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Volumn , Issue , 2016, Pages 1179-1187

Why reinvent the wheel? Building new proteins based on ready-made parts

Author keywords

antibody; bioinformatics; evolution; protein design; Rosetta; propeller; barrel

Indexed keywords

ANTIBODY; PROTEIN;

EID: 84976578559     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2892     Document Type: Review
Times cited : (37)

References (72)
  • 2
    • 0033694923 scopus 로고    scopus 로고
    • De novo design of helical bundles as models for understanding protein folding and function
    • Hill RB, Raleigh DP, Lombardi A, DeGrado WF (2000) De novo design of helical bundles as models for understanding protein folding and function. Acc Chem Res 33:745–754.
    • (2000) Acc Chem Res , vol.33 , pp. 745-754
    • Hill, R.B.1    Raleigh, D.P.2    Lombardi, A.3    DeGrado, W.F.4
  • 3
    • 0025040232 scopus 로고
    • De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence
    • Hecht MH, Richardson JS, Richardson DC, Ogden RC (1990) De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. Science 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
  • 4
    • 0023812695 scopus 로고
    • Characterization of a helical protein designed from first principles
    • Regan L, DeGrado WF (1988) Characterization of a helical protein designed from first principles. Science 241:976–978.
    • (1988) Science , vol.241 , pp. 976-978
    • Regan, L.1    DeGrado, W.F.2
  • 6
    • 84950276750 scopus 로고    scopus 로고
    • De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy
    • Fernandez Velasco DA
    • Huang PS, Feldmeier K, Parmeggiani F, Fernandez Velasco DA, Höcker B, Baker D (2016) De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nat Chem Biol. 12:29–34.
    • (2016) Nat Chem Biol. , vol.12 , pp. 29-34
    • Huang, P.S.1    Feldmeier, K.2    Parmeggiani, F.3    Höcker, B.4    Baker, D.5
  • 8
    • 84859765617 scopus 로고    scopus 로고
    • Role of the biomolecular energy gap in protein design, structure, and evolution
    • Fleishman SJ, Baker D (2012) Role of the biomolecular energy gap in protein design, structure, and evolution. Cell 149:262–273.
    • (2012) Cell , vol.149 , pp. 262-273
    • Fleishman, S.J.1    Baker, D.2
  • 10
    • 84892615437 scopus 로고    scopus 로고
    • Computational design of a pH-sensitive IgG binding protein
    • Strauch EM, Fleishman SJ, Baker D (2014) Computational design of a pH-sensitive IgG binding protein. Proc Natl Acad Sci USA 111:675–680.
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 675-680
    • Strauch, E.M.1    Fleishman, S.J.2    Baker, D.3
  • 13
    • 84855685292 scopus 로고    scopus 로고
    • Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer
    • Der BS, Machius M, Miley MJ, Mills JL, Szyperski T, Kuhlman B (2012) Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. J Am Chem Soc 134:375–385.
    • (2012) J Am Chem Soc , vol.134 , pp. 375-385
    • Der, B.S.1    Machius, M.2    Miley, M.J.3    Mills, J.L.4    Szyperski, T.5    Kuhlman, B.6
  • 16
    • 84863000087 scopus 로고    scopus 로고
    • Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59
    • Khersonsky O, Kiss G, Rothlisberger D, Dym O, Albeck S, Houk KN, Baker D, Tawfik DS (2012) Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59. Proc Natl Acad Sci US 109:10358–10363.
    • (2012) Proc Natl Acad Sci US , vol.109 , pp. 10358-10363
    • Khersonsky, O.1    Kiss, G.2    Rothlisberger, D.3    Dym, O.4    Albeck, S.5    Houk, K.N.6    Baker, D.7    Tawfik, D.S.8
  • 17
    • 84873024403 scopus 로고    scopus 로고
    • A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds
    • Stranges PB, Kuhlman B (2013) A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds. Protein Sci 22:74–82.
    • (2013) Protein Sci , vol.22 , pp. 74-82
    • Stranges, P.B.1    Kuhlman, B.2
  • 18
    • 84876020987 scopus 로고    scopus 로고
    • Emerging themes in the computational design of novel enzymes and protein–protein interfaces
    • Khare SD, Fleishman SJ (2013) Emerging themes in the computational design of novel enzymes and protein–protein interfaces. FEBS Lett 587:1147–1154.
