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Volumn 18, Issue 4, 2007, Pages 305-311

Progress in computational protein design

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; CATALYSIS; ENTROPY; INCLUSIONS; SOLVENTS;

EID: 34548528158     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2007.04.009     Document Type: Review
Times cited : (177)

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    • Allen B.D., and Mayo S.L. Dramatic performance enhancements for the FASTER optimization algorithm. J Comput Chem 27 (2006) 1071-1075. FASTER is an efficient stochastic optimizer for protein design that starts by placing the rotamer with the best one-body energy at each position and then refines the design through an iterative series of improvements that involve relaxations and perturbations. The use of a short MC simulation to create a collection of high quality starting structures and focusing relaxation steps on positions that interact strongly with perturbed positions together were found to lead to significant quality and speed enhancements (up to two orders of magnitude faster).
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    • The authors redesigned the colicin E7 DNase-Im7 immunity protein complex to exhibit a new hydrogen-bond network and at least a 300-fold specificity switch over one of the cognate interactions. They used both a negative and positive design strategy, and sampled rigid-body orientations mimicking the natural specificity determinant. One of 11 initial designs, from the affinity protocol, was crystallized and used as the basis for the second-round design.
    • Joachimiak L.A., Kortemme T., Stoddard B.L., and Baker D. Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J Mol Biol 361 (2006) 195-208. The authors redesigned the colicin E7 DNase-Im7 immunity protein complex to exhibit a new hydrogen-bond network and at least a 300-fold specificity switch over one of the cognate interactions. They used both a negative and positive design strategy, and sampled rigid-body orientations mimicking the natural specificity determinant. One of 11 initial designs, from the affinity protocol, was crystallized and used as the basis for the second-round design.
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    • The endonuclease I-MsoI was redesigned to specifically recognize a target sequence with two base-pair changes. A disrupting base-pair change was found computationally, and then amino acids were redesigned to accommodate the new base pair. This is the first study to computationally switch endonuclease recognition specificity.
    • Ashworth J., Havranek J.J., Duarte C.M., Sussman D., Monnat R.J., Stoddard B.L., and Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441 (2006) 656-659. The endonuclease I-MsoI was redesigned to specifically recognize a target sequence with two base-pair changes. A disrupting base-pair change was found computationally, and then amino acids were redesigned to accommodate the new base pair. This is the first study to computationally switch endonuclease recognition specificity.
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    • The authors designed a single amino-acid sequence that can adopt either a zinc finger-like fold or a trimeric coiled-coil, depending upon pH or the presence of transition metals.
    • Ambroggio X.I., and Kuhlman B. Computational design of a single amino acid sequence that can switch between two distinct protein folds. J Am Chem Soc 128 (2006) 1154-1161. The authors designed a single amino-acid sequence that can adopt either a zinc finger-like fold or a trimeric coiled-coil, depending upon pH or the presence of transition metals.
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    • Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion
    • Song G., Lazar G.A., Kortemme T., Shimaoka M., Desjarlais J.R., Baker D., and Springer T.A. Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. J Biol Chem 281 (2006) 5042-5049
    • (2006) J Biol Chem , vol.281 , pp. 5042-5049
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    • Recapitulation and design of protein binding peptide structures and sequences
    • Sood V.D., and Baker D. Recapitulation and design of protein binding peptide structures and sequences. J Mol Biol 357 (2006) 917-927
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    • Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor
    • The authors developed computational design methodology to engineer a protein that binds a specificied cofactor. They designed a four-helix bundle to bind a DPP-Fe cofactor.
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    • Computational prediction of native protein ligand-binding and enzyme active site sequences
    • The sequences of protein ligand-binding and enzyme active sites were predicted by optimizing binding affinity. Constraints based on known catalytic mechanism were used to capture the active sites of diverse enzymes.
    • Chakrabarti R., Klibanov A.M., and Friesner R.A. Computational prediction of native protein ligand-binding and enzyme active site sequences. Proc Natl Acad Sci USA 102 (2005) 10153-10158. The sequences of protein ligand-binding and enzyme active sites were predicted by optimizing binding affinity. Constraints based on known catalytic mechanism were used to capture the active sites of diverse enzymes.
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    • (2005) Protein Eng Des Sel , vol.18 , pp. 161-163
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    • Triose phosphate isomerase activity was introduced into ribose-binding protein. Substrate recognition was first introduced, and then catalytic residues were incorporated. This is the first report of a computationally designed enzyme.
    • Dwyer M.A., Looger L.L., and Hellinga H.W. Computational design of a biologically active enzyme. Science 304 (2004) 1967-1971. Triose phosphate isomerase activity was introduced into ribose-binding protein. Substrate recognition was first introduced, and then catalytic residues were incorporated. This is the first report of a computationally designed enzyme.
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    • Computational thermostabilization of an enzyme
    • The enzyme yeast cytosine deaminase was redesigned to be 10 °C more thermostable while maintaining its wild-type catalytic efficiency. The authors fixed the active site and contacting sites, and combined three separate single mutations for the overall improvement.
    • Korkegian A., Black M.E., Baker D., and Stoddard B.L. Computational thermostabilization of an enzyme. Science 308 (2005) 857-860. The enzyme yeast cytosine deaminase was redesigned to be 10 °C more thermostable while maintaining its wild-type catalytic efficiency. The authors fixed the active site and contacting sites, and combined three separate single mutations for the overall improvement.
    • (2005) Science , vol.308 , pp. 857-860
    • Korkegian, A.1    Black, M.E.2    Baker, D.3    Stoddard, B.L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.