메뉴 건너뛰기




Volumn 351, Issue 5, 2005, Pages 1160-1168

Evolutionary protein stabilization in comparison with computational design

Author keywords

Computational protein design; In vitro selection; Phage display; Protein stability; Streptococcal protein G

Indexed keywords

BACTERIAL PROTEIN;

EID: 23644443403     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.06.059     Document Type: Article
Times cited : (30)

References (46)
  • 1
    • 1342324030 scopus 로고    scopus 로고
    • Exploring folding free energy landscapes using computational protein design
    • B. Kuhlman, and D. Baker Exploring folding free energy landscapes using computational protein design Curr. Opin. Struct. Biol. 14 2004 89 95
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 89-95
    • Kuhlman, B.1    Baker, D.2
  • 2
    • 0036266942 scopus 로고    scopus 로고
    • Conformational strain in the hydrophobic core and its implications for protein folding and design
    • S. Ventura, M.C. Vega, E. Lacroix, I. Angrand, L. Spagnolo, and L. Serrano Conformational strain in the hydrophobic core and its implications for protein folding and design Nature Struct. Biol. 9 2002 485 493
    • (2002) Nature Struct. Biol. , vol.9 , pp. 485-493
    • Ventura, S.1    Vega, M.C.2    Lacroix, E.3    Angrand, I.4    Spagnolo, L.5    Serrano, L.6
  • 3
    • 0041387567 scopus 로고    scopus 로고
    • A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins
    • G. Dantas, B. Kuhlman, D. Callender, M. Wong, and D. Baker A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins J. Mol. Biol. 332 2003 449 460
    • (2003) J. Mol. Biol. , vol.332 , pp. 449-460
    • Dantas, G.1    Kuhlman, B.2    Callender, D.3    Wong, M.4    Baker, D.5
  • 4
    • 14144256681 scopus 로고    scopus 로고
    • Energy functions for protein design: Adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity
    • N. Pokala, and T.M. Handel Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity J. Mol. Biol. 347 2005 203 227
    • (2005) J. Mol. Biol. , vol.347 , pp. 203-227
    • Pokala, N.1    Handel, T.M.2
  • 5
  • 6
    • 0033779402 scopus 로고    scopus 로고
    • Temperature adaptation of enzymes: Lessons from laboratory evolution
    • P.L. Wintrode, and F.H. Arnold Temperature adaptation of enzymes: lessons from laboratory evolution Advan. Protein Chem. 55 2000 161 225
    • (2000) Advan. Protein Chem. , vol.55 , pp. 161-225
    • Wintrode, P.L.1    Arnold, F.H.2
  • 8
    • 3042693137 scopus 로고    scopus 로고
    • Evolutionary optimization of a nonbiological ATP binding protein for improved folding stability
    • J.C. Chaput, and J.W. Szostak Evolutionary optimization of a nonbiological ATP binding protein for improved folding stability Chem. Biol 11 2004 865 874
    • (2004) Chem. Biol , vol.11 , pp. 865-874
    • Chaput, J.C.1    Szostak, J.W.2
  • 10
    • 0031729179 scopus 로고    scopus 로고
    • Selecting proteins with improved stability by a phage-based method
    • V. Sieber, A. Plückthun, and F.X. Schmid Selecting proteins with improved stability by a phage-based method Nature Biotechnol. 16 1998 955 960
    • (1998) Nature Biotechnol. , vol.16 , pp. 955-960
    • Sieber, V.1    Plückthun, A.2    Schmid, F.X.3
  • 11
    • 0031759422 scopus 로고    scopus 로고
    • Proteolytic selection for protein folding using filamentous bacteriophages
    • P. Kristensen, and G. Winter Proteolytic selection for protein folding using filamentous bacteriophages Fold. Des. 3 1998 321 328
    • (1998) Fold. Des. , vol.3 , pp. 321-328
    • Kristensen, P.1    Winter, G.2
  • 12
    • 0035827175 scopus 로고    scopus 로고
    • In vitro selection of highly stabilized protein variants with optimized surface
