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Volumn 45, Issue 41, 2006, Pages 12547-12559

Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide

Author keywords

[No Author keywords available]

Indexed keywords

BIOSENSORS; CALCIUM COMPOUNDS; CELLS; COMPLEXATION; MUTAGENESIS; PROTEINS;

EID: 33750058234     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi060857u     Document Type: Article
Times cited : (33)

References (62)
  • 2
    • 0029149085 scopus 로고
    • Molecular and structural basis of target recognition by calmodulin
    • Crivici, A., and Ikura, M. (1995) Molecular and structural basis of target recognition by calmodulin, Annu. Rev. Biophys. Biomol. Struct. 24, 85-116.
    • (1995) Annu. Rev. Biophys. Biomol. Struct. , vol.24 , pp. 85-116
    • Crivici, A.1    Ikura, M.2
  • 3
    • 0037318056 scopus 로고    scopus 로고
    • Novel aspects of calmodulin target recognition and activation
    • Vetter, S. W., and Leclerc, E. (2003) Novel aspects of calmodulin target recognition and activation, Eur. J. Biochem. 270, 404-414.
    • (2003) Eur. J. Biochem. , vol.270 , pp. 404-414
    • Vetter, S.W.1    Leclerc, E.2
  • 4
    • 0030945196 scopus 로고    scopus 로고
    • Sequence motifs for calmodulin recognition
    • Rhoads, A. R., and Friedberg, F. (1997) Sequence motifs for calmodulin recognition, FASEB J. 11, 331-340.
    • (1997) FASEB J. , vol.11 , pp. 331-340
    • Rhoads, A.R.1    Friedberg, F.2
  • 5
    • 0030002422 scopus 로고    scopus 로고
    • Alanine substitutions in calmodulin-binding peptides result in unexpected affinity enhancement
    • Montigiani, S., Neri, G., Neri, P., and Neri, D. (1996) Alanine substitutions in calmodulin-binding peptides result in unexpected affinity enhancement, J. Mol. Biol. 258, 6-13.
    • (1996) J. Mol. Biol. , vol.258 , pp. 6-13
    • Montigiani, S.1    Neri, G.2    Neri, P.3    Neri, D.4
  • 6
    • 4744372036 scopus 로고    scopus 로고
    • Systematic delineation of a calmodulin peptide interaction
    • Hultschig, C., Hecht, H. J., and Frank, R. (2004) Systematic delineation of a calmodulin peptide interaction, J. Mol. Biol. 343, 559-568.
    • (2004) J. Mol. Biol. , vol.343 , pp. 559-568
    • Hultschig, C.1    Hecht, H.J.2    Frank, R.3
  • 7
    • 0026577811 scopus 로고
    • A single step purification for recombinant proteins. Characterization of a microtubule associated protein (MAP 2) fragment which associates with the type II cAMP-dependent protein kinase
    • Stofko-Hahn, R. E., Carr, D. W., and Scott, J. D. (1992) A single step purification for recombinant proteins. Characterization of a microtubule associated protein (MAP 2) fragment which associates with the type II cAMP-dependent protein kinase, FEBS Lett. 302, 274-278.
    • (1992) FEBS Lett. , vol.302 , pp. 274-278
    • Stofko-Hahn, R.E.1    Carr, D.W.2    Scott, J.D.3
  • 8
    • 0028939489 scopus 로고
    • Calmodulin as a versatile tag for antibody fragments
    • Neri, D., de Lalla, C., Petrul, H., Neri, P., and Winter, G. (1995) Calmodulin as a versatile tag for antibody fragments, Biotechnology 13, 373-377.
    • (1995) Biotechnology , vol.13 , pp. 373-377
    • Neri, D.1    De Lalla, C.2    Petrul, H.3    Neri, P.4    Winter, G.5
  • 9
    • 0032030220 scopus 로고    scopus 로고
    • Cell separation based on the reversible interaction between calmodulin and a calmodulin-binding peptide
    • Colinas, R. J., and Walsh, A. C. (1998) Cell separation based on the reversible interaction between calmodulin and a calmodulin-binding peptide, J. Immunol. Methods 212, 69-78.
