Document Detail


Molecular dynamics of the anti-fluorescein 4-4-20 antigen-binding fragment. 1. Computer simulations.
MedLine Citation:
PMID:  7766606     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Two 174 ps molecular dynamics simulations of the solvated, 4-4-20 antigen-binding fragment (Fab) were performed: one with antigen (fluorescein) in the antigen-combining site and another with it removed. At the beginning of the second simulation, fluorescein was relocated from the antigen-combining site to a point outside the cutoff distance for nonbonded interactions by applying a "pulling force". Initially, the antigen-combining site collapsed when fluorescein was removed but gradually re-formed as the simulation progressed. In addition, several other differences were observed between the two simulations. These included (i) structural rearrangements of key contact residues in the antigen-combining site, (ii) significant differences in the degree of hydration of the antigen-combining site, (iii) a more acute elbow bend angle in the case of the unliganded form, and (iv) less correlated motions of amino acid residues in the unliganded form. These observations suggested that the Fab without fluorescein exhibited a greater degree of segmental flexibility than the Fab with fluorescein. Time-resolved fluorescence experiments were performed in order to validate this prediction, and the results are described in the following paper [Lim et al. (1995) Biochemistry 34, 6975-6984].
Authors:
K Lim; J N Herron
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  Biochemistry     Volume:  34     ISSN:  0006-2960     ISO Abbreviation:  Biochemistry     Publication Date:  1995 May 
Date Detail:
Created Date:  1995-07-03     Completed Date:  1995-07-03     Revised Date:  2007-11-14    
Medline Journal Info:
Nlm Unique ID:  0370623     Medline TA:  Biochemistry     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  6962-74     Citation Subset:  IM    
Affiliation:
Department of Pharmaceutics and Bioengineering, University of Utah, Salt Lake City 84112, USA.
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MeSH Terms
Descriptor/Qualifier:
Antigens / immunology*
Computer Graphics
Computer Simulation
Crystallography, X-Ray
Fluorescein
Fluoresceins*
Immunoglobulin Fab Fragments / chemistry*,  immunology
Protein Conformation
Spectrometry, Fluorescence
Grant Support
ID/Acronym/Agency:
AI 22898/AI/NIAID NIH HHS
Chemical
Reg. No./Substance:
0/Antigens; 0/Fluoresceins; 0/Immunoglobulin Fab Fragments; 2321-07-5/Fluorescein

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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