메뉴 건너뛰기




Volumn 18, Issue 4, 2008, Pages 499-506

Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; SERINE; TYROSINE;

EID: 49549102657     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2008.06.004     Document Type: Review
Times cited : (28)

References (41)
  • 1
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson T., and Wells J.A. A hot spot of binding energy in a hormone-receptor interface. Science 267 (1995) 383-386
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 2
    • 0036469060 scopus 로고    scopus 로고
    • Unraveling hot spots in binding interfaces: progress and challenges
    • DeLano W.L. Unraveling hot spots in binding interfaces: progress and challenges. Curr Opin Struct Biol 12 (2002) 14-20
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 14-20
    • DeLano, W.L.1
  • 4
    • 28444488346 scopus 로고    scopus 로고
    • Filamentous phage display in the new millennium
    • Kehoe J.W., and Kay B.K. Filamentous phage display in the new millennium. Chem Rev 105 (2005) 4056-4072
    • (2005) Chem Rev , vol.105 , pp. 4056-4072
    • Kehoe, J.W.1    Kay, B.K.2
  • 5
    • 34548838274 scopus 로고    scopus 로고
    • Phage display for engineering and analyzing protein interaction interfaces
    • Sidhu S.S., and Koide S. Phage display for engineering and analyzing protein interaction interfaces. Curr Opin Struct Biol 17 (2007) 481-487
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 481-487
    • Sidhu, S.S.1    Koide, S.2
  • 6
    • 33746799726 scopus 로고    scopus 로고
    • Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning
    • Describes a new methodology termed quantitative saturation (QS) scanning that was used to introduce every amino acid type in every position (35 sites) in the hGH-hGH receptor interface. This is the most comprehensive analysis that has ever been performed.
    • Pal G., Kouadio J.L., Artis D.R., Kossiakoff A.A., and Sidhu S.S. Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning. J Biol Chem 281 (2006) 22378-22385. Describes a new methodology termed quantitative saturation (QS) scanning that was used to introduce every amino acid type in every position (35 sites) in the hGH-hGH receptor interface. This is the most comprehensive analysis that has ever been performed.
    • (2006) J Biol Chem , vol.281 , pp. 22378-22385
    • Pal, G.1    Kouadio, J.L.2    Artis, D.R.3    Kossiakoff, A.A.4    Sidhu, S.S.5
  • 8
    • 34250721751 scopus 로고    scopus 로고
    • Exploring and designing protein function with restricted diversity
    • Sidhu S.S., and Kossiakoff A.A. Exploring and designing protein function with restricted diversity. Curr Opin Chem Biol 11 (2007) 347-354
    • (2007) Curr Opin Chem Biol , vol.11 , pp. 347-354
    • Sidhu, S.S.1    Kossiakoff, A.A.2
  • 10
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan A.A., and Thorn K.S. Anatomy of hot spots in protein interfaces. J Mol Biol 280 (1998) 1-9
    • (1998) J Mol Biol , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 11
    • 21844442124 scopus 로고    scopus 로고
    • Shotgun alanine scanning shows that growth hormone can bind productively to its receptor through a drastically minimized interface
    • Shotgun Ala scanning was applied to make multiple simultaneous Ala mutations in a protein-protein interface. They determine that the interface can be 'shaved' significantly without causing significant deleterious effects on binding. This reinforces the concept of hot spot and shows that bystander residues play a secondary role in the interface.
    • Kouadio J.L., Horn J.R., Pal G., and Kossiakoff A.A. Shotgun alanine scanning shows that growth hormone can bind productively to its receptor through a drastically minimized interface. J Biol Chem 280 (2005) 25524-25532. Shotgun Ala scanning was applied to make multiple simultaneous Ala mutations in a protein-protein interface. They determine that the interface can be 'shaved' significantly without causing significant deleterious effects on binding. This reinforces the concept of hot spot and shows that bystander residues play a secondary role in the interface.
