메뉴 건너뛰기




Volumn 385, Issue 5, 2009, Pages 1470-1480

Computational Design of Calmodulin Mutants with up to 900-Fold Increase in Binding Specificity

Author keywords

calmodulin; computational protein design; protein binding specificity; protein protein interactions

Indexed keywords

CALMODULIN;

EID: 58549091879     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.09.053     Document Type: Article
Times cited : (51)

References (51)
  • 1
    • 0024403619 scopus 로고
    • High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis
    • Cunningham B.C., and Wells J.A. High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science 244 (1989) 1081-1085
    • (1989) Science , vol.244 , pp. 1081-1085
    • Cunningham, B.C.1    Wells, J.A.2
  • 2
    • 0027132013 scopus 로고
    • Comparison of a structural and a functional epitope
    • Cunningham B.C., and Wells J.A. Comparison of a structural and a functional epitope. J. Mol. Biol. 234 (1993) 554-563
    • (1993) J. Mol. Biol. , vol.234 , pp. 554-563
    • Cunningham, B.C.1    Wells, J.A.2
  • 3
    • 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
    • 14744305626 scopus 로고    scopus 로고
    • Intramolecular cooperativity in a protein binding site assessed by combinatorial shotgun scanning mutagenesis
    • Pal G., Ultsch M.H., Clark K.P., Currell B., Kossiakoff A.A., and Sidhu S.S. Intramolecular cooperativity in a protein binding site assessed by combinatorial shotgun scanning mutagenesis. J. Mol. Biol. 347 (2005) 489-494
    • (2005) J. Mol. Biol. , vol.347 , pp. 489-494
    • Pal, G.1    Ultsch, M.H.2    Clark, K.P.3    Currell, B.4    Kossiakoff, A.A.5    Sidhu, S.S.6
  • 5
    • 0037470140 scopus 로고    scopus 로고
    • Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain
    • Skelton N.J., Koehler M.F., Zobel K., Wong W.L., Yeh S., Pisabarro M.T., et al. Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain. J. Biol. Chem. 278 (2003) 7645-7654
    • (2003) J. Biol. Chem. , vol.278 , pp. 7645-7654
    • Skelton, N.J.1    Koehler, M.F.2    Zobel, K.3    Wong, W.L.4    Yeh, S.5    Pisabarro, M.T.6
  • 6
    • 0346749508 scopus 로고    scopus 로고
    • Dissecting cooperative and additive binding energetics in the affinity maturation pathway of a protein-protein interface
    • Yang J., Swaminathan C.P., Huang Y., Guan R., Cho S., Kieke M.C., et al. Dissecting cooperative and additive binding energetics in the affinity maturation pathway of a protein-protein interface. J. Biol. Chem. 278 (2003) 50412-50421
    • (2003) J. Biol. Chem. , vol.278 , pp. 50412-50421
    • Yang, J.1    Swaminathan, C.P.2    Huang, Y.3    Guan, R.4    Cho, S.5    Kieke, M.C.6
  • 7
    • 0242580779 scopus 로고    scopus 로고
    • Determinants of binding affinity and specificity for the interaction of TEM-1 and SME-1 beta-lactamase with beta-lactamase inhibitory protein
    • Zhang Z., and Palzkill T. Determinants of binding affinity and specificity for the interaction of TEM-1 and SME-1 beta-lactamase with beta-lactamase inhibitory protein. J. Biol. Chem. 278 (2003) 45706-45712
    • (2003) J. Biol. Chem. , vol.278 , pp. 45706-45712
    • Zhang, Z.1    Palzkill, T.2
  • 8
    • 33746799726 scopus 로고    scopus 로고
    • Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning
    • 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
    • (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
  • 9
    • 27144511241 scopus 로고    scopus 로고
    • Engineering novel binding proteins from nonimmunoglobulin domains
    • Binz H.K., Amstutz P., and Pluckthun A. Engineering novel binding proteins from nonimmunoglobulin domains. Nat. Biotechnol. 23 (2005) 1257-1268
    • (2005) Nat. Biotechnol. , vol.23 , pp. 1257-1268
    • Binz, H.K.1    Amstutz, P.2    Pluckthun, A.3
  • 10
    • 23644452792 scopus 로고    scopus 로고
    • Engineered proteins as specific binding reagents
    • Binz H.K., and Pluckthun A. Engineered proteins as specific binding reagents. Curr. Opin. Biotechnol. 16 (2005) 459-469