    • (1998) J. Immunol. Methods , vol.212 , pp. 69-78
    • Colinas, R.J.1    Walsh, A.C.2
  • 14
    • 0035129282 scopus 로고    scopus 로고
    • 2+ probe composed of a single green fluorescent protein
    • 2+ probe composed of a single green fluorescent protein, Nat. Biotechnol. 19, 137-141.
    • (2001) Nat. Biotechnol. , vol.19 , pp. 137-141
    • Nakai, J.1    Ohkura, M.2    Imoto, K.3
  • 15
    • 33749533603 scopus 로고    scopus 로고
    • Calcium sensors for magnetic resonance imaging based on superparamagnetic iron oxide nanoparticles and calmodulin
    • in press
    • Atanasijevic, T. A., Shusteff, M., Fam, P. S., and Jasanoff, A. (2006) Calcium sensors for magnetic resonance imaging based on superparamagnetic iron oxide nanoparticles and calmodulin, Proc. Natl. Acad. Sci. U.S.A., in press.
    • (2006) Proc. Natl. Acad. Sci. U.S.A.
    • Atanasijevic, T.A.1    Shusteff, M.2    Fam, P.S.3    Jasanoff, A.4
  • 16
    • 0037255597 scopus 로고    scopus 로고
    • Overview of tag protein fusions: From molecular and biochemical fundamentals to commercial systems
    • Terpe, K. (2003) Overview of tag protein fusions: From molecular and biochemical fundamentals to commercial systems, Appl. Microbiol. Biotechnol. 60, 523-533.
    • (2003) Appl. Microbiol. Biotechnol. , vol.60 , pp. 523-533
    • Terpe, K.1
  • 19
    • 0026669408 scopus 로고
    • Identification of amino acids essential for calmodulin binding and activation of smooth muscle myosin light chain kinase
    • Bagchi, I. C., Huang, Q. H., and Means, A. R. (1992) Identification of amino acids essential for calmodulin binding and activation of smooth muscle myosin light chain kinase, J. Biol. Chem. 267, 3024-3029.
    • (1992) J. Biol. Chem. , vol.267 , pp. 3024-3029
    • Bagchi, I.C.1    Huang, Q.H.2    Means, A.R.3
  • 20
    • 0027057114 scopus 로고
    • Identification of basic residues involved in activation and calmodulin binding of rabbit smooth muscle myosin light chain kinase
    • Fitzsimons, D. P., Herring, B. P., Stull, J. T., and Gallagher, P. J. (1992) Identification of basic residues involved in activation and calmodulin binding of rabbit smooth muscle myosin light chain kinase, J. Biol. Chem. 267, 23903-23909.
    • (1992) J. Biol. Chem. , vol.267 , pp. 23903-23909
    • Fitzsimons, D.P.1    Herring, B.P.2    Stull, J.T.3    Gallagher, P.J.4
  • 21
    • 0027483204 scopus 로고
    • Features of calmodulin that are important in the activation of the catalytic subunit of phosphorylase kinase
    • Farrar, Y. J., Lukas, T. J., Craig, T. A., Watterson, D. M., and Carlson, G. M. (1993) Features of calmodulin that are important in the activation of the catalytic subunit of phosphorylase kinase, J. Biol. Chem. 268, 4120-4125.
    • (1993) J. Biol. Chem. , vol.268 , pp. 4120-4125
    • Farrar, Y.J.1    Lukas, T.J.2    Craig, T.A.3    Watterson, D.M.4    Carlson, G.M.5
  • 22
    • 0030008340 scopus 로고    scopus 로고
    • Target recognition by calmodulin: Dissecting the kinetics and affinity of interaction using short peptide sequences
    • Bayley, P. M., Findlay, W. A., and Martin, S. R. (1996) Target recognition by calmodulin: Dissecting the kinetics and affinity of interaction using short peptide sequences, Protein Sci. 5, 1215-1228.
    • (1996) Protein Sci. , vol.5 , pp. 1215-1228
    • Bayley, P.M.1    Findlay, W.A.2    Martin, S.R.3
  • 23
    • 0036407643 scopus 로고    scopus 로고
    • Modulating calmodulin binding specificity through computational protein design
    • Shifman, J. M., and Mayo, S. L. (2002) Modulating calmodulin binding specificity through computational protein design, J. Mol. Biol. 323, 417-423.
    • (2002) J. Mol. Biol. , vol.323 , pp. 417-423
    • Shifman, J.M.1    Mayo, S.L.2
  • 24
    • 0344392711 scopus 로고    scopus 로고
    • Exploring the origins of binding specificity through the computational redesign of calmodulin
    • Shifman, J. M., and Mayo, S. L. (2003) Exploring the origins of binding specificity through the computational redesign of calmodulin, Proc. Natl. Acad. Sci. U.S.A. 100, 13274-13279.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 13274-13279
    • Shifman, J.M.1    Mayo, S.L.2
  • 25
    • 0028237287 scopus 로고
    • Optimal sequence selection in proteins of known structure by simulated evolution
    • Hellinga, H. W., and Richards, F. M. (1994) Optimal sequence selection in proteins of known structure by simulated evolution, Proc. Natl. Acad. Sci. U.S.A. 91, 5803-5807.
    • (1994) Proc. Natl. Acad. Sci. U.S.A. , vol.91 , pp. 5803-5807
    • Hellinga, H.W.1    Richards, F.M.2
  • 26
    • 0028220365 scopus 로고
    • De novo protein design using pairwise potentials and a genetic algorithm
    • Jones, D. T. (1994) De novo protein design using pairwise potentials and a genetic algorithm, Protein Sci. 3, 567-574.
    • (1994) Protein Sci. , vol.3 , pp. 567-574
    • Jones, D.T.1
  • 27
    • 0028858499 scopus 로고
    • De novo design of the hydrophobic cores of proteins
    • Desjarlais, J. R., and Handel, T. M. (1995) De novo design of the hydrophobic cores of proteins, Protein Sci. 4, 2006-2018.
    • (1995) Protein Sci. , vol.4 , pp. 2006-2018
    • Desjarlais, J.R.1    Handel, T.M.2
  • 28
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • Dahiyat, B. I., and Mayo, S. L. (1997) De novo protein design: Fully automated sequence selection, Science 278, 82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 29
    • 0032553587 scopus 로고    scopus 로고
    • High-resolution protein design with backbone freedom
    • Harbury, P. B., Plecs, J. J., Tidor, B., Alber, T., and Kim, P. S. (1998) High-resolution protein design with backbone freedom, Science 282, 1462-1467.
    • (1998) Science , vol.282 , pp. 1462-1467
    • Harbury, P.B.1    Plecs, J.J.2    Tidor, B.3    Alber, T.4    Kim, P.S.5
  • 30
    • 0033550206 scopus 로고    scopus 로고
    • De novo protein design. I. In search of stability and specificity
    • Koehl, P., and Levitt, M. (1999) De novo protein design. I. In search of stability and specificity, J. Mol. Biol. 293, 1161-1181.
    • (1999) J. Mol. Biol. , vol.293 , pp. 1161-1181
    • Koehl, P.1    Levitt, M.2
  • 31
    • 0345306764 scopus 로고    scopus 로고
    • Design of a novel globular protein fold with atomic-level accuracy
    • Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L., and Baker, D. (2003) Design of a novel globular protein fold with atomic-level accuracy, Science 302, 1364-1368.
    • (2003) Science , vol.302 , pp. 1364-1368
    • Kuhlman, B.1    Dantas, G.2    Ireton, G.C.3    Varani, G.4    Stoddard, B.L.5    Baker, D.6
  • 33
    • 0036713917 scopus 로고    scopus 로고
    • Rational cytokine design for increased lifetime and enhanced potency using pH-activated "histidine switching"
    • Sarkar, C. A., Lowenhaupt, K., Horan, T., Boone, T. C., Tidor, B., and Lauffenburger, D. A. (2002) Rational cytokine design for increased lifetime and enhanced potency using pH-activated "histidine switching", Nat. Biotechnol. 20, 908-913.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 908-913
    • Sarkar, C.A.1    Lowenhaupt, K.2    Horan, T.3    Boone, T.C.4    Tidor, B.5    Lauffenburger, D.A.6
  • 34
    • 0038752617 scopus 로고    scopus 로고
    • Computational design of receptor and sensor proteins with novel functions
    • Looger, L. L., Dwyer, M. A., Smith, J. J., and Hellinga, H. W. (2003) Computational design of receptor and sensor proteins with novel functions, Nature 423, 185-190.
