title: Automated identification of functional dynamic contact networks from X-ray crystallography.
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.
authors.affiliation: Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, Stanford, California, USA. vdbedem@slac.stanford.edu
authors.forename: Henry
authors.initials: H
authors.lastname: van den Bedem
authors.forename: Gira
authors.initials: G
authors.lastname: Bhabha
authors.forename: Kun
authors.initials: K
authors.lastname: Yang
authors.forename: Peter E
authors.initials: PE
authors.lastname: Wright
authors.forename: James S
authors.initials: JS
authors.lastname: Fraser
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D018360:Crystallography, X-Ray; D021984:Cyclophilin A / Q000737:chemistry / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D016296:Mutagenesis; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013329:Structure-Activity Relationship; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; D011506:Proteins; D013762:Tetrahydrofolate Dehydrogenase; D021984:Cyclophilin A
references.citation: Curr Opin Struct Biol. 2003 Dec;13(6):748-57
references.pmid: 14675554
references.citation: Annu Rev Biophys. 2012;41:429-52
references.pmid: 22577825
references.citation: J Mol Biol. 2011 Apr 1;407(3):391-412
references.pmid: 21277311
references.citation: Biochemistry. 2013 Jul 9;52(27):4605-19
references.pmid: 23758161
references.citation: Nature. 2009 Dec 3;462(7273):669-73
references.pmid: 19956261
references.citation: Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1393-405
references.pmid: 20944236
references.citation: Protein Sci. 2010 Jul;19(7):1420-31
references.pmid: 20499387
references.citation: Protein Sci. 2009 Apr;18(4):811-24
references.pmid: 19319933
references.citation: J Mol Biol. 2000 Sep 1;301(5):1237-56
references.pmid: 10966818
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32
references.pmid: 20124692
references.citation: Cell. 2010 Jan 22;140(2):246-56
references.pmid: 20141838
references.citation: Acta Crystallogr D Biol Crystallogr. 2007 May;63(Pt 5):597-610
references.pmid: 17452785
references.citation: Cell. 2009 Aug 21;138(4):774-86
references.pmid: 19703402
references.citation: J Biomol NMR. 1994 May;4(3):349-66
references.pmid: 8019142
references.citation: Trends Biochem Sci. 2009 Dec;34(12):601-11
references.pmid: 19846313
references.citation: Science. 2006 Sep 15;313(5793):1638-42
references.pmid: 16973882
references.citation: PLoS One. 2012;7(3):e33252
references.pmid: 22428003
references.citation: PLoS Comput Biol. 2009 Aug;5(8):e1000484
references.pmid: 19714199
references.citation: Proteins. 1991;10(4):340-58
references.pmid: 1946343
references.citation: Structure. 2007 Sep;15(9):1040-52
references.pmid: 17850744
references.citation: Acta Crystallogr D Biol Crystallogr. 2009 Oct;65(Pt 10):1107-17
references.pmid: 19770508
references.citation: Elife. 2012 Dec 18;1:e00311
references.pmid: 23251785
references.citation: Q Rev Biophys. 2010 Aug;43(3):295-332
references.pmid: 20819242
references.citation: Biochemistry. 1997 Jan 21;36(3):586-603
references.pmid: 9012674
references.citation: Science. 2012 Jul 20;337(6092):362-4
references.pmid: 22653729
references.citation: Nature. 2005 Nov 3;438(7064):117-21
references.pmid: 16267559
references.citation: Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6980-5
references.pmid: 12756296
references.citation: Nat Chem Biol. 2008 Aug;4(8):474-82
references.pmid: 18641628
references.citation: PLoS Comput Biol. 2011 Sep;7(9):e1002168
references.pmid: 21980271
references.citation: Nat Chem Biol. 2010 May;6(5):352-8
references.pmid: 20383153
references.citation: Science. 2011 Apr 8;332(6026):234-8
references.pmid: 21474759
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
references.pmid: 20124702
references.citation: Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4282-7
references.pmid: 15767576
references.citation: J Chem Theory Comput. 2009 Sep 8;5(9):2486-2502
references.pmid: 20161451
references.citation: Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):4793-8
references.pmid: 15051877
references.citation: Proc Natl Acad Sci U S A. 2005 May 10;102(19):6679-85
references.pmid: 15870208
references.citation: Cell Mol Life Sci. 2011 Jun;68(11):1829-41
references.pmid: 21190057
references.citation: Biochemistry. 2001 Aug 21;40(33):9846-59
references.pmid: 11502178
references.citation: J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
references.pmid: 19461840
references.citation: Cell. 2001 Apr 6;105(1):115-26
references.pmid: 11301007
references.citation: Acta Crystallogr D Biol Crystallogr. 2008 Apr;64(Pt 4):383-96
references.pmid: 18391405
references.citation: Protein Sci. 1997 Jul;6(7):1375-86
references.pmid: 9232638
references.citation: Nature. 2005 Jan 13;433(7022):128-32
references.pmid: 15650731
references.citation: Acta Crystallogr D Biol Crystallogr. 2013 Jul;69(Pt 7):1260-73
references.pmid: 23793152
references.citation: Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16247-52
references.pmid: 21918110