    • (2005) Curr. Opin. Biotechnol. , vol.16 , pp. 459-469
    • Binz, H.K.1    Pluckthun, A.2
  • 11
    • 1042298843 scopus 로고    scopus 로고
    • Computational design of protein-protein interactions
    • Kortemme T., and Baker D. Computational design of protein-protein interactions. Curr. Opin. Chem. Biol. 8 (2004) 91-97
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 91-97
    • Kortemme, T.1    Baker, D.2
  • 12
    • 0032516785 scopus 로고    scopus 로고
    • From synthetic coiled coils to functional proteins: automated design of a receptor for the calmodulin-binding domain of calcineurin
    • Ghirlanda G., Lear J.D., Lombardi A., and DeGrado W.F. From synthetic coiled coils to functional proteins: automated design of a receptor for the calmodulin-binding domain of calcineurin. J. Mol. Biol. 281 (1998) 379-391
    • (1998) J. Mol. Biol. , vol.281 , pp. 379-391
    • Ghirlanda, G.1    Lear, J.D.2    Lombardi, A.3    DeGrado, W.F.4
  • 14
    • 0037217406 scopus 로고    scopus 로고
    • Automated design of specificity in molecular recognition
    • Havranek J.J., and Harbury P.B. Automated design of specificity in molecular recognition. Nat. Struct. Biol. 10 (2003) 45-52
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 45-52
    • Havranek, J.J.1    Harbury, P.B.2
  • 16
    • 0036407643 scopus 로고    scopus 로고
    • Modulating calmodulin specificity through computational protein design
    • Shifman J.M., and Mayo S.L. Modulating calmodulin specificity through computational protein design. J. Mol. Biol. 323 (2002) 417-423
    • (2002) J. Mol. Biol. , vol.323 , pp. 417-423
    • Shifman, J.M.1    Mayo, S.L.2
  • 17
    • 0344392711 scopus 로고    scopus 로고
    • Exploring the origins of binding specificity through the computational redesign of calmodulin
    • Shifman J.M., and Mayo S.L. Exploring the origins of binding specificity through the computational redesign of calmodulin. Proc. Natl Acad. Sci. USA 100 (2003) 13274-13279
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 13274-13279
    • Shifman, J.M.1    Mayo, S.L.2
  • 20
    • 33745927413 scopus 로고    scopus 로고
    • Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface
    • 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
    • (2006) J. Mol. Biol. , vol.361 , pp. 195-208
    • Joachimiak, L.A.1    Kortemme, T.2    Stoddard, B.L.3    Baker, D.4
  • 21
    • 0033923367 scopus 로고    scopus 로고
    • Rational design of faster associating and tighter binding protein complexes
    • Selzer T., Albeck S., and Schreiber G. Rational design of faster associating and tighter binding protein complexes. Nat. Struct. Biol. 7 (2000) 537-541
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 537-541
    • Selzer, T.1    Albeck, S.2    Schreiber, G.3
  • 22
    • 3042594710 scopus 로고    scopus 로고
    • Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex
    • Kiel C., Selzer T., Shaul Y., Schreiber G., and Herrmann C. Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex. Proc. Natl Acad. Sci. USA 101 (2004) 9223-9228
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 9223-9228
    • Kiel, C.1    Selzer, T.2    Shaul, Y.3    Schreiber, G.4    Herrmann, C.5
  • 24
    • 0026536335 scopus 로고
    • Solution structure of calmodulin-target peptide complex by multidimensional NMR
    • Ikura M., Clore G.M., Gronenborn A.M., Guang Z., Klee C.B., and Bax A. Solution structure of calmodulin-target peptide complex by multidimensional NMR. Science 256 (1992) 632-638
    • (1992) Science , vol.256 , pp. 632-638
    • Ikura, M.1    Clore, G.M.2    Gronenborn, A.M.3    Guang, Z.4    Klee, C.B.5    Bax, A.6
  • 25
    • 0026794065 scopus 로고
    • Target enzyme recognition by calmodulin: 2.4 Å structure of a calmodulin-peptide complex
    • Meador W.E., Means A.R., and Quiocho F.A. Target enzyme recognition by calmodulin: 2.4 Å structure of a calmodulin-peptide complex. Science 257 (1992) 1251-1255
