Automated identification of functional dynamic contact networks from X-ray crystallography View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-08-04

AUTHORS

Henry van den Bedem, Gira Bhabha, Kun Yang, Peter E Wright, James S Fraser

ABSTRACT

Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active-site conformations and consequently alter protein function. Observing alternative conformations at low levels of electron density, in addition to comparison of independently determined X-ray crystal structures, can provide mechanistic insights into conformational dynamics. Here we report a new algorithm, CONTACT, that identifies contact networks of conformationally heterogeneous residues directly from high-resolution X-ray crystallography data. Contact networks determined for Escherichia coli dihydrofolate reductase (ecDHFR) predict the observed long-range pattern of NMR chemical shift perturbations of an allosteric mutation. A comparison of contact networks in wild-type and mutant ecDHFR suggests that mutations that alter optimized contact networks of coordinated motions can impair catalytic function. CONTACT-guided mutagenesis can exploit the structure-dynamics-function relationship in protein engineering and design. More... »

PAGES

896-902

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nmeth.2592

DOI

http://dx.doi.org/10.1038/nmeth.2592

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1035803529

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/23913260


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314 schema:name Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA.
315 Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
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317 https://www.grid.ac/institutes/grid.266102.1 schema:alternateName University of California, San Francisco
318 schema:name Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
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320 https://www.grid.ac/institutes/grid.419677.a schema:alternateName Joint Center for Structural Genomics
321 schema:name Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, Stanford, California, USA.
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