Towards a quantum mechanical force field for carbohydrates: a reparametrized semi-empirical MO approach

McNamara, Jonathan P.; Muslim, Abdul-Mueed; Abdel-Aal, Hoda; Wang, Hong; Mohr, Matthias; Hillier, Ian H.; Bryce, Richard A.

doi:10.1016/j.cplett.2004.07.037

Cited by 46 publications

(47 citation statements)

References 19 publications

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“…This is most likely attributable to a known limitation of this method with respect to representing glycosidic torsions. 23 Interestingly, SCC-DFTB-D outperformed both of the other methods with respect to computing the effect of hexosamine 4-sulfation on linkage 3D-conformation and acetamido libration, suggesting quantifiable benefits of including dispersion when sulfate is present.…”

Section: Discussionmentioning

confidence: 96%

“…2C) Interestingly, previous carbohydrate studies using PM3-CARB1 have not reported the conversion from 4 C 1 to 1 C 4 chair observed here, probably due to the fact that earlier work was on the sub-nanosecond timescale. 23 The principal improvement of PM3-CARB1 over standard PM3 is the correct energetic ranking of 4 C 1 and 1 C 4 conformations. The 1 C 4 chair can therefore be expected to be more populated in standard PM3 trajectories.…”

Section: Comparison Of Computed and Experimental Monosaccharide Geometrymentioning

confidence: 99%

“…The SCC-DFTB method, which is $2-3 orders of magnitude faster than standard DFT calculations using a DZP basis set, has also been previously applied to carbohydrates. 26 However, only a handful of glycosaminoglycan semi-empirical QM/MM molecular dynamics simulations exist in the literature, 23,27,28 none investigating the effects of epimerization or sulfation and no comparisons between them. The other computational chemistry methods for exploring glycosaminoglycan 3D-structure are the more approximate coarse grained [29][30][31] and molecular mechanics force-field formalisms.…”

Section: Introductionmentioning

confidence: 99%

“…However, many semi-empirical methods have not performed well for glycosaminoglycans. 21,22 Among the most promising approaches are PM3-CARB1 23 (a re-parameterization of PM3 24 for carbohydrates) and the self-consistent charge density functional tightbinding method 25 (SCC-DFTB-D), an approximate method based on a second-order expansion of the DFT total energy expression and including an empirical energetic correction for dispersion. The efficiency of such methods (compared with DFT) stems from usage of a minimal basis.…”

Section: Introductionmentioning

confidence: 99%

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Less is more when simulating unsulfated glycosaminoglycan 3D‐structure: Comparison of GLYCAM06/TIP3P, PM3‐CARB1/TIP3P, and SCC‐DFTB‐D/TIP3P predictions with experiment

Sattelle¹,

Almond²

2010

J Comput Chem

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The 3D-structure of extracellular matrix glycosaminoglycans is central to function, but is currently poorly understood. Resolving this will provide insight into their heterogeneous biological roles and help to realize their significant therapeutic potential. Glycosaminoglycan chemical isoforms are too numerous to study experimentally and simulation provides a tractable alternative. However, best practice for accurate calculation of glycosaminoglycan 3D-structure within biologically relevant nanosecond timescales is uncertain. Here, we evaluate the ability of three potentials to reproduce experimentally observed glycosaminoglycan monosaccharide puckering, disaccharide 3D-conformation, and characteristic solvent interactions. Temporal dynamics of unsulfated chondroitin, chondroitin-4-sulfate, and hyaluronan β(1→3) disaccharides were simulated within TIP3P explicit solvent unrestrained for 20 ns using the GLYCAM06 force-field and two semi-empirical quantum mechanics methods, PM3-CARB1 and SCC-DFTB-D (both within a hybrid QM/MM formalism). Comparison of calculated and experimental properties (vicinal couplings, nuclear Overhauser enhancements, and glycosidic linkage geometries) showed that the carbohydrate-specific parameterization of PM3-CARB1 imparted quantifiable benefits on monosaccharide puckering and that the SCC-DFTB-D method (including an empirical correction for dispersion) best modeled the effects of hexosamine 4-sulfation. However, paradoxically, the most approximate approach (GLYCAM06/TIP3P) was the best at predicting monosaccharide puckering, 3D-conformation, and solvent interactions. Our data contribute to the debate and emerging consensus on the relative performance of these levels of theory for biological molecules.

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Section: Discussionmentioning

confidence: 96%

Section: Comparison Of Computed and Experimental Monosaccharide Geometrymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Less is more when simulating unsulfated glycosaminoglycan 3D‐structure: Comparison of GLYCAM06/TIP3P, PM3‐CARB1/TIP3P, and SCC‐DFTB‐D/TIP3P predictions with experiment

Sattelle¹,

Almond²

2010

J Comput Chem

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“…Standard semiempirical molecular orbital methods have significant shortcomings for carbohydrates, but reparametrized variants have been developed, which give better descriptions of carbohydrate conformation (e.g. PM3CARB-1; McNamara et al 2004). …”

Section: Empirical 'Mm' Force Fields For Biomoleculesmentioning

confidence: 99%

Biomolecular simulation and modelling: status, progress and prospects

Kamp

Shaw

Woods

et al. 2008

J. R. Soc. Interface.

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Molecular simulation is increasingly demonstrating its practical value in the investigation of biological systems. Computational modelling of biomolecular systems is an exciting and rapidly developing area, which is expanding significantly in scope. A range of simulation methods has been developed that can be applied to study a wide variety of problems in structural biology and at the interfaces between physics, chemistry and biology. Here, we give an overview of methods and some recent developments in atomistic biomolecular simulation. Some recent applications and theoretical developments are highlighted.

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Correlated ab initio quantum chemical calculations of di‐ and trisaccharide conformations

2007

Self Cite

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High level correlated quantum chemical calculations, using MP2 and local MP2 theory, have been performed for conformations of the disaccharide, beta-maltose, and the trisaccharide, 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose. For beta-maltose, MP2 and local MP2 calculations using the 6-311++G** basis set are in good agreement, predicting a global minimum gas-phase conformation with a counterclockwise hydrogen bond network and the experimentally-observed intersaccharide hydrogen bonding arrangement. For conformations of 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose, MP2/6-311++G**, and local MP2/6-311++G** calculations do not provide a consensus prediction of relative energetics, with the MP2 method finding large differences in stability between extended and folded trisaccharide conformations. Local MP2 calculations, less susceptible to intramolecular basis set superposition errors, predict a narrower range of trisaccharide energetics, in line with estimates from Hartree-Fock theory and B3LYP and BP86 density functionals. All levels of theory predict compact, highly hydrogen-bonded conformations as lowest in energy on the in vacuo potential energy surface of the trisaccharide. These high level, correlated local MP2/6-311++G** calculations of di- and trisaccharide energetics constitute potential reference data in the development and testing of improved empirical and semiempirical potentials for modeling of carbohydrates in the condensed phase.

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Towards a quantum mechanical force field for carbohydrates: a reparametrized semi-empirical MO approach

Cited by 46 publications

References 19 publications

Less is more when simulating unsulfated glycosaminoglycan 3D‐structure: Comparison of GLYCAM06/TIP3P, PM3‐CARB1/TIP3P, and SCC‐DFTB‐D/TIP3P predictions with experiment

Less is more when simulating unsulfated glycosaminoglycan 3D‐structure: Comparison of GLYCAM06/TIP3P, PM3‐CARB1/TIP3P, and SCC‐DFTB‐D/TIP3P predictions with experiment

Biomolecular simulation and modelling: status, progress and prospects

Correlated ab initio quantum chemical calculations of di‐ and trisaccharide conformations

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