    • (2013) FEBS Lett , vol.587 , pp. 1147-1154
    • Khare, S.D.1    Fleishman, S.J.2
  • 19
    • 77957316716 scopus 로고    scopus 로고
    • An exciting but challenging road ahead for computational enzyme design
    • Baker D (2010) An exciting but challenging road ahead for computational enzyme design. Protein Sci 19:1817–1819.
    • (2010) Protein Sci , vol.19 , pp. 1817-1819
    • Baker, D.1
  • 20
    • 84870372750 scopus 로고    scopus 로고
    • Experimental support for the foldability-function tradeoff hypothesis: segregation of the folding nucleus and functional regions in fibroblast growth factor-1
    • Longo L, Lee J, Blaber M (2012) Experimental support for the foldability-function tradeoff hypothesis: segregation of the folding nucleus and functional regions in fibroblast growth factor-1. Protein Sci 21:1911–1920.
    • (2012) Protein Sci , vol.21 , pp. 1911-1920
    • Longo, L.1    Lee, J.2    Blaber, M.3
  • 23
    • 84877754586 scopus 로고    scopus 로고
    • Energy functions in de novo protein design: current challenges and future prospects
    • Li Z, Yang Y, Zhan J, Dai L, Zhou Y (2013) Energy functions in de novo protein design: current challenges and future prospects. Annu Rev Biophys 42:315–335.
    • (2013) Annu Rev Biophys , vol.42 , pp. 315-335
    • Li, Z.1    Yang, Y.2    Zhan, J.3    Dai, L.4    Zhou, Y.5
  • 25
    • 84874036318 scopus 로고    scopus 로고
    • Flexible backbone sampling methods to model and design protein alternative conformations
    • Ollikainen N, Smith CA, Fraser JS, Kortemme T (2013) Flexible backbone sampling methods to model and design protein alternative conformations. Methods Enzymol 523:61–85.
    • (2013) Methods Enzymol , vol.523 , pp. 61-85
    • Ollikainen, N.1    Smith, C.A.2    Fraser, J.S.3    Kortemme, T.4
  • 28
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536–540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 29
    • 22244450719 scopus 로고    scopus 로고
    • Protein families and their evolution—a structural perspective
    • Orengo CA, Thornton JM (2005) Protein families and their evolution—a structural perspective. Annu Rev Biochem 74:867–900.
    • (2005) Annu Rev Biochem , vol.74 , pp. 867-900
    • Orengo, C.A.1    Thornton, J.M.2
  • 31
    • 0034923923 scopus 로고    scopus 로고
    • Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies
    • Gerlt JA, Babbitt PC (2001) Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem 70:209–246.
    • (2001) Annu Rev Biochem , vol.70 , pp. 209-246
    • Gerlt, J.A.1    Babbitt, P.C.2
  • 33
    • 84906322381 scopus 로고    scopus 로고
    • Evolutionary relationship of two ancient protein superfolds
    • Farias-Rico JA, Schmidt S, Hocker B (2014) Evolutionary relationship of two ancient protein superfolds. Nat Chem Biol 10:710–715.
    • (2014) Nat Chem Biol , vol.10 , pp. 710-715
    • Farias-Rico, J.A.1    Schmidt, S.2    Hocker, B.3
  • 34
    • 31544483652 scopus 로고    scopus 로고
    • Biochemistry. Loop grafting and the origins of enzyme species
    • Tawfik DS (2006) Biochemistry. Loop grafting and the origins of enzyme species. Science 311:475–476.
    • (2006) Science , vol.311 , pp. 475-476
    • Tawfik, D.S.1
  • 35
    • 15244362640 scopus 로고    scopus 로고
    • Structural similarity of loops in protein families: toward the understanding of protein evolution
    • Panchenko AR, Madej T (2005) Structural similarity of loops in protein families: toward the understanding of protein evolution. BMC Evol Biol 5:10.
