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WaterLOGSY NMR Experiments in Conjunction with Molecular‐Dynamics Simulations Identify Immobilized Water Molecules That Bridge Peptide Mimic MDWNMHAA to Anticarbohydrate Antibody SYA/J6
Author(s) -
Szczepina Monica G.,
Bleile Dustin W.,
Müllegger Johannes,
Lewis Andrew R.,
Pinto B. Mario
Publication year - 2011
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.201101464
Subject(s) - molecular dynamics , chemistry , molecule , bound water , peptide , nuclear magnetic resonance spectroscopy , spectroscopy , stereochemistry , computational chemistry , biochemistry , organic chemistry , physics , quantum mechanics
X‐ray crystallographic data of the carbohydrate mimic MDWNMHAA when bound to an anti‐ Shigella flexneri Y mAb SYA/J6 indicate the immobilization of water molecules, that is, the presence of “bound” waters, in the active site. Water Ligand Observed via Gradient Spectroscopy (WaterLOGSY) was used in conjunction with saturation transfer difference (STD)‐NMR spectroscopy to probe the existence of immobilized water molecules in the complex of MDWNMHAA 1 bound to mAb SYA/J6. Molecular dynamics simulations using the ZymeCAD Molecular Dynamics platform were then used to specify the likely locations of these water molecules. Of note, those waters involved in providing complementarity between the peptide and mAb SYA/J6 remained throughout the course of the simulation. Together, the experimental and computational protocols have been used to identify the bound water molecules present in the antibody‐peptide complex.