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Volumn 22, Issue 4, 2012, Pages 442-450

Designing proteins from simple motifs: Opportunities in Top-Down Symmetric Deconstruction

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; FIBROBLAST GROWTH FACTOR 1; INTERLEUKIN 1BETA; POLYPEPTIDE; PROTEIN; TREFOIL PEPTIDE;

EID: 84865279549     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2012.05.008     Document Type: Review
Times cited : (23)

References (49)
  • 3
    • 23444436172 scopus 로고
    • Protein design by binary patterning of polar and nonpolar amino acids
    • Kamtekar S., Schiffer J.M., Xiong H., Babik J.M., Hecht M.H. Protein design by binary patterning of polar and nonpolar amino acids. Science 1993, 262:1680-1685.
    • (1993) Science , vol.262 , pp. 1680-1685
    • Kamtekar, S.1    Schiffer, J.M.2    Xiong, H.3    Babik, J.M.4    Hecht, M.H.5
  • 4
    • 0028567868 scopus 로고
    • De novo design of beta-sheet proteins
    • Hecht M.H. De novo design of beta-sheet proteins. Proc Natl Acad Sci U S A 1994, 91:8729-8730.
    • (1994) Proc Natl Acad Sci U S A , vol.91 , pp. 8729-8730
    • Hecht, M.H.1
  • 5
    • 0023812695 scopus 로고
    • Characterization of a helical protein designed from first principles
    • Regan L., DeGrado W.F. Characterization of a helical protein designed from first principles. Science 1988, 241:976-978.
    • (1988) Science , vol.241 , pp. 976-978
    • Regan, L.1    DeGrado, W.F.2
  • 6
    • 0025040232 scopus 로고
    • De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence
    • Hecht M.H., Richardson J.S., Richardson D.C., Ogden R.C. De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. Science 1990, 249:884-891.
    • (1990) Science , vol.249 , pp. 884-891
    • Hecht, M.H.1    Richardson, J.S.2    Richardson, D.C.3    Ogden, R.C.4
  • 9
    • 0034284955 scopus 로고    scopus 로고
    • Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion
    • Lang D., Thoma R., Henn-Sax M., Sterner R., Wilmanns M. Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science 2000, 289:1546-1550.
    • (2000) Science , vol.289 , pp. 1546-1550
    • Lang, D.1    Thoma, R.2    Henn-Sax, M.3    Sterner, R.4    Wilmanns, M.5
  • 11
    • 33751415081 scopus 로고    scopus 로고
    • Reconstruction of functional β-propeller lectins via homo-oligomeric assembly of shorter fragments
    • Yadid I., Tawfik D.S. Reconstruction of functional β-propeller lectins via homo-oligomeric assembly of shorter fragments. J Mol Biol 2007, 365:10-17.
    • (2007) J Mol Biol , vol.365 , pp. 10-17
    • Yadid, I.1    Tawfik, D.S.2
  • 13
    • 78650425278 scopus 로고    scopus 로고
    • Functional β-propeller lectins by tandem duplications of repetitive units
    • Yadid I., Tawfik D.S. Functional β-propeller lectins by tandem duplications of repetitive units. Protein Eng Des Sel 2011, 24:185-195.
    • (2011) Protein Eng Des Sel , vol.24 , pp. 185-195
    • Yadid, I.1    Tawfik, D.S.2
  • 14
    • 33746536641 scopus 로고    scopus 로고
    • Engineering of β-propellor protein scaffolds by multiple gene duplication and fusion of an idealized WD repeat
    • Nikkhah M., Jawad-Alami Z., Demydchuk M., Ribbons D., Paoli M. Engineering of β-propellor protein scaffolds by multiple gene duplication and fusion of an idealized WD repeat. Biomol Eng 2006, 23:185-194.
