모듈성 단백질의 재설계 및 개량
Engineering Hybrid Proteins by Modular Recombination and Evolutionary Optimization.
0
조회
0
다운로드
0
인용
0
참고문헌
초록
Many proteins consist of distinctive domains that can act independently or cooperatively to achieve a unique function. As these domains evolve from a naturally existing repertoire of functional domains, this implies that domain organization is an intrinsic element involved in building the complex structure and function of proteins. Thus, identifying functional domains would appear to be critical to the elucidation of questions related to protein evolution, folding, and the engineering of hybrid proteins for tailored applications. However, the simple application of “ego-like assembly”to the engineering of hybrid proteins is an oversimplification, as many hybrid constructs lack structural stability, usually due to unfavorable domain contacts. Thus, directed evolution, along with computational studies, may help to engineer hybrid proteins with improved physico-chemical properties. Accordingly, this paper introduces several approaches to functional hybrid protein engineering that potentially can be used to create modulators of gene transcription and cell signaling, and novel biosensors to analyze biological functions in vivo.
Abstract
Many proteins consist of distinctive domains that can act independently or cooperatively to achieve a unique function. As these domains evolve from a naturally existing repertoire of functional domains, this implies that domain organization is an intrinsic element involved in building the complex structure and function of proteins. Thus, identifying functional domains would appear to be critical to the elucidation of questions related to protein evolution, folding, and the engineering of hybrid proteins for tailored applications. However, the simple application of “ego-like assembly”to the engineering of hybrid proteins is an oversimplification, as many hybrid constructs lack structural stability, usually due to unfavorable domain contacts. Thus, directed evolution, along with computational studies, may help to engineer hybrid proteins with improved physico-chemical properties. Accordingly, this paper introduces several approaches to functional hybrid protein engineering that potentially can be used to create modulators of gene transcription and cell signaling, and novel biosensors to analyze biological functions in vivo.
참고문헌 (47)
- Allert, M., "Local encoding of computationally designed enzyme activity", J. Mol. Biol, 366, pp.945~953 (2007)
- Arnold, F. H., "Combinatorial and computational challenges for biocatalyst design", Nature, 409, pp.253~257 (2001)
- Arnold, F. H., "Method in Molecular Biology, vol.230, Directed enzyme evolution: Screening and selection methods" (2003), Human Press Inc
- Bhattacharyya, R. P., "Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits", Annu. Rev. Biochem, 75, pp.655~680 (2006)
- Bishop, A., "Unnatural ligands for engineered proteins: new tools for chemical genetics", Ann. Rev. Biophys. Biomol. Struct, 29, pp.577~606 (2000)
- A hierarchical approach to protein molecular evolution, "Bogarad, L. D.", ~, pp.PNAS 96: 2591- 2595 (1999)
- Chang, M. C. Y., "Engineering Escherichia coli for production of functionalized terpenoids using plant P450s", Nat. Chem. Biol, 3, pp.274~277 (2007)
- Chevalier, B. S., "Design, activity, and structure of a highly specific artificial endonuclease", Mol. Cell, 10, pp.895~905 (2002)
- 최수림, "Tyrosine Phenol-Lyase의 고속탐색기술 개발 및 방향성 분자진화", 한국미생물·생명공학회지, 34(1), pp.58~62 (2006), 한국미생물·생명공학회
- Crameri, A., "DNA shuffling of genes from diverse species accelerates directed evolution", Nature, 391, pp.288~291 (1998)
- De Lorimier, R. M., "Construction of a fluorescent biosensor family", Protein Sci, 11, pp.2655~2675 (2002)
- Deuschle, K., "Construction and optimization of a family of genetically encoded metabolite sensors by semirational protein engineering", Protein Sci, 14, pp.2304~2314 (2005)
- Dong, M., "Using fluorescent sensors to detect botulinum neurotoxin activity in vitro and in living cells", PNAS, 101, pp.14701~14706 (2004)
- Dwyer, M. A., "Computational design of a Zn2+ receptor that controls bacterial gene expression", PNAS, 100, pp.11255~11260 (2003)