    • (2003) Nature , vol.423 , pp. 185-190
    • Looger, L.L.1    Dwyer, M.A.2    Smith, J.J.3    Hellinga, H.W.4
  • 35
    • 24644518008 scopus 로고    scopus 로고
    • Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface
    • Green, D. F., and Tidor, B. (2005) Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface, Proteins 60, 644-657.
    • (2005) Proteins , vol.60 , pp. 644-657
    • Green, D.F.1    Tidor, B.2
  • 37
    • 33750076395 scopus 로고    scopus 로고
    • The Research Collaboratory for Structural Bioinformatics (RCSB), http://www.rcsb.org/pdb/.
  • 38
    • 0026536335 scopus 로고
    • Solution structure of a calmodulin-target peptide complex by multidimensional NMR
    • Ikura, M., Clore, G. M., Gronenborn, A. M., Zhu, G., Klee, C. B., and Bax, A. (1992) Solution structure of a calmodulin-target peptide complex by multidimensional NMR, Science 256, 632-638.
    • (1992) Science , vol.256 , pp. 632-638
    • Ikura, M.1    Clore, G.M.2    Gronenborn, A.M.3    Zhu, G.4    Klee, C.B.5    Bax, A.6
  • 39
    • 0024250301 scopus 로고
    • Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
    • Brünger, A. T., and Karplus, M. (1988) Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison, Proteins 4, 148-156.
    • (1988) Proteins , vol.4 , pp. 148-156
    • Brünger, A.T.1    Karplus, M.2
  • 41
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • Desmet, J., de Maeyer, M., Hazes, B., and Lasters, I. (1992) The dead-end elimination theorem and its use in protein side-chain positioning, Nature 356, 539-542.
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    De Maeyer, M.2    Hazes, B.3    Lasters, I.4
  • 42
    • 0028826985 scopus 로고
    • Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains
    • Lasters, I., de Maeyer, M., and Desmet, J. (1995) Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains, Protein Eng. 8, 815-822.
    • (1995) Protein Eng. , vol.8 , pp. 815-822
    • Lasters, I.1    De Maeyer, M.2    Desmet, J.3
  • 43
    • 0031717560 scopus 로고    scopus 로고
    • Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm
    • Leach, A. R., and Lemon, A. P. (1998) Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm, Proteins 33, 227-239.
    • (1998) Proteins , vol.33 , pp. 227-239
    • Leach, A.R.1    Lemon, A.P.2
  • 44
    • 0001686478 scopus 로고    scopus 로고
    • Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination therom
    • Gordon, D. B., and Mayo, S. L. (1998) Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination therom, J. Comput. Chem. 19, 1505-1514.
    • (1998) J. Comput. Chem. , vol.19 , pp. 1505-1514
    • Gordon, D.B.1    Mayo, S.L.2
  • 45
    • 0034575680 scopus 로고    scopus 로고
    • The dead-end elimination theorem: Mathematical aspects, implementation, optimizations, evaluation, and performance
    • de Maeyer, M., Desmet, J., and Lasters, I. (2000) The dead-end elimination theorem: Mathematical aspects, implementation, optimizations, evaluation, and performance, Methods Mol. Biol. 143, 265-304.
    • (2000) Methods Mol. Biol. , vol.143 , pp. 265-304
    • De Maeyer, M.1    Desmet, J.2    Lasters, I.3
  • 46
    • 0035896029 scopus 로고    scopus 로고
    • Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics
    • Looger, L. L., and Hellinga, H. W. (2001) Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics, J. Mol. Biol. 307, 429-445.
    • (2001) J. Mol. Biol. , vol.307 , pp. 429-445
    • Looger, L.L.1    Hellinga, H.W.2
  • 47
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins. Application to side-chain prediction
    • Dunbrack, R. L., Jr., and Karplus, M. (1993) Backbone-dependent rotamer library for proteins. Application to side-chain prediction, J. Mol. Biol. 230, 543-574.
    • (1993) J. Mol. Biol. , vol.230 , pp. 543-574
    • Dunbrack Jr., R.L.1    Karplus, M.2
  • 48
    • 84988087911 scopus 로고
    • Calculating the electrostatic potential of molecules in solution: Method and error assessment
    • Gilson, M. K., Sharp, K. A., and Honig, B. (1988) Calculating the electrostatic potential of molecules in solution: Method and error assessment, J. Comput. Chem. 9, 327-335.