    • (2006) Biomol Eng , vol.23 , pp. 185-194
    • Nikkhah, M.1    Jawad-Alami, Z.2    Demydchuk, M.3    Ribbons, D.4    Paoli, M.5
  • 16
    • 0029952910 scopus 로고    scopus 로고
    • Symmetry and the energy landscapes of biomolecules
    • Wolynes P.G. Symmetry and the energy landscapes of biomolecules. Proc Natl Acad Sci U S A 1996, 93:14249-14255.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 14249-14255
    • Wolynes, P.G.1
  • 17
    • 28644437048 scopus 로고    scopus 로고
    • The importance of sequence diversity in the aggregation and evolution of proteins
    • Wright C.F., Teichmann S.A., Clarke J., Dobson C.M. The importance of sequence diversity in the aggregation and evolution of proteins. Nature 2005, 438:878-881.
    • (2005) Nature , vol.438 , pp. 878-881
    • Wright, C.F.1    Teichmann, S.A.2    Clarke, J.3    Dobson, C.M.4
  • 19
    • 0029036051 scopus 로고
    • Second-generation octarellins: two new de novo (beta/alpha)8 polypeptides designed for investigating the influence of beta-residue packing on the alpha/beta-barrel structure stability
    • Houbrechts A., Moreau B., Abagyan R., Mainfroid V., Preaux G., Lamproye A., Poncin A., Goormaghtigh E., Ruysschaert J.M., Martial J.A. Second-generation octarellins: two new de novo (beta/alpha)8 polypeptides designed for investigating the influence of beta-residue packing on the alpha/beta-barrel structure stability. Protein Eng 1995, 8:249-259.
    • (1995) Protein Eng , vol.8 , pp. 249-259
    • Houbrechts, A.1    Moreau, B.2    Abagyan, R.3    Mainfroid, V.4    Preaux, G.5    Lamproye, A.6    Poncin, A.7    Goormaghtigh, E.8    Ruysschaert, J.M.9    Martial, J.A.10
  • 20
    • 0035187229 scopus 로고    scopus 로고
    • Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a β-trefoil
    • Brych S.R., Blaber S.I., Logan T.M., Blaber M. Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a β-trefoil. Protein Sci 2001, 10:2587-2599.
    • (2001) Protein Sci , vol.10 , pp. 2587-2599
    • Brych, S.R.1    Blaber, S.I.2    Logan, T.M.3    Blaber, M.4
  • 21
    • 0036304410 scopus 로고    scopus 로고
    • Three topologically equivalent core residues affect the transition state ensemble in a protein folding reaction
    • Heidary D.K., Jennings P.A. Three topologically equivalent core residues affect the transition state ensemble in a protein folding reaction. J Mol Biol 2002, 316:789-798.
    • (2002) J Mol Biol , vol.316 , pp. 789-798
    • Heidary, D.K.1    Jennings, P.A.2
  • 22
    • 0345276586 scopus 로고    scopus 로고
    • Accommodation of a highly symmetric core within a symmetric protein superfold
    • Brych S.R., Kim J., Logan T.M., Blaber M. Accommodation of a highly symmetric core within a symmetric protein superfold. Protein Sci 2003, 12:2704-2718.
    • (2003) Protein Sci , vol.12 , pp. 2704-2718
    • Brych, S.R.1    Kim, J.2    Logan, T.M.3    Blaber, M.4
  • 23
    • 7944227948 scopus 로고    scopus 로고
    • Symmetric primary and tertiary structure mutations within a symmetric superfold: a solution, not a constraint, to achieve a foldable polypeptide
    • Brych S.R., Dubey V.K., Bienkiewicz E., Lee J., Logan T.M., Blaber M. Symmetric primary and tertiary structure mutations within a symmetric superfold: a solution, not a constraint, to achieve a foldable polypeptide. J Mol Biol 2004, 344:769-780.
    • (2004) J Mol Biol , vol.344 , pp. 769-780
    • Brych, S.R.1    Dubey, V.K.2    Bienkiewicz, E.3    Lee, J.4    Logan, T.M.5    Blaber, M.6
  • 24
    • 84863177542 scopus 로고    scopus 로고
    • An empirical phase diagram approach to investigate conformational stability of 'second-generation' functional mutants of acidic fibroblast growth factor (FGF-1)
    • Alsenaidy M.A., Wang T., Kim J.H., Joshi S.B., Lee J., Blaber M., Volkin D.B., Middaugh C.R. An empirical phase diagram approach to investigate conformational stability of 'second-generation' functional mutants of acidic fibroblast growth factor (FGF-1). Protein Sci 2012, 21:418-432.