- Fehr, M., "Visualization of maltose uptake in living yeast cells by fluorescent nanosensor", PNAS, 99, pp.9846~9851 (2002)
- Fehr, M., "In vivo imaging of the dynamic of glucose uptake in the cytosol of COS-7 cells by fluorescent nanosensors", J. Biol. Chem, 278, pp.19127~19133 (2003)
- Fehr, M., "Minimally invasive dynamic imaging of ions and metabolites in living cells", Curr. Opin. Plant Biol, 7, pp.345~351 (2004)
- Fraser, H. B., "Modularity and evolutionary constraint on proteins", Nat. Genet, 37, pp.351~352 (2005)
- Frase, H. B., "Coevolution, modularity and human disease", Curr. Opin. Genet. Dev, 16, pp.637~644 (2005)
- WO 03, "025220", Frommer, W. B., 2003, WO 03[DOI]
- Guntas, G., "Directed evolution of protein switches and their application to the creation of ligand-binding proteins", PNAS, 102, pp.11224~11229 (2005)
- Ha, J. S., "Design and application of highly responsive fluorescence resonance energy transfer biosensors for detection of sugar in living Saccharomyces cerevisiae cells", Appl. Environmen. Microbiol, 73, pp.7408~7414 (2007)
- Hocker, B., "Stability, catalytic versatility and evolution of the (β", α)8- barrel fold, 2001, pp.12, 376~381
- Joern, J. M., "A versatile high throughput screen for dioxygenase activity using solid-phase digital imaging", J. Biomol. Screen, 6, pp.219~230 (2001)
- Kawarasaki, Y., "Enhanced crossover SCRATCHY: construction and highthroughput screening of a combinatorial library containing multiple non-homologous crossovers", Nucleic Acids Res, 31, pp.126~ (2003)
- Kuchner, O., "Directed evolution of enzyme catalysts", Trends Biotechnol, 15, pp.523~530 (1997)
- Lager, I., "Development of a fluorescent nanosensor for ribos", FEBS Lett, 553, pp.85~89 (2003)
- Looger, L. L., "Computational design of receptor and sensor proteins with novel functions", Nature, 423, pp.185~190 (2003)
- Mainfroid, V., "Replacing the (βα)-unit 8 of E. coli TIM with its chicken homologue leads to a stable and active hybrid enzyme", Protein Eng, 6, pp.893~900 (1993)
- Marvin, J. S., "The rational design of allosteric interactions in a monomeric protein and its applications to the construction of biosensors", PNAS, 94, pp.4366~4371 (1997)
- Michnick, S. W., "Protein fragment complementation strategies for biochemical network mapping", Curr. Opin. Biotech, 14, pp.610~617 (2003)
- Miyawaki, A., "Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin", Nature, 388, pp.882~887 (1997)
- Mochizuki, N., "Spatio-temporal images of growth-factor-induced activation of Ras and Rap1", Nature, 411, pp.1065~1068 (2001)
- Moore, G. L., "Identifying residueresidue clashes in protein hybrids by using a second-order mean-field approach", PNAS, 100, pp.5091~5096 (2003)
- Mootz, H. D., "Construction of hybrid peptide synthetases by module and domain fusions", PNAS, 97, pp.5848~5853 (2000)
- Nagai, T., "Circularly permutated green fluorescent proteins engineered to sense Ca2+", PNAS, 98, pp.3197~3203 (2001)
- Nagai, T., "Expanded dynamic range of fluorescent indicators for Ca2+ by circularly permuted yellow fluorescent proteins", PNAS, 101, pp.10554~10559 (2004)
- Okumoto, S., "Detection of glutamate release from neurons by genetically encoded surface-displayed FRET nanosensors", PNAS, 102, pp.8740~8745 (2005)
- Olsen, M., "High-throughput screening of enzyme libraries", Curr. Opin. Biotechnol, 11, pp.331~337 (2000)
- Ostermeier, M., "A combinatorial approach to hybrid enzymes independent of DNA homology", Nat. Biotechnol, 17, pp.1205~1209 (1999)
- Park, H.-S., "Design and evolution of new catalytic activity with an existing protein scaffold", Science, 311, pp.535~538 (2006)
- Ponting, C. P., "The natural history of protein domains", Annu. Rev. Biophys. Biomol. Struct, 31, pp.45~71 (2002)
- Stemmer, W. P. C., "DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution", PNAS, 91, pp.10747~10751 (1994)
- Tanimura, A., "Fluorescent biosensor for quantitative real-time measurements of inositol 1,4,5-triphosphate in single living cells", J. Biol. Chem, 279, pp.38095~38098 (2004)
- WO 98, "40477", Tsien, R. Y., 1998, WO 98[DOI]
- Voigt, C. A., "Protein building blocks preserved by recombination", Nat. Struct. Biol, 9, pp.553~558 (2002)
- Zhao, H., "Staggered Extension process in vitro DNA recombination", Methods Enzymol, 388, pp.42~49 (2004)
