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Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry
Article first published online: 6 JAN 2010
DOI: 10.1002/pro.327
Copyright © 2010 The Protein Society
Additional Information
How to Cite
Wang, C., Vernon, R., Lange, O., Tyka, M. and Baker, D. (2010), Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry. Protein Science, 19: 494–506. doi: 10.1002/pro.327
Publication History
- Issue published online: 22 FEB 2010
- Article first published online: 6 JAN 2010
- Accepted manuscript online: 6 JAN 2010 12:00AM EST
- Manuscript Accepted: 11 DEC 2009
- Manuscript Revised: 9 DEC 2009
- Manuscript Received: 11 OCT 2009
Funded by
- Henry Wellcome Fellowship Grant
References
- 1, ( 1987) Zinc in DNA replication and transcription. Annu Rev Nutr 7: 251–272.
- 2( 1995) The influence of zinc on apoptosis. Ann Clin Lab Sci 25: 134–142.
- 3, ( 2008) Intracellular zinc homeostasis and zinc signaling. Cancer Sci 99: 1515–1522.Direct Link:
- 4, , ( 2000) Function and mechanism of zinc metalloenzymes. J Nutr 130: 1437S–1446S.
- 5, ( 1996) The galvanization of biology: a growing appreciation for the roles of zinc. Science 271: 1081–1085.
- 6, , , ( 2006) Counting the zinc-proteins encoded in the human genome. J Proteome Res 5: 196–201.
- 7, , , , , , , ( 2000) The Protein Data Bank. Nucleic acids Res 28: 235–242.
- 8( 1991) Structural biology of zinc. Adv Protein Chem 42: 281–355.
- 9( 2001) Zinc coordination sphere in biochemical zinc sites. Biometals 14: 271–313.
- 10, , ( 2007) Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures. Biochim Biophys Acta 1774: 1247–1253.
- 11, , ( 2003) Structural classification of zinc fingers: survey and summary. Nucleic Acids Res 31: 532–550.
- 12, , ( 2008) Evolution of binding sites for zinc and calcium ions playing structural roles. Proteins 71: 813–830.Direct Link:
- 13, , ( 2008) Prediction of zinc-binding sites in proteins from sequence. Bioinformatics 24: 775–782.
- 14, , , , , ( 2004) Predicting metal-binding site residues in low-resolution structural models. J Mol Biol 342: 307–320.
- 15, , , , , ( 2005) Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci USA 102: 10147–10152.
- 16, , , ( 2006) Identification of zinc-ligated cysteine residues based on 13Calpha and 13Cbeta chemical shift data. J Biomol NMR 34: 259–269.
- 17, , , ( 2008) Modeling of metal interaction geometries for protein-ligand docking. Proteins 71: 1237–1254.Direct Link:
- 18( 2001) Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method. Proteins 45: 183–189.Direct Link:
- 19, , , , , , , ( 2008) Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement. Structure 16: 210–215.
- 20, ( 2001) Protein structure prediction and structural genomics. Science 294: 93–96.
- 21, , , ( 2004) Protein structure prediction using Rosetta. Methods Enzymol 383: 66–93.
- 22, ( 2008) Macromolecular modeling with rosetta. Annu Rev Biochem 77: 363–382.
- 23, , ( 2005) Toward high-resolution de novo structure prediction for small proteins. Science 309: 1868–1871.
- 24, , , , , , , , , , , , , , , , ( 2007) Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 69 ( Suppl 8): 118–128.Direct Link:
- 25, , , , , , ( 2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450: 259–264.
- 26, ( 2006) Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins 65: 922–929.Direct Link:
- 27, , ( 2007) Protein-protein docking with backbone flexibility. J Mol Biol 373: 503–519.
- 28, ( 2009) RosettaLigand docking with full ligand and receptor flexibility. J Mol Biol 385: 381–392.
- 29, , , ( 2000) Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach. Protein Sci 9: 1857–1865.
- 30, , , , , , , , , , , , , , , ( 2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105: 4685–4690.
- 31, , , ( 2009) De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR 43: 63–78.
- 32, , , ( 2004) Modeling structurally variable regions in homologous proteins with rosetta. Proteins 55: 656–677.Direct Link:
- 33, ( 2003) Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 12: 963–972.Direct Link:
- 34, ( 1987) Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 84: 6611–6615.
- 35( 2001) Handbook of metalloproteins. Chichester: Wiley.
- 36
- 37, ( 2001) Metalloprotein and redox protein design. Curr Opin Struct Biol 11: 485–490.
- 38, ( 2005) Probing metal-protein interactions using a de novo design approach. Curr Opin Chem Biol 9: 97–103.
- 39, ( 1990) Denovo design of a Zn2+-binding protein. J Am Chem Soc 112: 6710–6711.
- 40, , ( 1991) Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin. J Mol Biol 222: 787–803.
- 41, , , , ( 1995) Novel metal-binding proteins by design. Nat Struct Biol 2: 368–373.
- 42, , ( 1998) Construction of a family of Cys2His2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design. Biochemistry 37: 8269–8277.
- 43, , , , , , , , , , ( 2007) De novo design of a single-chain diphenylporphyrin metalloprotein. J Am Chem Soc 129: 10732–10740.
- 44, , , , , ( 2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302: 1364–1368.
- 45, , , , ( 2009) Alteration of enzyme specificity by computational loop remodeling and design. Proc Natl Acad Sci USA 106: 9215–9220.
- 46, , , ( 1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268: 209–225.
- 47, ( 1995) Zinc binding in proteins and solution: a simple but accurate nonbonded representation. Proteins 23: 12–31.Direct Link: