A comparison and chemometric analysis of several molecular mechanics force fields and parameter sets applied to carbohydrates

Pérez, Serge; Imberty, Anne; Engelsen, Søren B.; Gruza, Jan; Mazeau, K.; Jiménez‐Barbero, Jesús; Poveda, Ana; Espinosa, Juan F.; Eyck, B.P. van; Johnson, Glenn P.; French, Alfred D.; Kouwijzer, Milou; Grootenuis, Peter D.J; Bernardi, Anna; Raimondi, Laura; Senderowitz, Hanoch; Durier, V.; Vergoten, Gérard; Rasmussen, Kjeld

doi:10.1016/s0008-6215(98)00305-x

Cited by 155 publications

(90 citation statements)

References 30 publications

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“…The problem of reproducing some carbohydrates peculiarities, such as the rotameric distribution of the hydroxymethyl group or the anomeric and exo-anomeric effects, have been addressed in various force fields, and the reader can find some comparative analyses in Refs. [29][30][31]. However, considerably less attention has been devoted so far to the correct reproduction of the ring conformational properties.…”

Section: Introductionmentioning

confidence: 99%

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation

Autieri

Sega

Pederiva

et al. 2010

The Journal of Chemical Physics

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We present the results of a combined metadynamics-umbrella sampling investigation of the puckered conformers of pyranoses described using the gromos 45a4 force field. The free energy landscape of Cremer-Pople puckering coordinates has been calculated for the whole series of α and β aldohexoses, showing that the current force field parameters fail in reproducing proper puckering free energy differences between chair conformers. We suggest a modification to the gromos 45a4 parameter set which improves considerably the agreement of simulation results with theoretical and experimental estimates of puckering free energies. We also report on the experimental measurement of altrose conformers populations by means of NMR spectroscopy, which show good agreement with the predictions of current theoretical models.

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Section: Introductionmentioning

confidence: 99%

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation

Autieri

Sega

Pederiva

et al. 2010

The Journal of Chemical Physics

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“…MM3 is considered one of the best force fields for carbohydrates because it allows full relaxation of the glycosidic residues taking into account the exo-anomeric effect (29,30). The notations used for the torsion angles of the glycosidic linkage are as follows: ⌽ ϭ O5-C1-O1-CX, ⌿ ϭ C1-O1-CX-CXϩ1, and ϭ O5-C5-C6-O6.…”

Section: Methodsmentioning

confidence: 99%

Role of Water Molecules in Structure and Energetics of Pseudomonas aeruginosa Lectin I Interacting with Disaccharides

Nurisso

Blanchard

Audfray

et al. 2010

Journal of Biological Chemistry

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Calcium-dependent lectin I from Pseudomonas aeruginosa (PA-IL) binds specifically to oligosaccharides presenting an ␣-galactose residue at their nonreducing end, such as the disaccharides ␣Gal1-2␤GalOMe, ␣Gal1-3␤GalOMe, and ␣Gal1-4␤GalOMe. This provides a unique model for studying the effect of the glycosidic linkage of the ligands on structure and thermodynamics of the complexes by means of experimental and theoretical tools. The structural features of PA-IL in complex with the three disaccharides were established by docking and molecular dynamics simulations and compared with those observed in available crystal structures, including PA-IL⅐␣Gal1-2␤GalOMe complex, which was solved at 2.4 Å resolution and reported herein. The role of a structural bridge water molecule in the binding site of PA-IL was also elucidated through molecular dynamics simulations and free energy calculations. This water molecule establishes three very stable hydrogen bonds with O6 of nonreducing galactose, oxygen from Pro-51 main chain, and nitrogen from Gln-53 main chain of the lectin binding site. Binding free energies for PA-IL in complex with the three disaccharides were investigated, and the results were compared with the experimental data determined by titration microcalorimetry. When the bridge water molecule was included in the free energy calculations, the simulations predicted the correct binding affinity trends with the 1-2-linked disaccharide presenting three times stronger affinity ligand than the other two. These results highlight the role of the water molecule in the binding site of PA-IL and indicate that it should be taken into account when designing glycoderivatives active against P. aeruginosa adhesion.

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“…Somente para citar, diferentes campos de força quando são avaliados segundo a capacidade de descrever o ordenamento anomérico alfa-beta, podem apresentar diferenças de até 14 kcal/mol para o mesmo sistema, havendo por vezes, inclusive, inversão da preferência. 28,29 E esta pode ser uma informação preocupante, haja vista que mais de 90% dos trabalhos teóricos existentes utilizam simulações moleculares com campos de força, por conta da facilidade na varredura do espaço conformacional que estes métodos oferecem. Talvez, pelo menos para monossacarídeos, já haja alternativa... Nesta situação, somente métodos eletrônicos mais detalhados como aqueles quanto-mecânicos teriam mais chance de propriamente quantificar este efeito esteoeletrônico, que a evolução parece ter selecionado de modo sutil, porém preciso.…”

Section: Considerações Finaisunclassified

Anomeric Effect in Carbohydrates: Facts and Hypothesis

Silva¹

2011

Revista Virtual De Química

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Abstract:The anomeric effect is responsible for the determination of conformations in many systems, although it is related mainly to the determination of conformations in carbohydrates, due to two reasons: firstly, because it was from the study of some carbohydrate reactions that it was identified for the first time. Secondly, because carbohydrates occur naturally in several distinct conformations, in which such effect plays a key role. Very often, it's clear definition is merged with its controversial origin, leading to misunderstandings about the comprehension of the anomeric effect. This text intends to present separately the facts and the suppositions about the origin of the anomeric effect. Taking into account some examples, the text is pretended to be an easy reading about this subject. It discusses some situations where such effect determines the compound chemistry: preferably D-glicose molecule in the most abundant axial and equatorial conformations.Keywords: anomeric effect; stereoelectronic effects; carbohydrates. ResumoO efeito anomérico é responsável pela determinação da conformação de muitos sistemas, muito embora esteja ligado principalmente à determinação da conformação de carboidratos, por duas razões: primeiramente porque foi através da reatividade destes compostos que foi identificado pela primeira vez, e segundo, por conta da diversidade conformacional que tais compostos apresentam, onde este efeito tem papel determinante. Muito frequentemente a sua inequívoca definição vem confundida com a sua controversa origem, e o conceito então, incorporado de modo indevido. O presente texto tem por objetivo apresentar, em separado, o que é fato sobre o efeito anomérico, daquilo que é suposição. Valendo-se de vários exemplos de sua manifestação, o texto pretende ser de fácil leitura, e ilustra diversas situações onde o efeito é determinante na química do composto em análise: na maior parte dos casos, a molécula de D-glicose nas duas conformações (axial e equatorial) mais abundantes.Palavras-chave: efeito anomérico; efeitos estereoeletrônicos; carboidratos.

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A comparison and chemometric analysis of several molecular mechanics force fields and parameter sets applied to carbohydrates

Cited by 155 publications

References 30 publications

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation

Role of Water Molecules in Structure and Energetics of Pseudomonas aeruginosa Lectin I Interacting with Disaccharides

Anomeric Effect in Carbohydrates: Facts and Hypothesis

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