    • (1992) Science , vol.257 , pp. 1251-1255
    • Meador, W.E.1    Means, A.R.2    Quiocho, F.A.3
  • 26
    • 0027759276 scopus 로고
    • Modulation of calmodulin plasticity in molecular recognition on the basis of X-ray structures
    • Meador W.E., Means A.R., and Quiocho F.A. Modulation of calmodulin plasticity in molecular recognition on the basis of X-ray structures. Science 262 (1993) 1718-1721
    • (1993) Science , vol.262 , pp. 1718-1721
    • Meador, W.E.1    Means, A.R.2    Quiocho, F.A.3
  • 28
    • 0035823139 scopus 로고    scopus 로고
    • Target-induced conformational adaptation of calmodulin revealed by the crystal structure of a complex with nematode Ca(2+)/calmodulin-dependent kinase kinase peptide
    • Kurokawa H., Osawa M., Kurihara H., Katayama N., Tokumitsu H., Swindells M.B., et al. Target-induced conformational adaptation of calmodulin revealed by the crystal structure of a complex with nematode Ca(2+)/calmodulin-dependent kinase kinase peptide. J. Mol. Biol. 312 (2001) 59-68
    • (2001) J. Mol. Biol. , vol.312 , pp. 59-68
    • Kurokawa, H.1    Osawa, M.2    Kurihara, H.3    Katayama, N.4    Tokumitsu, H.5    Swindells, M.B.6
  • 29
    • 0031574184 scopus 로고    scopus 로고
    • Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering
    • Wall M.E., Clarage J.B., and Phillips G.N. Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. Structure 5 (1997) 1599-1612
    • (1997) Structure , vol.5 , pp. 1599-1612
    • Wall, M.E.1    Clarage, J.B.2    Phillips, G.N.3
  • 30
    • 2242474818 scopus 로고    scopus 로고
    • Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: studies of the kinase activation mechanism
    • Clapperton J.A., Martin S.R., Smerdon S.J., Gamblin S.J., and Bayley P.M. Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: studies of the kinase activation mechanism. Biochemistry 41 (2002) 14669-14679
    • (2002) Biochemistry , vol.41 , pp. 14669-14679
    • Clapperton, J.A.1    Martin, S.R.2    Smerdon, S.J.3    Gamblin, S.J.4    Bayley, P.M.5
  • 31
    • 28844497233 scopus 로고    scopus 로고
    • Structure of calmodulin bound to the hydrophobic IQ domain of the cardiac Ca(v)1.2 calcium channel
    • Fallon J.L., Halling D.B., Hamilton S.L., and Quiocho F.A. Structure of calmodulin bound to the hydrophobic IQ domain of the cardiac Ca(v)1.2 calcium channel. Structure 13 (2005) 1881-1886
    • (2005) Structure , vol.13 , pp. 1881-1886
    • Fallon, J.L.1    Halling, D.B.2    Hamilton, S.L.3    Quiocho, F.A.4
  • 32
    • 22144464877 scopus 로고    scopus 로고
    • Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family
    • Contessa G.M., Orsale M., Melino S., Torre V., Paci M., Desideri A., and Cicero D.O. Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family. J. Biomol. NMR 31 (2005) 185-199
    • (2005) J. Biomol. NMR , vol.31 , pp. 185-199
    • Contessa, G.M.1    Orsale, M.2    Melino, S.3    Torre, V.4    Paci, M.5    Desideri, A.6    Cicero, D.O.7
  • 34
    • 33749246223 scopus 로고    scopus 로고
    • Complex of calmodulin with a ryanodine receptor target reveals a novel, flexible binding mode
    • Maximciuc A.A., Putkey J.A., Shamoo Y., and Mackenzie K.R. Complex of calmodulin with a ryanodine receptor target reveals a novel, flexible binding mode. Structure 14 (2006) 1547-1556
    • (2006) Structure , vol.14 , pp. 1547-1556
    • Maximciuc, A.A.1    Putkey, J.A.2    Shamoo, Y.3    Mackenzie, K.R.4
  • 38
    • 0037165139 scopus 로고    scopus 로고
    • Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin
    • Drum C.L., Yan S.Z., Bard J., Shen Y.Q., Lu D., Soelaiman S., et al. Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin. Nature 415 (2002) 396-402
    • (2002) Nature , vol.415 , pp. 396-402
    • Drum, C.L.1    Yan, S.Z.2    Bard, J.3    Shen, Y.Q.4    Lu, D.5    Soelaiman, S.6
  • 39
    • 0028306195 scopus 로고
    • Dual role of calmodulin in autophosphorylation of multifunctional CaM kinase may underlie decoding of calcium signals