    • (2005) BMC Evol Biol , vol.5 , pp. 10
    • Panchenko, A.R.1    Madej, T.2
  • 37
    • 0036384350 scopus 로고    scopus 로고
    • One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions
    • Nagano N, Orengo CA, Thornton JM (2002) One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol 321:741–765.
    • (2002) J Mol Biol , vol.321 , pp. 741-765
    • Nagano, N.1    Orengo, C.A.2    Thornton, J.M.3
  • 38
    • 84879549646 scopus 로고    scopus 로고
    • What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs
    • Dellus-Gur E, Toth-Petroczy A, Elias M, Tawfik DS (2013) What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs. J Mol Biol 425:2609–2621.
    • (2013) J Mol Biol , vol.425 , pp. 2609-2621
    • Dellus-Gur, E.1    Toth-Petroczy, A.2    Elias, M.3    Tawfik, D.S.4
  • 39
    • 77952303485 scopus 로고    scopus 로고
    • Computational and experimental evidence for the evolution of a (beta alpha)8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds
    • Richter M, Bosnali M, Carstensen L, Seitz T, Durchschlag H, Blanquart S, Merkl R, Sterner R (2010) Computational and experimental evidence for the evolution of a (beta alpha)8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds. J Mol Biol 398:763–773.
    • (2010) J Mol Biol , vol.398 , pp. 763-773
    • Richter, M.1    Bosnali, M.2    Carstensen, L.3    Seitz, T.4    Durchschlag, H.5    Blanquart, S.6    Merkl, R.7    Sterner, R.8
  • 40
    • 41149106300 scopus 로고    scopus 로고
    • Evolution of the beta-propeller fold
    • Chaudhuri I, Soding J, Lupas AN (2008) Evolution of the beta-propeller fold. Proteins 71:795–803.
    • (2008) Proteins , vol.71 , pp. 795-803
    • Chaudhuri, I.1    Soding, J.2    Lupas, A.N.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 (2011) Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Proc Natl Acad Sci USA 108:126–130.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 126-130
    • Lee, J.1    Blaber, M.2
  • 42
    • 0041428117 scopus 로고    scopus 로고
    • The folding and design of repeat proteins: reaching a consensus
    • Main ER, Jackson SE, Regan L (2003) The folding and design of repeat proteins: reaching a consensus. Curr Opin Struct Biol 13:482–489.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 482-489
    • Main, E.R.1    Jackson, S.E.2    Regan, L.3
  • 43
    • 0041317258 scopus 로고    scopus 로고
    • More than the sum of their parts: on the evolution of proteins from peptides
    • Soding J, Lupas AN (2003) More than the sum of their parts: on the evolution of proteins from peptides. Bioessays 25:837–846.
    • (2003) Bioessays , vol.25 , pp. 837-846
    • Soding, J.1    Lupas, A.N.2
  • 44
    • 84901378640 scopus 로고    scopus 로고
    • Design of proteins from smaller fragments-learning from evolution
    • Hocker B (2014) Design of proteins from smaller fragments-learning from evolution. Curr Opin Struct Biol 27:56–62.
    • (2014) Curr Opin Struct Biol , vol.27 , pp. 56-62
    • Hocker, B.1
  • 45
    • 0028050350 scopus 로고
    • Rapid evolution of a protein in-vitro by DNA shuffling
    • Stemmer WPC (1994) Rapid evolution of a protein in-vitro by DNA shuffling. Nature 370:389–391.
    • (1994) Nature , vol.370 , pp. 389-391
    • Stemmer, W.P.C.1
  • 46
    • 84865306330 scopus 로고    scopus 로고
    • Directed enzyme evolution: beyond the low-hanging fruit
    • Goldsmith M, Tawfik DS (2012) Directed enzyme evolution: beyond the low-hanging fruit. Curr Opin Struct Biol 22:406–412.
    • (2012) Curr Opin Struct Biol , vol.22 , pp. 406-412
    • Goldsmith, M.1    Tawfik, D.S.2
  • 47
    • 84874032890 scopus 로고    scopus 로고
    • Efficient sampling of SCHEMA chimera families to identify useful sequence elements
    • Heinzelman P, Romero PA, Arnold FH (2013) Efficient sampling of SCHEMA chimera families to identify useful sequence elements. Method Enzymol 523:351–368.