    • A. Martin, V. Sieber, and F.X. Schmid In vitro selection of highly stabilized protein variants with optimized surface J. Mol. Biol. 309 2001 717 726
    • (2001) J. Mol. Biol. , vol.309 , pp. 717-726
    • Martin, A.1    Sieber, V.2    Schmid, F.X.3
  • 13
    • 0036310988 scopus 로고    scopus 로고
    • Origins of the high stability of an in vitro-selected cold-shock protein
    • A. Martin, I. Kather, and F.X. Schmid Origins of the high stability of an in vitro-selected cold-shock protein J. Mol. Biol. 318 2002 1341 1349
    • (2002) J. Mol. Biol. , vol.318 , pp. 1341-1349
    • Martin, A.1    Kather, I.2    Schmid, F.X.3
  • 14
    • 0037427448 scopus 로고    scopus 로고
    • Evolutionary stabilization of the gene-3-protein of phage fd reveals the principles that govern the thermodynamic stability of two-domain proteins
    • A. Martin, and F.X. Schmid Evolutionary stabilization of the gene-3-protein of phage fd reveals the principles that govern the thermodynamic stability of two-domain proteins J. Mol. Biol. 328 2003 863 875
    • (2003) J. Mol. Biol. , vol.328 , pp. 863-875
    • Martin, A.1    Schmid, F.X.2
  • 15
    • 0141888974 scopus 로고    scopus 로고
    • Proside: A phage based method for selecting thermostable proteins
    • A. Martin, F.X. Schmid, and V. Sieber Proside: a phage based method for selecting thermostable proteins Methods Mol. Biol. 230 2003 57 70
    • (2003) Methods Mol. Biol. , vol.230 , pp. 57-70
    • Martin, A.1    Schmid, F.X.2    Sieber, V.3
  • 16
    • 2342528494 scopus 로고    scopus 로고
    • Selection of stably folded proteins by phage-display with proteolysis
    • Y.W. Bai, and H. Feng Selection of stably folded proteins by phage-display with proteolysis Eur. J. Biochem. 271 2004 1609 1614
    • (2004) Eur. J. Biochem. , vol.271 , pp. 1609-1614
    • Bai, Y.W.1    Feng, H.2
  • 17
    • 2442441204 scopus 로고    scopus 로고
    • Stabilization of antibody VH-domains by proteolytic selection
    • H. Ueda, P. Kristensen, and G. Winter Stabilization of antibody VH-domains by proteolytic selection J. Mol. Catal. B 28 2004 173 179
    • (2004) J. Mol. Catal. B , vol.28 , pp. 173-179
    • Ueda, H.1    Kristensen, P.2    Winter, G.3
  • 18
    • 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
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 19
    • 0030987610 scopus 로고    scopus 로고
    • Probing the role of packing specificity in protein design
    • B.I. Dahiyat, and S.L. Mayo Probing the role of packing specificity in protein design Proc. Natl Acad. Sci. USA 94 1997 10172 10177
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 10172-10177
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 20
    • 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
    • Malakauskas, S.M.1    Mayo, S.L.2
  • 22
    • 0027421911 scopus 로고
    • Identification of the contact surface of a streptococcal protein G domain complexed with a human Fc fragment
    • A.M. Gronenborn, and G.M. Clore Identification of the contact surface of a streptococcal protein G domain complexed with a human Fc fragment J. Mol. Biol. 233 1993 331 335
    • (1993) J. Mol. Biol. , vol.233 , pp. 331-335
    • Gronenborn, A.M.1    Clore, G.M.2
  • 23
    • 0028354429 scopus 로고
    • Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR
    • T. Gallagher, P. Alexander, P. Bryan, and G.L. Gilliland Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR Biochemistry 33 1994 4721 4729
    • (1994) Biochemistry , vol.33 , pp. 4721-4729
    • Gallagher, T.1    Alexander, P.2    Bryan, P.3    Gilliland, G.L.4
  • 24
    • 0025273561 scopus 로고
    • Dissection of functional domains in phage fd adsorption protein. Discrimination between attachment and penetration sites
