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Volumn 342, Issue 1, 2004, Pages 289-297

Structural test of the parameterized-backbone method for protein design

Author keywords

parameterized backbone; protein design; RH3; structure

Indexed keywords

BINDING PROTEIN; PROTEIN RH3; TETRAMER; UNCLASSIFIED DRUG;

EID: 4143120071     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.06.051     Document Type: Article
Times cited : (19)

References (40)
  • 1
    • 0035807809 scopus 로고    scopus 로고
    • Enzyme-like proteins by computational design
    • D.N. Bolon, and S.L. Mayo Enzyme-like proteins by computational design Proc. Natl Acad. Sci. USA 98 2001 14274 14279
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 14274-14279
    • Bolon1    Mayo, S.L.D.N.2
  • 3
    • 0035979773 scopus 로고    scopus 로고
    • Design of bioelectronic interfaces by exploiting hinge-bending motions in proteins
    • D.E. Benson, D.W. Conrad, R.M. de Lorimier, S.A. Trammell, and H.W. Hellinga Design of bioelectronic interfaces by exploiting hinge-bending motions in proteins Science 293 2001 1641 1644
    • (2001) Science , vol.293 , pp. 1641-1644
    • Benson, D.E.1    Conrad, D.W.2    De Lorimier, R.M.3    Trammell4    Hellinga, H.W.S.A.5
  • 4
    • 0036300662 scopus 로고    scopus 로고
    • Accurate computer-based design of a new backbone conformation in the second turn of protein L
    • B. Kuhlman, J.W. O'Neill, D.E. Kim, K.Y. Zhang, and D. Baker Accurate computer-based design of a new backbone conformation in the second turn of protein L J. Mol. Biol. 315 2002 471 477
    • (2002) J. Mol. Biol. , vol.315 , pp. 471-477
    • Kuhlman, B.1    O'Neill, J.W.2    Kim, D.E.3    Zhang4    Baker, D.K.Y.5
  • 5
    • 0033516509 scopus 로고    scopus 로고
    • Side-chain and backbone flexibility in protein core design
    • J.R. Desjarlais, and T.M. Handel Side-chain and backbone flexibility in protein core design J. Mol. Biol. 290 1999 305 318
    • (1999) J. Mol. Biol. , vol.290 , pp. 305-318
    • Desjarlais1    Handel, T.M.J.R.2
  • 6
    • 0032835617 scopus 로고    scopus 로고
    • De novo design and structural characterization of proteins and metalloproteins
    • W.F. DeGrado, C.M. Summa, V. Pavone, F. Nastri, and A. Lombardi De novo design and structural characterization of proteins and metalloproteins Annu. Rev. Biochem. 68 1999 779 819
    • (1999) Annu. Rev. Biochem. , vol.68 , pp. 779-819
    • Degrado, W.F.1    Summa, C.M.2    Pavone, V.3    Nastri4    Lombardi, A.F.5
  • 8
    • 0032546610 scopus 로고    scopus 로고
    • Construction of a novel redox protein by rational design: Conversion of a disulfide bridge into a mononuclear iron-sulfur center
    • D.E. Benson, M.S. Wisz, W. Liu, and H.W. Hellinga Construction of a novel redox protein by rational design: conversion of a disulfide bridge into a mononuclear iron-sulfur center Biochemistry 37 1998 7070 7076
    • (1998) Biochemistry , vol.37 , pp. 7070-7076
    • Benson, D.E.1    Wisz, M.S.2    Liu3    Hellinga, H.W.W.4
  • 9
    • 0031779918 scopus 로고    scopus 로고
    • Design, structure and stability of a hyperthermophilic protein variant
    • S.M. Malakauskas, and S.L. Mayo Design, structure and stability of a hyperthermophilic protein variant Nature Struct. Biol. 5 1998 470 475
    • (1998) Nature Struct. Biol. , vol.5 , pp. 470-475
    • Malakauskas1    Mayo, S.L.S.M.2
