Article
You have full text access to this OnlineOpen article
OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold
Article first published online: 2 DEC 2008
DOI: 10.1002/pro.2
Copyright © 2008 The Protein Society
Additional Information
How to Cite
Fazelinia, H., Cirino, P. C. and Maranas, C. D. (2009), OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold. Protein Science, 18: 180–195. doi: 10.1002/pro.2
Publication History
- Issue published online: 16 DEC 2008
- Article first published online: 2 DEC 2008
- Accepted manuscript online: 2 DEC 2008 12:00AM EST
- Manuscript Accepted: 26 SEP 2008
- Manuscript Received: 18 JUL 2008
Funded by
- National Science Foundation Award. Grant Number: CBET-0639962
References
- 1, , ( 2003) Computational design of a Zn2+ receptor that controls bacterial gene expression. Proc Natl Acad Sci USA 100: 11255–11260.
- 2, , , ( 2004) Computational design of receptors for an organophosphate surrogate of the nerve agent soman. Proc Natl Acad Sci USA 101: 7907–7912.
- 3, ( 2004) De novo design of catalytic proteins. Proc Natl Acad Sci USA 101: 11566–11570.
- 4, , , ( 2005) Computational thermostabilization of an enzyme. Science 308: 857–860.
- 5, , , , , , , ( 2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15: 2785–2794.Direct Link:
- 6, , ( 2007) Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications. Protein Sci 16: 582–588.Direct Link:
- 7, , ( 2007) Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity. Biophys J 92: 2120–2130.
- 8, , , , , , ( 2007) Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity. J Biol Chem 282: 30658–30666.
- 9, , , , , ( 2007) Full-sequence computational design and solution structure of a thermostable protein variant. J Mol Biol 372: 1–6.
- 10, , , ( 2007) Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function. Proc Natl Acad Sci USA 104: 48–53.
- 11, , , , , , , , , , , , , ( 2008) De novo computational design of retro-aldol enzymes. Science 319: 1387–1391.
- 12, , , , , , , , , , , , , ( 2008) Kemp elimination catalysts by computational enzyme design. Nature 453: 190–195.
- 13, , , , , , ( 2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441: 656–659.
- 14, ( 1991) Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with predefined geometry. J Mol Biol 222: 763–785.
- 15, ( 1995) Metal search: a computer program that helps design tetrahedral metal-binding sites. Proteins 23: 256–263.Direct Link:
- 16, ( 1997) De novo protein design: fully automated sequence selection. Science 278: 82–87.
- 17, , , , , , ( 2003) Turnover-based in vitro selection and evolution of biocatalysts from a fully synthetic antibody library. Nat Biotechnol 21: 679–685.
- 18, , , , ( 2005) Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity. Proc Natl Acad Sci USA 102: 6855–6860.
- 19, ( 2007) Selection and evolution of enzymes from a partially randomized non-catalytic scaffold. Nature 448: 828–831.
- 20, , ( 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.
- 21, , , , ( 1995) Novel metal-binding proteins by design. Nat Struct Biol 2: 368–373.
- 22, , ( 1998) Construction of a family of Cys2His2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design. Biochemistry 37: 8269–8277.
- 23, , ( 2000) Rational design of nascent metalloenzymes. Proc Natl Acad Sci USA 97: 6292–6297.
- 24, , , ( 2002) Structural analysis, identification, and design of calcium-binding sites in proteins. Proteins 47: 344–356.Direct Link:
- 25, , , , , , ( 1990) Antibody remodeling: a general solution to the design of a metal-coordination site in an antibody binding pocket. Proc Natl Acad Sci USA 87: 6654–6658.
- 26, , , ( 2003) Computational design of receptor and sensor proteins with novel functions. Nature 423: 185–190.
- 27, , ( 2002) Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. Biochemistry 41: 3262–3269.
- 28( 1988) Structure of azurin from Alcaligenes denitrificans refinement at 1.8 A resolution and comparison of the two crystallographically independent molecules. J Mol Biol 203: 1071–1095.
- 29, , ( 1988) Refinement of the structure of pseudoazurin from Alcaligenes faecalis S-6 at 1.55 A resolution. Acta crystallographica 44(Pt 6): 628–636.
- 30, , , , , ( 1993) The 1.5-A crystal structure of plastocyanin from the green alga Chlamydomonas reinhardtii. Biochemistry 32: 10560–10567.
