HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Kroon, G. J.A. Articles by Wright, P. E. Search for Related Content PubMed PubMed Citation Articles by Kroon, G. J.A. Articles by Wright, P. E. Social Bookmarking                   What's this?

Changes in structure and dynamics of the Fv fragment of a catalytic antibody upon binding of inhibitor

Department of Molecular Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA

Reprint requests to: Peter E. Wright or H. Jane Dyson, Department of Molecular Biology, MB2, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla CA 92037, USA; e-mail: wright{at}scripps.edu or dyson{at}scripps.edu; fax: (858) 784-9822.

Binding of the product inhibitor p-nitrophenol to the monoclonal esterolytic antibody NPN43C9 has been investigated by performing NMR spectroscopy of the heterodimeric variable-domain fragment (Fv) of the antibody in the presence and absence of inhibitor. Structural information from changes in chemical shift upon binding has been related to the changes in local dynamics in the active site of the catalytic antibody using NMR relaxation measurements. Significant changes in the chemical shifts of the backbone resonances upon binding extend beyond the immediate vicinity of the antigen binding site into the interface between the two associated polypeptides that form the Fv heterodimer, a possible indication that the binding of ligand causes a change in the relative orientations of the component light (V_L) and heavy (V_H) chain polypeptides. Significant differences in backbone dynamics were observed between the free Fv and the complex with p-nitrophenol. A number of resonances, including almost all of the third hypervariable loop of the light chain (L3), were greatly broadened in the free form of the protein. Other residues in the antigen-binding site showed less broadening of resonances, but still required exchange terms (R_ex) in the model-free dynamics analysis, consistent with motion on a slow timescale in the active site region of the free Fv. Binding of p-nitrophenol caused these resonances to sharpen, but some R_ex terms are still required in the analysis of the backbone dynamics. We conclude that the slow timescale motions in the antigen-binding site are very different in the bound and free forms of the Fv, presumably due to the damping of large-amplitude motions by the bound inhibitor.

Keywords: Catalysis; NMR; relaxation measurements; anisotropy; model-free analysis

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				I. F. Thorpe and C. L. Brooks III Molecular evolution of affinity and flexibility in the immune system PNAS, May 22, 2007; 104(21): 8821 - 8826. [Abstract] [Full Text] [PDF]