    • Hanson P.I., Meyer T., Stryer L., and Schulman H. Dual role of calmodulin in autophosphorylation of multifunctional CaM kinase may underlie decoding of calcium signals. Neuron 12 (1994) 943-956
    • (1994) Neuron , vol.12 , pp. 943-956
    • Hanson, P.I.1    Meyer, T.2    Stryer, L.3    Schulman, H.4
  • 40
    • 0026718175 scopus 로고
    • Calmodulin trapping by calcium-calmodulin-dependent protein kinase
    • Meyer T., Hanson P.I., Stryer L., and Schulman H. Calmodulin trapping by calcium-calmodulin-dependent protein kinase. Science 256 (1992) 1199-1202
    • (1992) Science , vol.256 , pp. 1199-1202
    • Meyer, T.1    Hanson, P.I.2    Stryer, L.3    Schulman, H.4
  • 41
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: fully automated sequence selection
    • Dahiyat B.I., and Mayo S.L. De novo protein design: fully automated sequence selection. Science 278 (1997) 82-87
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 42
    • 31044452100 scopus 로고    scopus 로고
    • Structure of calmodulin bound to a calcineurin peptide: a new way of making an old binding mode
    • Ye Q., Li X., Wong A., Wei Q., and Jia Z. Structure of calmodulin bound to a calcineurin peptide: a new way of making an old binding mode. Biochemistry 45 (2006) 738-745
    • (2006) Biochemistry , vol.45 , pp. 738-745
    • Ye, Q.1    Li, X.2    Wong, A.3    Wei, Q.4    Jia, Z.5
  • 43
    • 0031841279 scopus 로고    scopus 로고
    • The HSSP database of protein structure sequence alignments and family profiles
    • Dodge C., Schneider R., and Sander C. The HSSP database of protein structure sequence alignments and family profiles. Nucleic Acids Res. 26 (1998) 313-315
    • (1998) Nucleic Acids Res. , vol.26 , pp. 313-315
    • Dodge, C.1    Schneider, R.2    Sander, C.3
  • 44
    • 34547571461 scopus 로고    scopus 로고
    • Structure-based protocol for identifying mutations that enhance protein-protein binding affinities
    • Sammond D.W., Eletr Z.M., Purbeck C., Kimple R.J., Siderovski D.P., and Kuhlman B. Structure-based protocol for identifying mutations that enhance protein-protein binding affinities. J. Mol. Biol. 371 (2007) 1392-1404
    • (2007) J. Mol. Biol. , vol.371 , pp. 1392-1404
    • Sammond, D.W.1    Eletr, Z.M.2    Purbeck, C.3    Kimple, R.J.4    Siderovski, D.P.5    Kuhlman, B.6
  • 45
    • 0033900165 scopus 로고    scopus 로고
    • Computational design of an integrin I domain stabilized in the open high affinity conformation
    • Shimaoka M., Shifman J.M., Jing H., Takagi J., Mayo S.L., and Springer T.A. Computational design of an integrin I domain stabilized in the open high affinity conformation. Nat. Struct. Biol. 7 (2000) 674-678
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 674-678
    • Shimaoka, M.1    Shifman, J.M.2    Jing, H.3    Takagi, J.4    Mayo, S.L.5    Springer, T.A.6
  • 46
    • 0034863015 scopus 로고    scopus 로고
    • Manipulation of ligand binding affinity by exploitation of conformational coupling
    • Marvin J.S., and Hellinga H.W. Manipulation of ligand binding affinity by exploitation of conformational coupling. Nat. Struct. Biol. 8 (2001) 795-798
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 795-798
    • Marvin, J.S.1    Hellinga, H.W.2
  • 47
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins. Applications to side-chain predictions
    • Dunbrack R.L., and Karplus M. Backbone-dependent rotamer library for proteins. Applications to side-chain predictions. J. Mol. Biol. 230 (1993) 543-574
    • (1993) J. Mol. Biol. , vol.230 , pp. 543-574
    • Dunbrack, R.L.1    Karplus, M.2
  • 50
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in side chain packing problem
    • Desmet J., De Maeyer M., Hazes B., and Lasters I. The dead-end elimination theorem and its use in side chain packing problem. Nature 356 (1992) 539-542
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    De Maeyer, M.2    Hazes, B.3    Lasters, I.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.