Structure/thermodynamics relationships of lectin-saccharide complexes: the Erythrina corallodendron case.
Molecular dynamics (MD) simulations of Erythrina corallodendron lectin binding to a monosaccharide, alpha-galactose, and a disaccharide, N-acetyl lactosamine, have been performed in order to investigate the relationship between structure and thermodynamics. A simulated annealing protocol has been used to generate ensembles of structures for the two complexes, from which both qualitative and quantitative information on binding dynamics have been extracted. The ensembled averaged lectin-saccharide interaction enthalpy is equivalent for both sugars, whereas the calculation based on the X-ray structures does show a difference. Within large statistical errors, the calculated 'binding enthalpy' is also the same for the two systems. These errors arise largely from terms involving solvent and are a typical limitation of current MD simulations. Significant qualitative differences in binding between the two complexes are, however, observed over the ensembles. These could be important for unraveling the structure/thermodynamic relationship. Stated simply, there are a greater number of binding options available to the disaccharide compared to the monosaccharide. The implications of alternative binding states on thermodynamic parameters and the 'breaking of enthalpy-entropy compensation' are discussed. The role of solvent in lectin-saccharide complex formation is suggested to be significant.
Bradbrook
G M
GM
CERMAV-CNRS, BP 53-38041 Grenoble, France. gail@cermav.cnrs.fr
Forshaw
J R
JR
Pérez
S
S
D000606:Amino Sugars / Q000737:chemistry / Q000378:metabolism; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004187:Disaccharides / Q000737:chemistry* / Q000378:metabolism; D004895:Erythrina / Q000737:chemistry*; D005690:Galactose / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D037102:Lectins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009005:Monosaccharides / Q000737:chemistry* / Q000378:metabolism; D037121:Plant Lectins; D010946:Plants, Medicinal; D011485:Protein Binding; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000378:metabolism
D000606:Amino Sugars; D004187:Disaccharides; D037102:Lectins; D009005:Monosaccharides; D037121:Plant Lectins; D014867:Water; C000458:N-acetyllactosamine; D005690:Galactose