    • I. Stengele, P. Bross, X. Garces, J. Giray, and I. Rasched Dissection of functional domains in phage fd adsorption protein. Discrimination between attachment and penetration sites J. Mol. Biol. 212 1990 143 149
    • (1990) J. Mol. Biol. , vol.212 , pp. 143-149
    • Stengele, I.1    Bross, P.2    Garces, X.3    Giray, J.4    Rasched, I.5
  • 25
    • 15244350748 scopus 로고    scopus 로고
    • Stabilization of the cold shock protein CspB from Bacillus subtilis by evolutionary optimization of Coulombic interactions
    • M. Wunderlich, A. Martin, and F.X. Schmid Stabilization of the cold shock protein CspB from Bacillus subtilis by evolutionary optimization of Coulombic interactions J. Mol. Biol. 347 2005 1063 1076
    • (2005) J. Mol. Biol. , vol.347 , pp. 1063-1076
    • Wunderlich, M.1    Martin, A.2    Schmid, F.X.3
  • 26
    • 0028792105 scopus 로고
    • Guidelines for protein design: The energetics of beta sheet side chain interactions
    • C.K. Smith, and L. Regan Guidelines for protein design: the energetics of beta sheet side chain interactions Science 270 1995 980 982
    • (1995) Science , vol.270 , pp. 980-982
    • Smith, C.K.1    Regan, L.2
  • 27
    • 0028175780 scopus 로고
    • A thermodynamic scale for the beta-sheet forming tendencies of the amino acids
    • C.K. Smith, J.M. Withka, and L. Regan A thermodynamic scale for the beta-sheet forming tendencies of the amino acids Biochemistry 33 1994 5510 5517
    • (1994) Biochemistry , vol.33 , pp. 5510-5517
    • Smith, C.K.1    Withka, J.M.2    Regan, L.3
  • 28
    • 0033571653 scopus 로고    scopus 로고
    • Sidechain interactions in parallel beta sheets: The energetics of cross-strand pairings
    • J.S. Merkel, J.M. Sturtevant, and L. Regan Sidechain interactions in parallel beta sheets: the energetics of cross-strand pairings Struct. Fold. Des. 7 1999 1333 1343
    • (1999) Struct. Fold. Des. , vol.7 , pp. 1333-1343
    • Merkel, J.S.1    Sturtevant, J.M.2    Regan, L.3
  • 29
    • 0033871567 scopus 로고    scopus 로고
    • Critical role of beta-hairpin formation in protein G folding
    • E.L. McCallister, E. Alm, and D. Baker Critical role of beta-hairpin formation in protein G folding Nature Struct. Biol. 7 2000 669 673
    • (2000) Nature Struct. Biol. , vol.7 , pp. 669-673
    • McCallister, E.L.1    Alm, E.2    Baker, D.3
  • 30
    • 0034964196 scopus 로고    scopus 로고
    • Computer-based redesign of a protein folding pathway
    • S. Nauli, B. Kuhlman, and D. Baker Computer-based redesign of a protein folding pathway Nature Struct. Biol. 8 2001 602 605
    • (2001) Nature Struct. Biol. , vol.8 , pp. 602-605
    • Nauli, S.1    Kuhlman, B.2    Baker, D.3
  • 31
    • 0033551039 scopus 로고    scopus 로고
    • a values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions
    • a values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions Biochemistry 38 1999 4896 4903
    • (1999) Biochemistry , vol.38 , pp. 4896-4903
    • Kuhlman, B.1    Luisi, D.L.2    Young, P.3    Raleigh, D.P.4
  • 32
    • 0033852796 scopus 로고    scopus 로고
    • Charge-charge interactions influence the denatured state ensemble and contribute to protein stability
    • C.N. Pace, R.W. Alston, and K.L. Shaw Charge-charge interactions influence the denatured state ensemble and contribute to protein stability Protein Sci. 9 2000 1395 1398
    • (2000) Protein Sci. , vol.9 , pp. 1395-1398
    • Pace, C.N.1    Alston, R.W.2    Shaw, K.L.3
  • 33
    • 0035843136 scopus 로고    scopus 로고
    • Combinatorial and computational challenges for biocatalyst design
    • F.H. Arnold Combinatorial and computational challenges for biocatalyst design Nature 409 2001 253 257
