Essential dynamics from NMR clusters: Dynamic properties of the Myb DNA-binding domain and a hinge-bending enhancing variant

Van Aalten, D. M. F., Grotewold, E., Joshua-Tor, L. (March 1998) Essential dynamics from NMR clusters: Dynamic properties of the Myb DNA-binding domain and a hinge-bending enhancing variant. Methods, 14 (3). pp. 318-328. ISSN 10462023 (ISSN)

URL: https://www.ncbi.nlm.nih.gov/pubmed/9571087
DOI: 10.1006/meth.1998.0587

Abstract

Application of the 'essential dynamics' method to the NMR cluster of structures for the R2R3 DNA-binding domain of the mouse c-Myb transcriptional activator is described. Using this method, large concerted fluctuations of atoms are extracted showing a hinge-bending motion between the two (R2 and R3) Myb repeats on the basis of NMR data alone. Molecular dynamics simulation of the same protein allowed quantitative comparison of the large concerted motions calculated from experimental and theoretical data, showing a significant degree of similarity. Detailed inspection of the motions reveals a conserved proline that plays a key role in determining hinge flexibility. The proline-to-alanine mutation at this position, which has previously been characterized biochemically, was subjected to molecular dynamics and subsequent essential dynamics analysis. The hingebending motion between the two repeats was found to be enhanced for the mutant. The approach described should have general applications, predicting the effect of mutations on protein dynamic properties of other proteins.

Item Type: Paper
Uncontrolled Keywords: DNA binding protein mutant protein proline transcription factor article molecular dynamics nuclear magnetic resonance oncogene c myb priority journal protein domain protein variant structure activity relation Binding Sites DNA DNA-Binding Proteins Magnetic Resonance Spectroscopy Proto-Oncogene Proteins Proto-Oncogene Proteins c-myb Trans-Activators Proto Oncogene
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein structure rendering
CSHL Authors:
Communities: CSHL labs > Joshua-Tor lab
Depositing User: CSHL Librarian
Date: March 1998
Date Deposited: 20 Mar 2012 20:51
Last Modified: 17 Jan 2017 17:22
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25501

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