    • (2012) Protein Sci , vol.21 , pp. 418-432
    • Alsenaidy, M.A.1    Wang, T.2    Kim, J.H.3    Joshi, S.B.4    Lee, J.5    Blaber, M.6    Volkin, D.B.7    Middaugh, C.R.8
  • 25
    • 0036384211 scopus 로고    scopus 로고
    • Structural basis of stability-function tradeoffs in enzymes
    • Beadle B.M., Shoichet B.K. Structural basis of stability-function tradeoffs in enzymes. J Mol Biol 2002, 321:285-296.
    • (2002) J Mol Biol , vol.321 , pp. 285-296
    • Beadle, B.M.1    Shoichet, B.K.2
  • 27
    • 18744380008 scopus 로고    scopus 로고
    • Consensus-derived structural determinants of the ankyrin repeat motif
    • Mosavi L.K., Minor D.L., Peng Z.Y. Consensus-derived structural determinants of the ankyrin repeat motif. Proc Natl Acad Sci U S A 2002, 99:16029-16034.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 16029-16034
    • Mosavi, L.K.1    Minor, D.L.2    Peng, Z.Y.3
  • 28
    • 0042780350 scopus 로고    scopus 로고
    • Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins
    • Binz H.K., Stumpp M.T., Forrer P., Amstutz P., Pluckthun A. Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J Mol Biol 2003, 332:489-503.
    • (2003) J Mol Biol , vol.332 , pp. 489-503
    • Binz, H.K.1    Stumpp, M.T.2    Forrer, P.3    Amstutz, P.4    Pluckthun, A.5
  • 29
    • 42649092133 scopus 로고    scopus 로고
    • Rerouting the folding pathway of the notch ankyrin domain by reshaping the energy landscape
    • Tripp K.W., Barrick D. Rerouting the folding pathway of the notch ankyrin domain by reshaping the energy landscape. J Am Chem Soc 2008, 130:5681-5688.
    • (2008) J Am Chem Soc , vol.130 , pp. 5681-5688
    • Tripp, K.W.1    Barrick, D.2
  • 30
    • 78349313323 scopus 로고    scopus 로고
    • Structural determinants for improved stability of designed ankyrin repeat proteins with a redesigned C-capping module
    • Kramer M.A., Wetzel S.K., Pluckthun A., Mittl P.R., Grutter M.G. Structural determinants for improved stability of designed ankyrin repeat proteins with a redesigned C-capping module. J Mol Biol 2010, 404:381-391.
    • (2010) J Mol Biol , vol.404 , pp. 381-391
    • Kramer, M.A.1    Wetzel, S.K.2    Pluckthun, A.3    Mittl, P.R.4    Grutter, M.G.5
  • 31
    • 9344235017 scopus 로고    scopus 로고
    • Mimicking enzyme evolution by generating new (beta-alpha)8-barrels from (beta-alpha)4-half-barrels
    • Hocker B., Claren J., Sterner R. Mimicking enzyme evolution by generating new (beta-alpha)8-barrels from (beta-alpha)4-half-barrels. Proc Natl Acad Sci U S A 2004, 101:16448-16453.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 16448-16453
    • Hocker, B.1    Claren, J.2    Sterner, R.3
  • 32
    • 34547662332 scopus 로고    scopus 로고
    • Stabilization of a (beta-alpha)8-barrel protein designed from identical half barrels
    • Seitz T., Bocola M., Claren J., Sterner R. Stabilization of a (beta-alpha)8-barrel protein designed from identical half barrels. J Mol Biol 2007, 372:114-129.
    • (2007) J Mol Biol , vol.372 , pp. 114-129
    • Seitz, T.1    Bocola, M.2    Claren, J.3    Sterner, R.4
  • 34
    • 79952735272 scopus 로고    scopus 로고
    • A polypeptide 'building block' for the β-trefoil fold identified by 'Top-Down Symmetric Deconstruction'
    • Lee J., Blaber S.I., Dubey V.K., Blaber M. A polypeptide 'building block' for the β-trefoil fold identified by 'Top-Down Symmetric Deconstruction'. J Mol Biol 2011, 407:744-763.