  • 10
    • 2642670311 scopus 로고    scopus 로고
    • Design of a 20-amino acid, three-stranded beta-sheet protein
    • T. Kortemme, M. Ramirez-Alvarado, and L. Serrano Design of a 20-amino acid, three-stranded beta-sheet protein Science 281 1998 253 256
    • (1998) Science , vol.281 , pp. 253-256
    • Kortemme, T.1    Ramirez-Alvarado2    Serrano, L.M.3
  • 11
    • 0142140800 scopus 로고    scopus 로고
    • Prediction of protein side-chain conformations: A study on the influence of backbone accuracy on conformation stability in the rotamer space
    • P. Tuffery, C. Etchebest, and S. Hazout Prediction of protein side-chain conformations: a study on the influence of backbone accuracy on conformation stability in the rotamer space Protein Eng. 10 1997 361 372
    • (1997) Protein Eng. , vol.10 , pp. 361-372
    • Tuffery, P.1    Etchebest2    Hazout, S.C.3
  • 12
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • B.I. Dahiyat, and S.L. Mayo De novo protein design: fully automated sequence selection Science 278 1997 82 87
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat1    Mayo, S.L.B.I.2
  • 13
    • 0031558762 scopus 로고    scopus 로고
    • De novo protein design: Towards fully automated sequence selection
    • B.I. Dahiyat, C.A. Sarisky, and S.L. Mayo De novo protein design: towards fully automated sequence selection J. Mol. Biol. 273 1997 789 796
    • (1997) J. Mol. Biol. , vol.273 , pp. 789-796
    • Dahiyat, B.I.1    Sarisky2    Mayo, S.L.C.A.3
  • 14
    • 0030992890 scopus 로고    scopus 로고
    • De novo design of the hydrophobic core of ubiquitin
    • G.A. Lazar, J.R. Desjarlais, and T.M. Handel De novo design of the hydrophobic core of ubiquitin Protein Sci. 6 1997 1167 1178
    • (1997) Protein Sci. , vol.6 , pp. 1167-1178
    • Lazar, G.A.1    Desjarlais2    Handel, T.M.J.R.3
  • 15
    • 0028858499 scopus 로고
    • De novo design of the hydrophobic cores of proteins
    • J.R. Desjarlais, and T.M. Handel De novo design of the hydrophobic cores of proteins Protein Sci. 4 1995 2006 2018
    • (1995) Protein Sci. , vol.4 , pp. 2006-2018
    • Desjarlais1    Handel, T.M.J.R.2
  • 16
    • 0028343413 scopus 로고
    • Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
    • P. Koehl, and M. Delarue Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy J. Mol. Biol. 239 1994 249 275
    • (1994) J. Mol. Biol. , vol.239 , pp. 249-275
    • Koehl1    Delarue, M.P.2
  • 17
    • 0028237287 scopus 로고
    • Optimal sequence selection in proteins of known structure by simulated evolution
    • H.W. Hellinga, and F.M. Richards Optimal sequence selection in proteins of known structure by simulated evolution Proc. Natl Acad. Sci. USA 91 1994 5803 5807
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 5803-5807
    • Hellinga1    Richards, F.M.H.W.2
  • 18
    • 0034612192 scopus 로고    scopus 로고
    • Retrostructural analysis of metalloproteins: Application to the design of a minimal model for diiron proteins
    • A. Lombardi, C.M. Summa, S. Geremia, L. Randaccio, V. Pavone, and W.F. DeGrado Retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins Proc. Natl Acad. Sci. USA 97 2000 6298 6305
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 6298-6305
    • Lombardi, A.1    Summa, C.M.2    Geremia, S.3    Randaccio, L.4    Pavone5    Degrado, W.F.V.6
  • 19
    • 0036385840 scopus 로고    scopus 로고
