Conformational analysis of diribosylribitol phosphate by NMR spectroscopy and molecular dynamics

Maestre, M.; Pérez, Carolina

doi:10.1002/(sici)1097-458x(200002)38:2<123::aid-mrc586>3.3.co;2-c

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“…Recently, an MD and NMR study was presented of the CPS from serotype b, which contains a ribitol phosphodiester in the repeating unit. Good agreement was found between NMR observables and the MD simulation which used the GROMOS force field …”

Section: Resultsmentioning

confidence: 75%

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Molecular Dynamics Simulations of the Phosphodiester-Linked Repeating Units of the Haemophilus influenzae Types c and f Capsular Polysaccharides

2001

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The three-dimensional structure of the repeating units of Haemophilus influenzae types c and f capsular polysaccharides (CPS) have been investigated by molecular dynamics simulations. The models consist of disaccharides joined by phosphodiester linkages, explicit water, and sodium as the counterion. Four 1 ns simulations were performed for each type, with either different starting conformations or different methods to handle long-range truncation effects, namely, Ewald summation or force shift truncation. For the average properties investigated, the choice of the method did not make any significant difference. Limited flexibility was observed close to the sugar residues, whereas at the phosphorus atom, the torsions showed major transitions. For comparison, 3 J H,P was measured on CPS material. On the basis of these spin-spin couplings, only small changes are required in the models of the disaccharide repeating unit to agree with data on the CPS. In addition, hydrogen bonding and radial and spatial distribution functions were analyzed to obtain a picture of solvent ordering around the disaccharides.

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Section: Resultsmentioning

confidence: 75%

“…Good agreement was found between NMR observables and the MD simulation which used the GROMOS force field. 24 III. Solvent Structure.…”

Section: Conformation and Flexibilitymentioning

confidence: 99%

Molecular Dynamics Simulations of the Phosphodiester-Linked Repeating Units of the Haemophilus influenzae Types c and f Capsular Polysaccharides

2001

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show abstract

Conformational analysis of diribosylribitol phosphate by NMR spectroscopy and molecular dynamics

Cited by 1 publication

References 0 publications

Molecular Dynamics Simulations of the Phosphodiester-Linked Repeating Units of the Haemophilus influenzae Types c and f Capsular Polysaccharides

Molecular Dynamics Simulations of the Phosphodiester-Linked Repeating Units of the Haemophilus influenzae Types c and f Capsular Polysaccharides

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