    • (1988) J. Comput. Chem. , vol.9 , pp. 327-335
    • Gilson, M.K.1    Sharp, K.A.2    Honig, B.3
  • 49
    • 0023779259 scopus 로고
    • Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
    • Gilson, M. K., and Honig, B. (1988) Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis, Proteins 4, 7-18.
    • (1988) Proteins , vol.4 , pp. 7-18
    • Gilson, M.K.1    Honig, B.2
  • 50
    • 0025283002 scopus 로고
    • Electrostatic interactions in macromolecules: Theory and applications
    • Sharp, K. A., and Honig, B. (1990) Electrostatic interactions in macromolecules: Theory and applications, Annu. Rev. Biophys. Biophys. Chem. 19, 301-332.
    • (1990) Annu. Rev. Biophys. Biophys. Chem. , vol.19 , pp. 301-332
    • Sharp, K.A.1    Honig, B.2
  • 51
    • 33751552991 scopus 로고
    • Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
    • Sharp, K. A., and Honig, B. (1990) Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation, J. Phys. Chem. 94, 7684-7692.
    • (1990) J. Phys. Chem. , vol.94 , pp. 7684-7692
    • Sharp, K.A.1    Honig, B.2
  • 52
    • 0020062918 scopus 로고
    • Calmodulin and the cell cycle: Involvement in regulation of cell-cycle progression
    • Chafouleas, J. G., Bolton, W. E., Hidaka, H., Boyd, A. E., III, and Means, A. R. (1982) Calmodulin and the cell cycle: Involvement in regulation of cell-cycle progression, Cell 28, 41-50.
    • (1982) Cell , vol.28 , pp. 41-50
    • Chafouleas, J.G.1    Bolton, W.E.2    Hidaka, H.3    Boyd III, A.E.4    Means, A.R.5
  • 53
    • 0020307706 scopus 로고
    • Quantitative determinations of calmodulin in the supernatant and particulate fractions of mammalian tissues
    • Kakiuchi, S., Yasuda, S., Yamazaki, R., Teshima, Y., Kanda, K., Kakiuchi, R., and Sobue, K. (1982) Quantitative determinations of calmodulin in the supernatant and particulate fractions of mammalian tissues, J. Biochem. 92, 1041-1048.
    • (1982) J. Biochem. , vol.92 , pp. 1041-1048
    • Kakiuchi, S.1    Yasuda, S.2    Yamazaki, R.3    Teshima, Y.4    Kanda, K.5    Kakiuchi, R.6    Sobue, K.7
  • 55
    • 0036138931 scopus 로고    scopus 로고
    • Calmodulin is a limiting factor in the cell
    • Persechini, A., and Stemmer, P. M. (2002) Calmodulin is a limiting factor in the cell, Trends Cardiovasc. Med. 12, 32-37.
    • (2002) Trends Cardiovasc. Med. , vol.12 , pp. 32-37
    • Persechini, A.1    Stemmer, P.M.2
  • 56
    • 0041589199 scopus 로고    scopus 로고
    • Intracellular coupling via limiting calmodulin
    • Tran, Q. K., Black, D. J., and Persechini, A. (2003) Intracellular coupling via limiting calmodulin, J. Biol. Chem. 278, 24247-24250.
    • (2003) J. Biol. Chem. , vol.278 , pp. 24247-24250
    • Tran, Q.K.1    Black, D.J.2    Persechini, A.3
  • 58
    • 0037217406 scopus 로고    scopus 로고
    • Automated design of specificity in molecular recognition
    • Havranek, J. J., and Harbury, P. B. (2003) Automated design of specificity in molecular recognition, Nat. Struct. Biol. 10, 45-52.
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 45-52
    • Havranek, J.J.1    Harbury, P.B.2
  • 60
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P. J. (1991) MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallogr. 24, 946-950.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 61
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • Merritt, E. A., and Bacon, D. J. (1997) Raster3D: Photorealistic molecular graphics, Methods Enzymol. 277, 505-524.
    • (1997) Methods Enzymol. , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2


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