Ligand-induced changes in the binding sites of proteins.
Classical molecular interaction potentials, in conjunction with other theoretical techniques, are used to analyze the dependence of the binding sites of representative proteins on the bound ligand. It is found that the ligand bound introduces in general small structural perturbations at the binding site of the protein. However, such small structural changes can lead to important alterations in the recognition pattern of the protein. The impact of these findings in docking procedures is discussed.
Fradera
Xavier
X
Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain.
De La Cruz
Xavier
X
Silva
Carlos H T P
CH
Gelpí
Jose Luis
JL
Luque
F J
FJ
Orozco
Modesto
M
D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D016000:Cluster Analysis; D030562:Databases, Protein; D008024:Ligands; D046911:Macromolecular Substances; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011485:Protein Binding / Q000235:genetics; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D020539:Sequence Analysis, Protein / Q000379:methods; D018709:Statistics, Nonparametric; D013329:Structure-Activity Relationship
D008024:Ligands; D046911:Macromolecular Substances; D011506:Proteins