The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Center for Research Resources or the National Institutes of Health.
1469-896X/asset/olbannerleft.gif?v=1&s=d218899ae53b2862ab119790ed504b8d72122fb3)
1469-896X/asset/olbannerright.gif?v=1&s=59470eb9a1d9b7b13b1be75e9445e6c46ee2214f)
Article
You have full text access to this OnlineOpen article
Motif-directed flexible backbone design of functional interactions†
Article first published online: 16 APR 2009
DOI: 10.1002/pro.142
Copyright © 2009 The Protein Society
Additional Information
How to Cite
Havranek, J. J. and Baker, D. (2009), Motif-directed flexible backbone design of functional interactions. Protein Science, 18: 1293–1305. doi: 10.1002/pro.142
- †
Publication History
- Issue published online: 26 MAY 2009
- Article first published online: 16 APR 2009
- Accepted manuscript online: 16 APR 2009 12:00AM EST
- Manuscript Accepted: 30 MAR 2009
- Manuscript Revised: 27 MAR 2009
- Manuscript Received: 31 OCT 2008
Funded by
- National Center for Research Resources. Grant Number: K99RR024107
References
- 1( 1983) Molecular technology-designing proteins and peptides. Nature 301: 200–200.
- 2, ( 1987) Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 193: 775–791.
- 3, , , , ( 1998) High-resolution protein design with backbone freedom. Science 282: 1462–1467.
- 4, , , , , ( 2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302: 1364–1368.
- 5, ( 1997) De novo protein design: fully automated sequence selection. Science 278: 82–87.
- 6, ( 1998) Design, structure, and stability of a hyperthermophilic protein variant. Nat Struct Biol 5: 470–475.
- 7, , , , ( 2003) A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol 332: 449–460.
- 8, , , , , ( 2007) Full-sequence computational design and solution structure of a thermostable protein variant. J Mol Biol 372: 1–6.
- 9, ( 1986) Computer-aided model-building strategies for protein design. Biochemistry 25: 5987–5991.
- 10, , , , , , ( 1986) An engineered intersubunit disulfide enhances the stability and DNA binding of the N-terminal domain of lambda repressor. Biochemistry 25: 5992–5998.
- 11, , ( 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.
- 12, , ( 1997) The rational design and construction of a cuboidal iron-sulfur protein. Proc Natl Acad Sci USA 94: 6635–6640.
- 13, , ( 1997) Construction of a catalytically active iron superoxide dismutase by rational protein design. Proc Natl Acad Sci USA 94: 5562–5567.
- 14, , , ( 1998) Construction of a novel redox protein by rational design: conversion of a disulfide bridge into a mononuclear iron-sulfur center. Biochemistry 37: 7070–7076.
- 15, , ( 1998) Construction of a family of Cys2His2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design. Biochemistry 37: 8269–8277.
- 16, , ( 2002) Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. Biochemistry 41: 3262–3269.
- 17, , , ( 2005) A “solvated rotamer” approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 58: 893–904.Direct Link:
- 18, , , , , , , , , , , , , ( 2008) Kemp elimination catalysts by computational enzyme design. Nature 453: 190–195.
- 19( 2002). The PyMOL molecular graphics system. San Carlos, CA: DeLano Scientific. Available at: http:/www.pymol.org. accessed June 2008.
- 20, , ( 2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res 29: 2860–2874.
- 21, , , , , ( 2004) AANT: the amino acid-nucleotide interaction database. Nucleic Acids Res 32: D174–D181.
- 22, , , , , , , ( 2000) The protein data bank. Nucleic Acids Res 28: 235–242.
- 23, , , , , , , ( 2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15: 2785–2794.Direct Link:
- 24, , , , , , , , , , , , , ( 2008) De novo computational design of retro-aldol enzymes. Science 319: 1387–1391.
- 25, ( 2001) Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res 29: 3757–3774.
- 26( 2000) Severe combined immunodeficiencies (SCID). Clin Exp Immunol 122: 143–149.Direct Link:
- 27, , ( 2007) Coevolution of a homing endonuclease and its host target sequence. J Mol Biol 372: 1305–1319.
- 28, , , ( 2006) The backrub motion: how protein backbone shrugs when a sidechain dances. Structure 14: 265–274.
- 29, ( 2008) Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol 380: 742–756.
- 30, , ( 2001) The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites. Nat Struct Biol 8: 312–316.
- 31, , , , , ( 2006) The structure of I-CeuI homing endonuclease: evolving asymmetric DNA recognition from a symmetric protein scaffold. Structure 14: 869–880.
- 32, , , , , , , , , , ( 2008) Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Proc Natl Acad Sci USA 105: 16888–16893.
- 33, , , , ( 2003) Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. J Mol Biol 329: 253–269.
- 34, , , , , , ( 2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450: 259–264.
- 35, , , , , , , , , , , , , , , , ( 2007) Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 8( 69 Suppl): 118–128.Direct Link:
- 36, , ( 1976) Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci USA 73: 804–808.
- 37( 1988) Protein-DNA interaction. No code for recognition. Nature 335: 294–295.
- 38, ( 2000) Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J Mol Biol 301: 597–624.
- 39, , ( 2004) A simple physical model for the prediction and design of protein-DNA interactions. J Mol Biol 344: 59–70.
- 40, , , ( 2005) Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res 33: 5781–5798.
- 41, , , ( 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.
- 42, ( 2003) Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 12: 963–972.Direct Link:
- 43, , , ( 1953) Equation of state calculations by fast computing machines. J Chem Phys 21: 1087–1092.