    • (2005) J Biol Chem , vol.280 , pp. 25524-25532
    • Kouadio, J.L.1    Horn, J.R.2    Pal, G.3    Kossiakoff, A.A.4
  • 13
    • 33750303565 scopus 로고    scopus 로고
    • Hot-spot mimicry of a cytokine receptor by a small molecule
    • Thanos C.D., DeLano W.L., and Wells J.A. Hot-spot mimicry of a cytokine receptor by a small molecule. Proc Natl Acad Sci U S A 103 (2006) 15422-15427
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 15422-15427
    • Thanos, C.D.1    DeLano, W.L.2    Wells, J.A.3
  • 14
    • 4344714933 scopus 로고    scopus 로고
    • Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition
    • Fellouse F.A., Wiesmann C., and Sidhu S.S. Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition. Proc Natl Acad Sci U S A 101 (2004) 12467-12472
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 12467-12472
    • Fellouse, F.A.1    Wiesmann, C.2    Sidhu, S.S.3
  • 15
    • 0025964038 scopus 로고
    • Structure, function and properties of antibody binding sites
    • Mian I.S., Bradwell A.R., and Olson A.J. Structure, function and properties of antibody binding sites. J Mol Biol 217 (1991) 133-151
    • (1991) J Mol Biol , vol.217 , pp. 133-151
    • Mian, I.S.1    Bradwell, A.R.2    Olson, A.J.3
  • 16
    • 0242551578 scopus 로고    scopus 로고
    • Expressed murine and human CDR-H3 intervals of equal length exhibit distinct repertoires that differ in their amino acid composition and predicted range of structures
    • Zemlin M., Klinger M., Link J., Zemlin C., Bauer K., Engler J.A., Schroeder Jr. H.W., and Kirkham P.M. Expressed murine and human CDR-H3 intervals of equal length exhibit distinct repertoires that differ in their amino acid composition and predicted range of structures. J Mol Biol 334 (2003) 733-749
    • (2003) J Mol Biol , vol.334 , pp. 733-749
    • Zemlin, M.1    Klinger, M.2    Link, J.3    Zemlin, C.4    Bauer, K.5    Engler, J.A.6    Schroeder Jr., H.W.7    Kirkham, P.M.8
  • 18
    • 1842555070 scopus 로고    scopus 로고
    • Rational protein crystallization by mutational surface engineering
    • Derewenda Z.S. Rational protein crystallization by mutational surface engineering. Structure (Camb) 12 (2004) 529-535
    • (2004) Structure (Camb) , vol.12 , pp. 529-535
    • Derewenda, Z.S.1
  • 19
    • 34250315356 scopus 로고    scopus 로고
    • Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL
    • Tyr residues in the paratope of an antibody were mutated and thermodynamic and structural effects were characterized, which shows the ability of Tyr to contribute to molecular recognition in multiple modes.
    • Shiroishi M., Tsumoto K., Tanaka Y., Yokota A., Nakanishi T., Kondo H., and Kumagai I. Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL. J Biol Chem 282 (2007) 6783-6791. Tyr residues in the paratope of an antibody were mutated and thermodynamic and structural effects were characterized, which shows the ability of Tyr to contribute to molecular recognition in multiple modes.
    • (2007) J Biol Chem , vol.282 , pp. 6783-6791
    • Shiroishi, M.1    Tsumoto, K.2    Tanaka, Y.3    Yokota, A.4    Nakanishi, T.5    Kondo, H.6    Kumagai, I.7
  • 20
    • 0029098489 scopus 로고
    • Role of Tyr residues in the contact region of anti-lysozyme monoclonal antibody HyHEL10 for antigen binding
    • Tsumoto K., Ogasahara K., Ueda Y., Watanabe K., Yutani K., and Kumagai I. Role of Tyr residues in the contact region of anti-lysozyme monoclonal antibody HyHEL10 for antigen binding. J Biol Chem 270 (1995) 18551-18557
    • (1995) J Biol Chem , vol.270 , pp. 18551-18557
    • Tsumoto, K.1    Ogasahara, K.2    Ueda, Y.3    Watanabe, K.4    Yutani, K.5    Kumagai, I.6
  • 21
    • 33644783935 scopus 로고    scopus 로고
    • Tyrosine plays a dominant functional role in the paratope of a synthetic antibody derived from a four amino acid code
    • Fellouse F.A., Barthelemy P.A., Kelley R.F., and Sidhu S.S. Tyrosine plays a dominant functional role in the paratope of a synthetic antibody derived from a four amino acid code. J Mol Biol 357 (2006) 100-114
    • (2006) J Mol Biol , vol.357 , pp. 100-114
    • Fellouse, F.A.1    Barthelemy, P.A.2    Kelley, R.F.3    Sidhu, S.S.4
  • 23
    • 34249852867 scopus 로고    scopus 로고
    • High-affinity single-domain binding proteins with a binary-code interface
    • A YS binary library in two recognition loops of the FN3 scaffold produced tight binders for several targets. A crystal structure shows the dominance of Tyr in mediating interactions and the importance of conformational diversity in achieving specific molecular recognition.