    • (2001) Nature , vol.409 , pp. 253-257
    • Arnold, F.H.1
  • 34
    • 0035957360 scopus 로고    scopus 로고
    • Computational method to reduce the search space for directed protein evolution
    • C.A. Voigt, S.L. Mayo, F.H. Arnold, and Z.G. Wang Computational method to reduce the search space for directed protein evolution Proc. Natl Acad. Sci. USA 98 2001 3778 3783
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 3778-3783
    • Voigt, C.A.1    Mayo, S.L.2    Arnold, F.H.3    Wang, Z.G.4
  • 35
    • 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
    • Desjarlais, J.R.1    Handel, T.M.2
  • 38
    • 0028111743 scopus 로고
    • Sequence statistics reliably predict stabilizing mutations in a protein domain
    • B. Steipe, B. Schiller, A. Plückthun, and S. Steinbacher Sequence statistics reliably predict stabilizing mutations in a protein domain J. Mol. Biol. 240 1994 188 192
    • (1994) J. Mol. Biol. , vol.240 , pp. 188-192
    • Steipe, B.1    Schiller, B.2    Plückthun, A.3    Steinbacher, S.4
  • 39
    • 0033059278 scopus 로고    scopus 로고
    • Evolutionary approaches to protein engineering
    • B. Steipe Evolutionary approaches to protein engineering Curr. Top. Microbiol. Immunol. 243 1999 55 86
    • (1999) Curr. Top. Microbiol. Immunol. , vol.243 , pp. 55-86
    • Steipe, B.1
  • 41
    • 18744380008 scopus 로고    scopus 로고
    • Consensus-derived structural determinants of the ankyrin repeat motif
    • L.K. Mosavi, D.L. Minor Jr, and Z.Y. Peng Consensus-derived structural determinants of the ankyrin repeat motif Proc. Natl Acad. Sci. USA 99 2002 16029 16034
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 16029-16034
    • Mosavi, L.K.1    Minor Jr., D.L.2    Peng, Z.Y.3
  • 42
    • 0037648552 scopus 로고    scopus 로고
    • Design of stable alpha-helical arrays from an idealized TPR motif
    • E.R. Main, Y. Xiong, M.J. Cocco, L. D'Andrea, and L. Regan Design of stable alpha-helical arrays from an idealized TPR motif Structure 11 2003 497 508
    • (2003) Structure , vol.11 , pp. 497-508
    • Main, E.R.1    Xiong, Y.2    Cocco, M.J.3    D'Andrea, L.4    Regan, L.5
  • 43
    • 0041428117 scopus 로고    scopus 로고
    • The folding and design of repeat proteins: Reaching a consensus
    • E.R.G. Main, S.E. Jackson, and L. Regan The folding and design of repeat proteins: reaching a consensus Curr. Opin. Struct. Biol. 13 2003 482 489
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 482-489
    • Main, E.R.G.1    Jackson, S.E.2    Regan, L.3
  • 44
    • 0023697408 scopus 로고
    • Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl α- Chymotrypsin using different denaturants
    • M.M. Santoro, and D.W. Bolen Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl α- chymotrypsin using different denaturants Biochemistry 27 1988 8063 8068
    • (1988) Biochemistry , vol.27 , pp. 8063-8068
    • Santoro, M.M.1    Bolen, D.W.2
  • 45
    • 0029049321 scopus 로고
    • Extremely rapid folding in the absence of intermediates: The cold-shock protein from Bacillus subtilis
    • T. Schindler, M. Herrler, M.A. Marahiel, and F.X. Schmid Extremely rapid folding in the absence of intermediates: the cold-shock protein from Bacillus subtilis Nature Struct. Biol. 2 1995 663 673
    • (1995) Nature Struct. Biol. , vol.2 , pp. 663-673
    • Schindler, T.1    Herrler, M.2    Marahiel, M.A.3    Schmid, F.X.4
  • 46
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • R. Koradi, M. Billeter, and K. Wüthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graph. 14 1996 51 55
    • (1996) J. Mol. Graph. , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wüthrich, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.