The SPASIBA force field as an essential tool for studying the structure and dynamics of saccharides

Vergoten, Gérard; Mazur, I. A.; Lagant, P.; Michalski, Jean‐Claude; Zanetta, Jean‐Pierre

doi:10.1016/s0300-9084(03)00052-x

Cited by 55 publications

(41 citation statements)

References 20 publications

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“…Torsional potentials related to ring bonds and exocylic hydroxyl groups were deduced from spectroscopic data on crystal forms of monosaccharides and extended to a variety of glycosidic linkages appearing in disaccharides. 14,15 Examination of the low-frequency region (76-300 cm -1 ) reveals a good agreement with the DFT predictions, in particular, for the monosaccharide ring normal modes involving CT-CT, CT-O5, and exocyclic hydroxyl group torsional librations and ring deformations.…”

Section: Resultssupporting

confidence: 70%

“…The SPASIBA force field is a spectroscopic molecular-mechanics-derived empirical potential function first devoted to proteins 13 and extended to a large variety of chemical groups such as alkanes, alkenes, amino acids, ethers, esters, thiols, alcohols, saccharides, and phospholipids. [14][15][16][17][18][19][20] Not only does this force field appear to be an adequate tool for molecular mechanics studies of monosaccharides, but it has also been extended to force constant determination related to various glycosidic linkages along the etablishment of Ramachandran's φ, ψ maps. 14,15 The SPASIBA force field has been developed in our group for many years.…”

Section: Methodsmentioning

confidence: 99%

“…[14][15][16][17][18][19][20] Not only does this force field appear to be an adequate tool for molecular mechanics studies of monosaccharides, but it has also been extended to force constant determination related to various glycosidic linkages along the etablishment of Ramachandran's φ, ψ maps. 14,15 The SPASIBA force field has been developed in our group for many years. It is able to reproduce at the same time structures energies and vibrational spectra with a much higher precision on the latter than commonly available force fields.…”

Section: Methodsmentioning

confidence: 99%

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The SPASIBA Force Field for Chondroitin Sulfate: Vibrational Analysis of d-Glucuronic and N-acetyl-d-Galactosamine 4-Sulfate Sodium Salts

et al. 2006

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Normal-mode analyses were carried out on the two components of the chondroitin 4-sulfate linear glycosaminoglycan, a copolymer implying alternate D-glucuronate beta-(1-->3) and N-acetyl-D-galactosamine 4-sulfate beta-(1-->4) (hereafter named D-galactosamine 4-sulfate) residues. Scaled quantum mechanical calculations (SQM) using the density functional theory approach at different levels of theory (B3LYP/6-31G** and B3LYP/6-31++G**) were performed to obtain correct vibrational assignments. The SPASIBA empirical force field parameters were then obtained from both theoretical predictions and observed IR and Raman data. It is shown that calculations including diffuse functions at the B3LP/6-31++G** level and the introduction of the Na+ counterion are necessary to give correct assignments of the CO2- symmetric (nu(s)) and antisymmetric (nu(a)) stretching modes for the glucuronic carboxylate residue.

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Section: Resultssupporting

confidence: 70%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

The SPASIBA Force Field for Chondroitin Sulfate: Vibrational Analysis of d-Glucuronic and N-acetyl-d-Galactosamine 4-Sulfate Sodium Salts

et al. 2006

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“…Additionally an empirical potential energy of interaction ∆E for the ranked complexes was evaluated using the simple expression ∆E(interaction) = E(complex) − (E(protein) + E(ligand) [ 44 , 45 ]. For that purpose, the Spectroscopic Emperical Potential Energy Function SPASIBA and the corresponding parameters are used [ 46 , 47 ]. Discovery Studio Visualizer 4.1 (Accelrys, San Diego, CA, USA) was used for viewing, Chimera version 1.8 (University of California, San Francisco, CA, USA) for figure preparation.…”

