Investigation of shape variations in the antibody binding site by molecular dynamics computer simulation

Delacruz, X, Mark, AE, Tormo, J, Fita, I and Vangunsteren, WF (1994) Investigation of shape variations in the antibody binding site by molecular dynamics computer simulation. Journal of Molecular Biology, 236 4: 1186-1195. doi:10.1016/0022-2836(94)90020-5


Author Delacruz, X
Mark, AE
Tormo, J
Fita, I
Vangunsteren, WF
Title Investigation of shape variations in the antibody binding site by molecular dynamics computer simulation
Journal name Journal of Molecular Biology   Check publisher's open access policy
ISSN 0022-2836
Publication date 1994-03-04
Sub-type Article (original research)
DOI 10.1016/0022-2836(94)90020-5
Volume 236
Issue 4
Start page 1186
End page 1195
Total pages 10
Language eng
Subject 2406 Virology
Abstract Molecular dynamics simulations have been used to investigate the flexibility and variations in the shape of the binding site of an antibody against human Rhinovirus serotype 2 (HRV2) and its complex with a 15 amino acid oligopeptide, the structure of which has been recently determined by X-ray crystallography. During the simulation of the unbound antibody the binding site, defined in terms of the hypervariable regions or complementarity determining regions (CDRs), shows significant fluctuations in shape. For the complex such variations in the shape of the binding site were reduced. The largest fluctuations in the unbound antibody occurred within the CDR-H3. The largest differences between the bound and unbound crystal structures are also associated with CDR-H3. The relative displacements of the loops have been analysed in terms of internal distortions, rigid body motions of the loops and changes with respect to the framework regions. The degree to which the motions of the loops are correlated and the variation in the volume of the binding pocket during the simulation have also been examined.
Keyword antibody-antigen recognition
computer simulation
human Rhinovirus
molecular dynamics
protein loop mobility
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
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