    • (2013) Method Enzymol , vol.523 , pp. 351-368
    • Heinzelman, P.1    Romero, P.A.2    Arnold, F.H.3
  • 48
    • 28444444163 scopus 로고    scopus 로고
    • Catalytic versatility, stability, and evolution of the (betaalpha)8-barrel enzyme fold
    • Sterner R, Hocker B (2005) Catalytic versatility, stability, and evolution of the (betaalpha)8-barrel enzyme fold. Chem Rev 105:4038–4055.
    • (2005) Chem Rev , vol.105 , pp. 4038-4055
    • Sterner, R.1    Hocker, B.2
  • 49
    • 50049096112 scopus 로고    scopus 로고
    • Experimental evidence for the existence of a stable half-barrel subdomain in the (beta/alpha)8-barrel fold
    • Akanuma S, Yamagishi A (2008) Experimental evidence for the existence of a stable half-barrel subdomain in the (beta/alpha)8-barrel fold. J Mol Biol 382:458–466.
    • (2008) J Mol Biol , vol.382 , pp. 458-466
    • Akanuma, S.1    Yamagishi, A.2
  • 50
    • 9344235017 scopus 로고    scopus 로고
    • Mimicking enzyme evolution by generating new (betaalpha)8-barrels from (betaalpha)4-half-barrels
    • Hocker B, Claren J, Sterner R (2004) Mimicking enzyme evolution by generating new (betaalpha)8-barrels from (betaalpha)4-half-barrels. Proc Natl Acad Sci USA 101:16448–16453.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 16448-16453
    • Hocker, B.1    Claren, J.2    Sterner, R.3
  • 51
    • 84883049489 scopus 로고    scopus 로고
    • Establishing catalytic activity on an artificial (betaalpha)8-barrel protein designed from identical half-barrels
    • Sperl JM, Rohweder B, Rajendran C, Sterner R (2013) Establishing catalytic activity on an artificial (betaalpha)8-barrel protein designed from identical half-barrels. FEBS Lett 587:2798–2805.
    • (2013) FEBS Lett , vol.587 , pp. 2798-2805
    • Sperl, J.M.1    Rohweder, B.2    Rajendran, C.3    Sterner, R.4
  • 52
    • 62649123200 scopus 로고    scopus 로고
    • Establishing wild-type levels of catalytic activity on natural and artificial (beta alpha)8-barrel protein scaffolds
    • Claren J, Malisi C, Hocker B, Sterner R (2009) Establishing wild-type levels of catalytic activity on natural and artificial (beta alpha)8-barrel protein scaffolds. Proc Natl Acad Sci USA 106:3704–3709.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 3704-3709
    • Claren, J.1    Malisi, C.2    Hocker, B.3    Sterner, R.4
  • 53
    • 84868531723 scopus 로고    scopus 로고
    • A highly stable protein chimera built from fragments of different folds
    • Shanmugaratnam S, Eisenbeis S, Hocker B (2012) A highly stable protein chimera built from fragments of different folds. Protein Eng Des Sel 25:699–703.
    • (2012) Protein Eng Des Sel , vol.25 , pp. 699-703
    • Shanmugaratnam, S.1    Eisenbeis, S.2    Hocker, B.3
  • 55
    • 84864645362 scopus 로고    scopus 로고
    • Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling
    • Afriat-Jurnou L, Jackson CJ, Tawfik DS (2012) Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling. Biochemistry 51:6047–6055.
    • (2012) Biochemistry , vol.51 , pp. 6047-6055
    • Afriat-Jurnou, L.1    Jackson, C.J.2    Tawfik, D.S.3
  • 59
    • 0025359825 scopus 로고
    • Synthesis, purification and initial structural characterization of octarellin, a de novo polypeptide modeled on the alpha beta-barrel proteins
    • Goraj K, Renard A, Martial JA (1990) Synthesis, purification and initial structural characterization of octarellin, a de novo polypeptide modeled on the alpha beta-barrel proteins. Protein Eng 3:259–266.
