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Domain motion and interdomain hot spots in a multidomain enzyme
Article first published online: 29 JUN 2010
DOI: 10.1002/pro.446
Copyright © 2010 The Protein Society
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How to Cite
Chuang, G.-Y., Mehra-Chaudhary, R., Ngan, C.-H., Zerbe, B. S., Kozakov, D., Vajda, S. and Beamer, L. J. (2010), Domain motion and interdomain hot spots in a multidomain enzyme. Protein Science, 19: 1662–1672. doi: 10.1002/pro.446
Publication History
- Issue published online: 23 AUG 2010
- Article first published online: 29 JUN 2010
- Manuscript Accepted: 10 JUN 2010
- Manuscript Revised: 8 JUN 2010
- Manuscript Received: 13 APR 2010
Funded by
- NIH. Grant Number: GM064700
- NSF. Grant Number: MCB-0918389
References
- 1, ( 2004) Searching for new allosteric sites in enzymes. Curr Opin Struct Biol 14: 1–10.
- 2, ( 1965) Evidence for conformation changes induced by substrates of phosphoglucomutase. J Biol Chem 240: 1593–602.
- 3, , , ( 2002) Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci 11: 184–197.Direct Link:
- 4, , , , , ( 2002) Allosterism and cooperativity in Pseudomonas aeruginosa GDP-mannose dehydrogenase. Biochemistry 2002; 41: 9637–9645.
- 5, ( 2001) Kinetic mechanism and pH dependence of the kinetic parameters of Pseudomonas aeruginosa phosphomannomutase/phosphoglucomutase. Arch Biochem Biophys 396: 111–118.
- 6, , , ( 2003) Roles of active site residues in P. aeruginosa phosphomannomutase/phosphoglucomutase. Biochemistry 42: 9946–9951.
- 7, ( 2005) Formation and reorientation of glucose 1,6-bisphosphate in the PMM/PGM reaction: transient-state kinetic studies. Biochemistry 44: 6831–6836.
- 8, , ( 2002) Crystal structure of PMM/PGM: an enzyme in the biosynthetic pathway of P. aeruginosa virulence factors. Structure 10: 269–279.
- 9, , , ( 2004) Structural basis of diverse substrate recognition by the enzyme PMM/PGM from P. aeruginosa. Structure 2004; 12: 55–63.
- 10, , ( 2006) Complexes of the enzyme phosphomannomutase/phosphoglucomutase with a slow substrate and an inhibitor. Acta Crystallograph Sect F Struct Biol Cryst Comm 62: 722–726.Direct Link:
- 11, , ( 2006) The reaction of phosphohexomutase from Pseudomonas aeruginosa: structural insights into a simple processive enzyme. J Biol Chem 281: 15564–15571.
- 12, , , ( 2008) Backbone flexibility, conformational change, and catalysis in a phosphohexomutase from Pseudomonas aeruginosa. Biochemistry 47: 9154–9162.
- 13, , ( 2002) Computational mapping identifies the binding sites of organic solvents on proteins. Proc Natl Acad Sci USA 99: 4290–4295.
- 14, , , , , ( 2003) Identification of substrate binding sites in enzymes by computational solvent mapping. J Mol Biol 332: 1095–1113.
- 15, , , , , , , ( 2009) Fragment-based identification of druggable ‘hot spots’ of proteins using fourier domain correlation techniques. Bioinformatics 25: 621–627.
- 16, , , , ( 2007) Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. J Med Chem 50: 1231–1240.
- 17, , ( 2005) Druggability indices for protein targets derived from NMR-based screening data, J Med Chem 48: 2518–2525.
- 18, , , , , , ( 2006) Multiple solvent crystal structures: probing binding sites, plasticity and hydration. J Mol Biol 357: 1471–1482.
- 19, ( 1996) Locating and characterizing binding sites on proteins. Nat Biotechnol 14: 595–599.
- 20, , , , , , , , , , , , ( 2009) Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J Comp Aided Mol Des.
- 21, , , ( 2005) Exploring the binding site structure of the PPAR-γ ligand binding domain by computational solvent mapping, Biochemistry 41: 1193–1209.
- 22, , , , , , ( 2008) Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des 71: 106–116.Direct Link:
- 23, , , , , and ( 2009) The structural basis of pregnane X receptor binding promiscuity. Biochemistry.
- 24, , , , , ( 2009) Binding hot spots and amantadine orientation in the influenza A virus M2 proton channel. Biophys J 97: 2846–2853.
- 25, , ( 2000) Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Eng 13: 77–82.
- 26, , , , , , , ( 2000) The protein data bank. Nucleic Acids Res 28: 235–242.
- 27, , , , , ( 1983) CHARMM: a program for macromolecular energy, minimzation, and dynamics calculations. J Com Chem 4: 187–217.Direct Link:
- 28CCP. ( 1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D 50: 760.Direct Link:
- 29. ( 2002) The PyMOL molecular graphics system. CA: DeLano Scientific.
- 30, , ( 1986) Understanding regression analysis: an introductory guide. CA: Sage Publications.

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