Section: Methodsmentioning

confidence: 99%

Sites for Dynamic Protein-Carbohydrate Interactions of O- and C-Linked Mannosides on the E. coli FimH Adhesin

et al. 2017

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Antagonists of the Escherichia coli type-1 fimbrial adhesin FimH are recognized as attractive alternatives for antibiotic therapies and prophylaxes against acute and recurrent bacterial infections. In this study α-d-mannopyranosides O- or C-linked with an alkyl, alkene, alkyne, thioalkyl, amide, or sulfonamide were investigated to fit a hydrophobic substituent with up to two aryl groups within the tyrosine gate emerging from the mannose-binding pocket of FimH. The results were summarized into a set of structure-activity relationships to be used in FimH-targeted inhibitor design: alkene linkers gave an improved affinity and inhibitory potential, because of their relative flexibility combined with a favourable interaction with isoleucine-52 located in the middle of the tyrosine gate. Of particular interest is a C-linked mannoside, alkene-linked to an ortho-substituted biphenyl that has an affinity similar to its O-mannosidic analog but superior to its para-substituted analog. Docking of its high-resolution NMR solution structure to the FimH adhesin indicated that its ultimate, ortho-placed phenyl ring is able to interact with isoleucine-13, located in the clamp loop that undergoes conformational changes under shear force exerted on the bacteria. Molecular dynamics simulations confirmed that a subpopulation of the C-mannoside conformers is able to interact in this secondary binding site of FimH.

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“…In the minimization procedures, the spectroscopic empirical energy function SPASIBA and the corresponding parameters are used. [45][46][47] A typical lowest energy structure for the complex LecA-G2b is shown in Fig. S3.…”

Section: In Silico Molecular Dockingmentioning

confidence: 99%

Importance of topology for glycocluster binding to Pseudomonas aeruginosa and Burkholderia ambifaria bacterial lectins

et al. 2015

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Pseudomonas aeruginosa (PA) and Burkholderia ambifaria (BA) are two opportunistic Gram negative bacteria and major infectious agents involved in lung infection of cystic fibrosis patients. Both bacteria can develop resistance to conventional antibiotherapies. An alternative strategy consists of targeting virulence factors in particular lectins with high affinity ligands such as multivalent glycoclusters. LecA (PA-IL) and LecB (PA-IIL) are two tetravalent lectins from PA that recognise galactose and fucose respectively. BambL lectin from BA is trimeric with 2 binding sites per monomer and is also specific for fucose. These three lectins are potential therapeutic targets in an anti-adhesive anti-bacterial approach. Herein, we report the synthesis of 18 oligonucleotide pentofuranose-centered or mannitol-centered glycoclusters leading to tri-, penta- or decavalent clusters with different topologies. The linker arm length between the core and the carbohydrate epitope was also varied leading to 9 galactoclusters targeting LecA and 9 fucoclusters targeting both LecB and BambL. Their dissociation constants (Kd) were determined using a DNA-based carbohydrate microarray technology. The trivalent xylo-centered galactocluster and the ribo-centered fucocluster exhibited the best affinity for LecA and LecB respectively while the mannitol-centered decafucocluster displayed the best affinity to BambL. These data demonstrated that the topology and nature of linkers were the predominant factors for achieving high affinity rather than valency.

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The SPASIBA force field as an essential tool for studying the structure and dynamics of saccharides

Cited by 55 publications

References 20 publications

The SPASIBA Force Field for Chondroitin Sulfate: Vibrational Analysis of d-Glucuronic and N-acetyl-d-Galactosamine 4-Sulfate Sodium Salts

The SPASIBA Force Field for Chondroitin Sulfate: Vibrational Analysis of d-Glucuronic and N-acetyl-d-Galactosamine 4-Sulfate Sodium Salts

Sites for Dynamic Protein-Carbohydrate Interactions of O- and C-Linked Mannosides on the E. coli FimH Adhesin

Importance of topology for glycocluster binding to Pseudomonas aeruginosa and Burkholderia ambifaria bacterial lectins

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