), AMBER (Kirschner et al 2008), and GROMOS (Lins and Hünenberger 2005), and parameterization of new carbohydrate force fields. Currently, there are high-level carbohydrate force fields that are used for computer simulations (Fadda and Woods 2010).…”

Section: Molecular Dynamics Simulations Of N-glycansmentioning

confidence: 99%

Conformational flexibility of N-glycans in solution studied by REMD simulations

Nishima

Miyashita³

et al. 2012

Biophys Rev

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Protein-glycan recognition regulates a wide range of biological and pathogenic processes. Conformational diversity of glycans in solution is apparently incompatible with specific binding to their receptor proteins. One possibility is that among the different conformational states of a glycan, only one conformer is utilized for specific binding to a protein. However, the labile nature of glycans makes characterizing their conformational states a challenging issue. All-atom molecular dynamics (MD) simulations provide the atomic details of glycan structures in solution, but fairly extensive sampling is required for simulating the transitions between rotameric states. This difficulty limits application of conventional MD simulations to small fragments like di-and tri-saccharides. Replica-exchange molecular dynamics (REMD) simulation, with extensive sampling of structures in solution, provides a valuable way to identify a family of glycan conformers. This article reviews recent REMD simulations of glycans carried out by us or other research groups and provides new insights into the conformational equilibria of N-glycans and their alteration by chemical modification. We also emphasize the importance of statistical averaging over the multiple conformers of glycans for comparing simulation results with experimental observables. The results support the concept of "conformer selection" in protein-glycan recognition.

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GLYCAM06: A generalizable biomolecular force field. Carbohydrates

Cited by 1,872 publications

References 148 publications

Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment

Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment

Molecular Dynamics of Cellulose Amphiphilicity at the Graphene–Water Interface

Conformational flexibility of N-glycans in solution studied by REMD simulations

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