    • Koide A., Gilbreth R.N., Esaki K., Tereshko V., and Koide S. High-affinity single-domain binding proteins with a binary-code interface. Proc Natl Acad Sci U S A 104 (2007) 6632-6637. A YS binary library in two recognition loops of the FN3 scaffold produced tight binders for several targets. A crystal structure shows the dominance of Tyr in mediating interactions and the importance of conformational diversity in achieving specific molecular recognition.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 6632-6637
    • Koide, A.1    Gilbreth, R.N.2    Esaki, K.3    Tereshko, V.4    Koide, S.5
  • 24
    • 40849097408 scopus 로고    scopus 로고
    • The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies
    • A systematic study show that an addition of Gly to the YS binary code enhances the functionality of synthetic antibody libraries, while Arg promotes nonspecific binding. These results reveal the intrinsic contributions of amino acid types to the formation of naïve protein-protein interaction interfaces and provide a clear guideline for the design of combinatorial libraries for synthetic binding proteins.
    • Birtalan S., Zhang Y., Fellouse F.A., Shao L., Schaefer G., and Sidhu S.S. The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies. J Mol Biol 377 (2008) 1518-1528. A systematic study show that an addition of Gly to the YS binary code enhances the functionality of synthetic antibody libraries, while Arg promotes nonspecific binding. These results reveal the intrinsic contributions of amino acid types to the formation of naïve protein-protein interaction interfaces and provide a clear guideline for the design of combinatorial libraries for synthetic binding proteins.
    • (2008) J Mol Biol , vol.377 , pp. 1518-1528
    • Birtalan, S.1    Zhang, Y.2    Fellouse, F.A.3    Shao, L.4    Schaefer, G.5    Sidhu, S.S.6
  • 25
    • 0037227422 scopus 로고    scopus 로고
    • Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen
    • Collis A.V., Brouwer A.P., and Martin A.C. Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen. J Mol Biol 325 (2003) 337-354
    • (2003) J Mol Biol , vol.325 , pp. 337-354
    • Collis, A.V.1    Brouwer, A.P.2    Martin, A.C.3
  • 26
    • 34848848421 scopus 로고    scopus 로고
    • High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries
    • Incremental additions of amino acid diversity to the YS binary code for CDR-H3 using a single Fab scaffold produced highly effective antibody library.
    • Fellouse F.A., Esaki K., Birtalan S., Raptis D., Cancasci V.J., Koide A., Jhurani P., Vasser M., Wiesmann C., Kossiakoff A.A., et al. High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J Mol Biol 373 (2007) 924-940. Incremental additions of amino acid diversity to the YS binary code for CDR-H3 using a single Fab scaffold produced highly effective antibody library.
