Molecular Conformations of Di-, Tri-, and Tetra-
conformational analysis
molecular dynamics
nuclear magnetic resonance
sialic acid
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
19 Dec 2019
19 Dec 2019
Historique:
received:
12
11
2019
revised:
12
12
2019
accepted:
14
12
2019
entrez:
22
12
2019
pubmed:
22
12
2019
medline:
6
5
2020
Statut:
epublish
Résumé
By using molecular dynamics simulations with an efficient enhanced sampling technique and in combination with nuclear magnetic resonance (NMR) spectroscopy quantitative structural information on α -2,8-linked sialic acids is presented. We used a bottom-up approach to obtain a set of larger ensembles for tetra- and deca-sialic acid from model dimer and trimer systems that are in agreement with the available J-coupling constants and nuclear Overhauser effects. The molecular dynamic (MD) simulations with enhanced sampling are used to validate the force field used in this study for its further use. This empowered us to couple NMR observables in the MD framework via J-coupling and distance restraining simulations to obtain conformations that are supported by experimental data. We used these conformations in thermodynamic integration and one-step perturbation simulations to calculate the free-energy of suggested helical conformations. This study brings most of the available NMR experiments together and supplies information to resolve the conflict on the structures of poly- α -2,8-linked sialic acid.
Identifiants
pubmed: 31861593
pii: ijms21010030
doi: 10.3390/ijms21010030
pmc: PMC6981865
pii:
doi:
Substances chimiques
N-Acetylneuraminic Acid
GZP2782OP0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Austrian Science Fund FWF
ID : W 1224
Pays : Austria
Organisme : Austrian Science Fund
ID : W1224
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