- 31, , , , ( 1992) Crystal structure at 2.8 A resolution of a soluble form of the cell adhesion molecule CD2. Nature 360: 232–239.
- 32, , , , , ( 2002) Metal-binding studies for a de novo designed calcium-binding protein. Protein Eng 15: 571–574.
- 33, , , , , , , , , , ( 2003) Rational design of a calcium-binding protein. J Am Chem Soc 125: 6165–6171.
- 34, , , , , ( 2003) A grafting approach to obtain site-specific metal-binding properties of EF-hand proteins. Protein Eng 16: 429–434.
- 35, , , , , , , , , ( 2005) Design of a calcium-binding protein with desired structure in a cell adhesion molecule. J Am Chem Soc 127: 2085–2093.
- 36, , , ( 2002) Structural analysis, identification, and design of calcium-binding sites in proteins. Proteins 47: 344–356.Direct Link:
- 37, , , ( 2007) Essential dynamics of helices provide a functional classification of EF-hand proteins. Journal of proteome research 6: 4245–4255.
- 38, , , , , ( 2008) Regulatory and structural EF-hand motifs of neuronal calcium sensor-1: Mg 2+ modulates Ca 2+ binding, Ca 2+-induced conformational changes, and equilibrium unfolding transitions. J Mol Biol 376: 1100–1115.
- 39, , , , , , ( 1990) Crystal structure of thermitase at 1.4 A resolution. J Mol Biol 214: 261–279.
- 40, , ( 1991) Calcium binding to thermitase. Crystallographic studies of thermitase at 0, 5, and 100 mM calcium. J Biol Chem 266: 2953–2961.
- 41, ( 1979) Lanthanide ion probes of structure in biology. Environmentally sensitive fine structure in laser-induced terbium(III) luminescence. Biochimica et biophysica acta 578: 135–144.
- 42, , , ( 1997) Characterization of lanthanide ion binding to the EF-hand protein S100 beta by luminescence spectroscopy. Biochemistry 36: 9674–9680.
- 43, , , , , , , ( 2005) Calcium-binding properties of wild-type and EF-hand mutants of S100B in the presence and absence of a peptide derived from the C-terminal negative regulatory domain of p53. Biochemistry 44: 7305–7314.
- 44( 1993) Luminescence spectroscopy. Methods Enzymol 226: 495–538.
- 45ILOG ( 2006) ILOG CPLEX 10.1 User's Manual. Sunnyvale, CA, USA: ILOG S.A. and ILOG, Inc.
- 46( 2000) Deterministic global optimization: theory, methods, and applications. Dordrecht: Kluwer Academic Publishers, p. xvii.
- 47, , , , , ( 2006) IPRO: an iterative computational protein library redesign and optimization procedure. Biophys J 90: 4167–4180.
- 48, , , , , , ( 1998) CHARMM: the energy function and its parameterization with an overview of the program. In: SchleyerR, editor. The encyclopedia of computational chemistry. Chichester, West Sussex, England: Wiley, pp. 271–277.
- 49, , , ( 2000) A new approach to the design of uniquely folded thermally stable proteins. Protein Sci 9: 403–416.Direct Link:
- 50
- 51, , , ( 2000) High-yield expression and purification of recombinant proteins in bacteria: a versatile vector for glutathione S-transferase fusion proteins containing two protease cleavage sites. Anal Biochem 281: 232–234.
- 52Amersham-Biosciences ( 2002) GST gene fusion system handbook. Piscataway, NJ, USA: Amersham-Biosciences.
- 53, ( 1976) A simple, one-step fluorometric method for determination of nanomolar concentrations of terbium. Anal Biochem 71: 351–357.
- 54, , , ( 1991) Quantitating and engineering the ion specificity of an EF-hand-like Ca2+ binding. Biochemistry 30: 8690–8697.
- 55, , ( 1996) Tuning the equilibrium ion affinity and selectivity of the EF-hand calcium binding motif: substitutions at the gateway position. Biochemistry 35: 6697–6705.

1469-896X/asset/olbannerleft.gif?v=1&s=d218899ae53b2862ab119790ed504b8d72122fb3)
1469-896X/asset/olbannerright.gif?v=1&s=59470eb9a1d9b7b13b1be75e9445e6c46ee2214f)