    • Computational de novo design and characterization of an A(2)B(2) diiron protein
    • C.M. Summa, M.M. Rosenblatt, J.K. Hong, J.D. Lear, and W.F. DeGrado Computational de novo design and characterization of an A(2)B(2) diiron protein J. Mol. Biol. 321 2002 923 938
    • (2002) J. Mol. Biol. , vol.321 , pp. 923-938
    • Summa, C.M.1    Rosenblatt, M.M.2    Hong, J.K.3    Lear4    Degrado, W.F.J.D.5
  • 21
    • 0345306764 scopus 로고    scopus 로고
    • Design of a novel globular protein fold with atomic-level accuracy
    • B. Kuhlman, G. Dantas, G.C. Ireton, G. Varani, B.L. Stoddard, and D. Baker Design of a novel globular protein fold with atomic-level accuracy Science 302 2003 1364 1368
    • (2003) Science , vol.302 , pp. 1364-1368
    • Kuhlman, B.1    Dantas, G.2    Ireton, G.C.3    Varani, G.4    Stoddard5    Baker, D.B.L.6
  • 22
    • 0029091449 scopus 로고
    • Repacking protein cores with backbone freedom: Structure prediction for coiled coils
    • P.B. Harbury, B. Tidor, and P.S. Kim Repacking protein cores with backbone freedom: structure prediction for coiled coils Proc. Natl Acad. Sci. USA 92 1995 8408 8412
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 8408-8412
    • Harbury, P.B.1    Tidor2    Kim, P.S.B.3
  • 23
    • 0032553587 scopus 로고    scopus 로고
    • High-resolution protein design with backbone freedom
    • P.B. Harbury, J.J. Plecs, B. Tidor, T. Alber, and P.S. Kim High-resolution protein design with backbone freedom Science 282 1998 1462 1467
    • (1998) Science , vol.282 , pp. 1462-1467
    • Harbury, P.B.1    Plecs, J.J.2    Tidor, B.3    Alber4    Kim, P.S.T.5
  • 24
    • 0000747247 scopus 로고
    • The Fourier transform of a coiled-coil
    • F. Crick The Fourier transform of a coiled-coil Acta Crystallog. 6 1953 685 689
    • (1953) Acta Crystallog. , vol.6 , pp. 685-689
    • Crick, F.1
  • 25
    • 0017620768 scopus 로고
    • Vitamin K-dependent formation of gamma-carboxyglutamic acid
    • J. Stenflo, and J.W. Suttie Vitamin K-dependent formation of gamma-carboxyglutamic acid Annu. Rev. Biochem. 46 1977 157 172
    • (1977) Annu. Rev. Biochem. , vol.46 , pp. 157-172
    • Stenflo1    Suttie, J.W.J.2
  • 26
    • 0028181062 scopus 로고
    • Differences in the metal ion structure between Sr- and Ca-prothrombin fragment 1
    • T.P. Seshadri, E. Skrzypczak-Jankun, M. Yin, and A. Tulinsky Differences in the metal ion structure between Sr- and Ca-prothrombin fragment 1 Biochemistry 33 1994 1087 1092
    • (1994) Biochemistry , vol.33 , pp. 1087-1092
    • Seshadri, T.P.1    Skrzypczak-Jankun, E.2    Yin3    Tulinsky, A.M.4
  • 27
    • 0027934571 scopus 로고
    • Crystal structure of an isoleucine-zipper trimer
    • P.B. Harbury, P.S. Kim, and T. Alber Crystal structure of an isoleucine-zipper trimer Nature 371 1994 80 83
    • (1994) Nature , vol.371 , pp. 80-83
    • Harbury, P.B.1    Kim2    Alber, T.P.S.3
  • 28
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • M.L. Connolly Solvent-accessible surfaces of proteins and nucleic acids Science 221 1983 709 713
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 29
    • 0026571898 scopus 로고
    • Mechanism of specificity in the Fos-Jun oncoprotein heterodimer
    • E.K. O'Shea, R. Rutkowski, and P.S. Kim Mechanism of specificity in the Fos-Jun oncoprotein heterodimer Cell 68 1992 699 708
    • (1992) Cell , vol.68 , pp. 699-708