    • (1990) Protein Eng , vol.3 , pp. 259-266
    • Goraj, K.1    Renard, A.2    Martial, J.A.3
  • 60
    • 33746536641 scopus 로고    scopus 로고
    • Engineering of beta-propeller protein scaffolds by multiple gene duplication and fusion of an idealized WD repeat
    • Nikkhah M, Jawad-Alami Z, Demydchuk M, Ribbons D, Paoli M (2006) Engineering of beta-propeller protein scaffolds by multiple gene duplication and fusion of an idealized WD repeat. Biomol Eng 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
  • 61
    • 78650425278 scopus 로고    scopus 로고
    • Functional beta-propeller lectins by tandem duplications of repetitive units
    • Yadid I, Tawfik DS (2011) Functional beta-propeller lectins by tandem duplications of repetitive units. Protein Engin Des Sel 24:185–195.
    • (2011) Protein Engin Des Sel , vol.24 , pp. 185-195
    • Yadid, I.1    Tawfik, D.S.2
  • 63
    • 33751415081 scopus 로고    scopus 로고
    • Reconstruction of functional beta-propeller lectins via homo-oligomeric assembly of shorter fragments
    • Yadid I, Tawfik DS (2007) Reconstruction of functional beta-propeller lectins via homo-oligomeric assembly of shorter fragments. J Mol Biol 365:10–17.
    • (2007) J Mol Biol , vol.365 , pp. 10-17
    • Yadid, I.1    Tawfik, D.S.2
  • 66
    • 0017614064 scopus 로고
    • Structural basis for specificity of antibody-antigen reactions and structural mechanisms for diversification of antigen-binding specificities
    • Padlan EA (1977) Structural basis for specificity of antibody-antigen reactions and structural mechanisms for diversification of antigen-binding specificities. Q Rev Biophys 10:35
    • (1977) Q Rev Biophys , vol.10 , pp. 35
    • Padlan, E.A.1
  • 67
    • 0017747498 scopus 로고
    • Unusual distributions of amino-acids in complementarity-determining (hypervariable) segments of heavy and light-chains of immunoglobulins and their possible roles in specificity of antibody-combining sites
    • Kabat EA, Wu TT, Bilofsky H (1977) Unusual distributions of amino-acids in complementarity-determining (hypervariable) segments of heavy and light-chains of immunoglobulins and their possible roles in specificity of antibody-combining sites. J Biol Chem 252:6609–6616.
    • (1977) J Biol Chem , vol.252 , pp. 6609-6616
    • Kabat, E.A.1    Wu, T.T.2    Bilofsky, H.3
  • 69
    • 0026094165 scopus 로고
    • Humanization of a mouse monoclonal antibody by CDR-grafting: the importance of framework residues on loop conformation
    • Kettleborough CA, Saldanha J, Heath VJ, Morrison CJ, Bendig MM (1991) Humanization of a mouse monoclonal antibody by CDR-grafting: the importance of framework residues on loop conformation. Protein Eng 4:773–783.
    • (1991) Protein Eng , vol.4 , pp. 773-783
    • Kettleborough, C.A.1    Saldanha, J.2    Heath, V.J.3    Morrison, C.J.4    Bendig, M.M.5
  • 70
    • 84937736814 scopus 로고    scopus 로고
    • AbDesign: an algorithm for combinatorial backbone design guided by natural conformations and sequences
    • Lapidoth GD, Baran D, Pszolla GM, Norn C, Alon A, Tyka MD, Fleishman SJ (2015) AbDesign: an algorithm for combinatorial backbone design guided by natural conformations and sequences. Proteins 83:1385–1406.
    • (2015) Proteins , vol.83 , pp. 1385-1406
    • Lapidoth, G.D.1    Baran, D.2    Pszolla, G.M.3    Norn, C.4    Alon, A.5    Tyka, M.D.6    Fleishman, S.J.7
  • 72
    • 79953169868 scopus 로고    scopus 로고
    • Restricted sidechain plasticity in the structures of native proteins and complexes
    • Fleishman SJ, Khare SD, Koga N, Baker D (2011) Restricted sidechain plasticity in the structures of native proteins and complexes. Protein Sci 20:753–757.
    • (2011) Protein Sci , vol.20 , pp. 753-757
    • Fleishman, S.J.1    Khare, S.D.2    Koga, N.3    Baker, D.4


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