    • (2011) J Mol Biol , vol.407 , pp. 744-763
    • Lee, J.1    Blaber, S.I.2    Dubey, V.K.3    Blaber, M.4
  • 35
    • 0033921704 scopus 로고    scopus 로고
    • The molecular evolutionary history of a winged bean α-chymotrypsin inhibitor and modeling of its mutations through structural analysis
    • Mukhopadhyay D. The molecular evolutionary history of a winged bean α-chymotrypsin inhibitor and modeling of its mutations through structural analysis. J Mol Evol 2000, 50:214-223.
    • (2000) J Mol Evol , vol.50 , pp. 214-223
    • Mukhopadhyay, D.1
  • 36
    • 0034612995 scopus 로고    scopus 로고
    • Identification of distant homologues of fibroblast growth factors suggests a common ancestor for all beta-trefoil proteins
    • Ponting C.P., Russell R.B. Identification of distant homologues of fibroblast growth factors suggests a common ancestor for all beta-trefoil proteins. J Mol Biol 2000, 302:1041-1047.
    • (2000) J Mol Biol , vol.302 , pp. 1041-1047
    • Ponting, C.P.1    Russell, R.B.2
  • 37
    • 0041387567 scopus 로고    scopus 로고
    • A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins
    • Dantas G., Kuhlman B., Callender D., Wong M., Baker D. A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol 2003, 332:449-460.
    • (2003) J Mol Biol , vol.332 , pp. 449-460
    • Dantas, G.1    Kuhlman, B.2    Callender, D.3    Wong, M.4    Baker, D.5
  • 39
    • 78649782932 scopus 로고    scopus 로고
    • 8-barrel protein as studied by fragmentation analysis
    • 8-barrel protein as studied by fragmentation analysis. Proteins 2011, 79:221-231.
    • (2011) Proteins , vol.79 , pp. 221-231
    • Akanuma, S.1    Yamagishi, A.2
  • 40
    • 0037116603 scopus 로고    scopus 로고
    • A common evolutionary origin of two elementary enzyme folds
    • Hocker B., Schmidt S., Sterner R. A common evolutionary origin of two elementary enzyme folds. FEBS Lett 2002, 510:133-135.
    • (2002) FEBS Lett , vol.510 , pp. 133-135
    • Hocker, B.1    Schmidt, S.2    Sterner, R.3
  • 41
    • 78651068037 scopus 로고    scopus 로고
    • Experimental support for the evolution of symmetric protein architecture from a simple peptide motif
    • Lee J., Blaber M. Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Proc Natl Acad Sci U S A 2011, 108:126-130.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 126-130
    • Lee, J.1    Blaber, M.2
  • 43
    • 27144517647 scopus 로고    scopus 로고
    • 8-barrel protein as studied by experimental and computational methods
    • 8-barrel protein as studied by experimental and computational methods. J Mol Biol 2005, 353:1161-1170.
    • (2005) J Mol Biol , vol.353 , pp. 1161-1170
    • Akanuma, S.1    Yamagishi, A.2
  • 47
    • 0036183061 scopus 로고    scopus 로고
    • Conserved and nonconserved features of the folding pathway of hisactophilin, a β-trefoil protein
    • Liu C., Gaspar J.A., Wong H.J., Meiering E.M. Conserved and nonconserved features of the folding pathway of hisactophilin, a β-trefoil protein. Protein Sci 2002, 11:669-679.
    • (2002) Protein Sci , vol.11 , pp. 669-679
    • Liu, C.1    Gaspar, J.A.2    Wong, H.J.3    Meiering, E.M.4
  • 49
    • 64349124286 scopus 로고    scopus 로고
    • High-resolution crystal structure of an artificial (betaalpha)(8)-barrel protein designed from identical half-barrels
    • Hocker B., Lochner A., Seitz T., Claren J., Sterner R. High-resolution crystal structure of an artificial (betaalpha)(8)-barrel protein designed from identical half-barrels. Biochemistry 2009, 48:1145-1147.
    • (2009) Biochemistry , vol.48 , pp. 1145-1147
    • Hocker, B.1    Lochner, A.2    Seitz, T.3    Claren, J.4    Sterner, R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.