    • O'Shea, E.K.1    Rutkowski2    Kim, P.S.R.3
  • 30
    • 0027949381 scopus 로고
    • The net energetic contribution of interhelical electrostatic attractions to coiled-coil stability
    • N.E. Zhou, C.M. Kay, and R.S. Hodges The net energetic contribution of interhelical electrostatic attractions to coiled-coil stability Protein Eng. 7 1994 1365 1372
    • (1994) Protein Eng. , vol.7 , pp. 1365-1372
    • Zhou, N.E.1    Kay2    Hodges, R.S.C.M.3
  • 31
    • 0027176792 scopus 로고
    • Dimerization specificity of the leucine zipper-containing bZIP motif on DNA binding: Prediction and rational design
    • C.R. Vinson, T. Hai, and S.M. Boyd Dimerization specificity of the leucine zipper-containing bZIP motif on DNA binding: prediction and rational design Genes Dev. 7 1993 1047 1058
    • (1993) Genes Dev. , vol.7 , pp. 1047-1058
    • Vinson, C.R.1    Hai2    Boyd, S.M.T.3
  • 32
    • 0029030233 scopus 로고
    • Measurement of interhelical electrostatic interactions in the GCN4 leucine zipper
    • K.J. Lumb, and P.S. Kim Measurement of interhelical electrostatic interactions in the GCN4 leucine zipper Science 268 1995 436 439
    • (1995) Science , vol.268 , pp. 436-439
    • Lumb1    Kim, P.S.K.J.2
  • 33
    • 0027756896 scopus 로고
    • A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants
    • P.B. Harbury, T. Zhang, P.S. Kim, and T. Alber A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants Science 262 1993 1401 1407
    • (1993) Science , vol.262 , pp. 1401-1407
    • Harbury, P.B.1    Zhang, T.2    Kim3    Alber, T.P.S.4
  • 34
    • 0027119143 scopus 로고
    • Internal stark effect measurement of the electric field at the amino terminus of an alpha helix
    • D.J. Lockhart, and P.S. Kim Internal stark effect measurement of the electric field at the amino terminus of an alpha helix Science 257 1992 947 951
    • (1992) Science , vol.257 , pp. 947-951
    • Lockhart1    Kim, P.S.D.J.2
  • 36
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project Number 4
    • Collaborative Computational Project Number 4 The CCP4 suite: programs for protein crystallography Acta Crystallog. sect. D 50 1994 760 763
    • (1994) Acta Crystallog. Sect. D , vol.50 , pp. 760-763
  • 37
    • 1242274650 scopus 로고    scopus 로고
    • Automated protein structure determination with Elves
    • J.M. Holton, and T. Alber Automated protein structure determination with Elves Proc. Natl Acad. Sci. USA 101 2004 1539 1542
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 1539-1542
    • Holton1    Alber, T.J.M.2
  • 38
    • 84889120137 scopus 로고
    • Kjeldgaard improved methods for building protein models in electron density maps and the location of errors in these models
    • T.A. Jones, J.Y. Zou, and S.W. Cowan Kjeldgaard improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallog. sect. A 47 1991 110 119
    • (1991) Acta Crystallog. Sect. a , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou2    Cowan, S.W.J.Y.3
  • 39
    • 0023140814 scopus 로고
    • Crystallographic R factor refinement by simulated annealing
    • A.T. Brunger, J. Kuriyan, and M. Karplus Crystallographic R factor refinement by simulated annealing Science 235 1987 458 460
    • (1987) Science , vol.235 , pp. 458-460
    • Brunger, A.T.1    Kuriyan2    Karplus, M.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.