    • (2007) J Mol Biol , vol.373 , pp. 924-940
    • Fellouse, F.A.1    Esaki, K.2    Birtalan, S.3    Raptis, D.4    Cancasci, V.J.5    Koide, A.6    Jhurani, P.7    Vasser, M.8    Wiesmann, C.9    Kossiakoff, A.A.10
  • 27
    • 47049105753 scopus 로고    scopus 로고
    • A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces
    • Gilbreth R.N., Esaki K., Koide A., Sidhu S.S., and Koide S. A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces. J Mol Biol 381 (2008) 407-418
    • (2008) J Mol Biol , vol.381 , pp. 407-418
    • Gilbreth, R.N.1    Esaki, K.2    Koide, A.3    Sidhu, S.S.4    Koide, S.5
  • 29
    • 0028890031 scopus 로고
    • Structure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans
    • Iwata S., Ostermeier C., Ludwig B., and Michel H. Structure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376 (1995) 660-669
    • (1995) Nature , vol.376 , pp. 660-669
    • Iwata, S.1    Ostermeier, C.2    Ludwig, B.3    Michel, H.4
  • 30
    • 0028991525 scopus 로고
    • Fv fragment-mediated crystallization of the membrane protein bacterial cytochrome c oxidase
    • Ostermeier C., Iwata S., Ludwig B., and Michel H. Fv fragment-mediated crystallization of the membrane protein bacterial cytochrome c oxidase. Nat Struct Biol 2 (1995) 842-846
    • (1995) Nat Struct Biol , vol.2 , pp. 842-846
    • Ostermeier, C.1    Iwata, S.2    Ludwig, B.3    Michel, H.4
  • 31
    • 0035499892 scopus 로고    scopus 로고
    • Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution
    • Zhou Y., Morais-Cabral J.H., Kaufman A., and MacKinnon R. Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution. Nature 414 (2001) 43-48
    • (2001) Nature , vol.414 , pp. 43-48
    • Zhou, Y.1    Morais-Cabral, J.H.2    Kaufman, A.3    MacKinnon, R.4
  • 32
    • 0036667741 scopus 로고    scopus 로고
    • Crystallisation of membrane proteins mediated by antibody fragments
    • Hunte C., and Michel H. Crystallisation of membrane proteins mediated by antibody fragments. Curr Opin Struct Biol 12 (2002) 503-508
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 503-508
    • Hunte, C.1    Michel, H.2
  • 37
    • 39149087988 scopus 로고    scopus 로고
    • The human combinatorial antibody library HuCAL GOLD combines diversification of all six CDRs according to the natural immune system with a novel display method for efficient selection of high-affinity antibodies
    • Rothe C., Urlinger S., Lohning C., Prassler J., Stark Y., Jager U., Hubner B., Bardroff M., Pradel I., Boss M., et al. The human combinatorial antibody library HuCAL GOLD combines diversification of all six CDRs according to the natural immune system with a novel display method for efficient selection of high-affinity antibodies. J Mol Biol 376 (2008) 1182-1200
    • (2008) J Mol Biol , vol.376 , pp. 1182-1200
    • Rothe, C.1    Urlinger, S.2    Lohning, C.3    Prassler, J.4    Stark, Y.5    Jager, U.6    Hubner, B.7    Bardroff, M.8    Pradel, I.9    Boss, M.10
  • 38
    • 33846363597 scopus 로고    scopus 로고
    • Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors
    • Inhibitors based on designed ankyrin-repeat proteins (DARPins) were selected for the multidrug exporter AcrB, an integral membrane protein, using the ribosome-display method. The 2.5 Å crystal structure of a DARPin/AcrB complex shows multiple conformations of the exporter subunits and identifies channels.
    • Sennhauser G., Amstutz P., Briand C., Storchenegger O., and Grutter M.G. Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors. PLoS Biol 5 (2007) e7. Inhibitors based on designed ankyrin-repeat proteins (DARPins) were selected for the multidrug exporter AcrB, an integral membrane protein, using the ribosome-display method. The 2.5 Å crystal structure of a DARPin/AcrB complex shows multiple conformations of the exporter subunits and identifies channels.
    • (2007) PLoS Biol , vol.5
    • Sennhauser, G.1    Amstutz, P.2    Briand, C.3    Storchenegger, O.4    Grutter, M.G.5
  • 39
    • 38349100453 scopus 로고    scopus 로고
    • Synthetic antibodies for specific recognition and crystallization of structured RNA
    • Tight and specific antibodies to a structured RNA target were generated from a synthetic Fab library. A high-resolution crystal structure of a Fab/RNA complex was determined. Together this work demonstrates the feasibility of producing anti-RNA antibodies and using them as crystallization chaperones.
    • Ye J.D., Tereshko V., Frederiksen J.K., Koide A., Fellouse F.A., Sidhu S.S., Koide S., Kossiakoff A.A., and Piccirilli J.A. Synthetic antibodies for specific recognition and crystallization of structured RNA. Proc Natl Acad Sci U S A 105 (2008) 82-87. Tight and specific antibodies to a structured RNA target were generated from a synthetic Fab library. A high-resolution crystal structure of a Fab/RNA complex was determined. Together this work demonstrates the feasibility of producing anti-RNA antibodies and using them as crystallization chaperones.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 82-87
    • Ye, J.D.1    Tereshko, V.2    Frederiksen, J.K.3    Koide, A.4    Fellouse, F.A.5    Sidhu, S.S.6    Koide, S.7    Kossiakoff, A.A.8    Piccirilli, J.A.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.