메뉴 건너뛰기




Volumn 20, Issue 3, 2010, Pages 377-384

Designing ensembles in conformational and sequence space to characterize and engineer proteins

Author keywords

[No Author keywords available]

Indexed keywords

BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; BETA LACTAMASE; DNA; MYOGLOBIN; TRANSCRIPTION FACTOR;

EID: 77955579347     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2010.02.004     Document Type: Review
Times cited : (26)

References (67)
  • 1
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: fully automated sequence selection
    • Dahiyat B.I., Mayo S.L. De novo protein design: fully automated sequence selection. Science 1997, 278:82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 2
    • 70350334391 scopus 로고    scopus 로고
    • Computer-aided design of functional protein interactions
    • Mandell D.J., Kortemme T. Computer-aided design of functional protein interactions. Nat Chem Biol 2009, 5:797-807.
    • (2009) Nat Chem Biol , vol.5 , pp. 797-807
    • Mandell, D.J.1    Kortemme, T.2
  • 3
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless S.W., Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 1999, 286:295-299.
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 4
    • 1842839788 scopus 로고    scopus 로고
    • Simulating protein evolution in sequence and structure space
    • Xia Y., Levitt M. Simulating protein evolution in sequence and structure space. Curr Opin Struct Biol 2004, 14:202-207.
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 202-207
    • Xia, Y.1    Levitt, M.2
  • 5
    • 44349161622 scopus 로고    scopus 로고
    • Intense neutral drifts yield robust and evolvable consensus proteins
    • Bershtein S., Goldin K., Tawfik D.S. Intense neutral drifts yield robust and evolvable consensus proteins. J Mol Biol 2008, 379:1029-1044.
    • (2008) J Mol Biol , vol.379 , pp. 1029-1044
    • Bershtein, S.1    Goldin, K.2    Tawfik, D.S.3
  • 6
    • 34250691635 scopus 로고    scopus 로고
    • Computational protein design: structure, function and combinatorial diversity
    • Kang S.G., Saven J.G. Computational protein design: structure, function and combinatorial diversity. Curr Opin Chem Biol 2007, 11:329-334.
    • (2007) Curr Opin Chem Biol , vol.11 , pp. 329-334
    • Kang, S.G.1    Saven, J.G.2
  • 7
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr D.D., Nussinov R., Wright P.E. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009, 5:789-796.
    • (2009) Nat Chem Biol , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 8
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • Tokuriki N., Tawfik D.S. Protein dynamism and evolvability. Science 2009, 324:203-207.
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 9
    • 0033516509 scopus 로고    scopus 로고
    • Side-chain and backbone flexibility in protein core design
    • Desjarlais J.R., Handel T.M. Side-chain and backbone flexibility in protein core design. J Mol Biol 1999, 290:305-318.
    • (1999) J Mol Biol , vol.290 , pp. 305-318
    • Desjarlais, J.R.1    Handel, T.M.2
  • 10
    • 34547121250 scopus 로고    scopus 로고
    • Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL
    • Fu X., Apgar J.R., Keating A.E. Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL. J Mol Biol 2007, 371:1099-1117.
    • (2007) J Mol Biol , vol.371 , pp. 1099-1117
    • Fu, X.1    Apgar, J.R.2    Keating, A.E.3
  • 11
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman B., Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 2000, 97:10383-10388.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 12
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • Desmet J., Maeyer M.D., Hazes B., Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 1992, 356:539-542.
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    Maeyer, M.D.2    Hazes, B.3    Lasters, I.4
  • 13
    • 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., Hellinga H.W. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. J Mol Biol 2001, 307:429-445.
    • (2001) J Mol Biol , vol.307 , pp. 429-445
    • Looger, L.L.1    Hellinga, H.W.2
  • 14
    • 5444230250 scopus 로고    scopus 로고
    • Preprocessing of rotamers for protein design calculations
    • Shah P.S., Hom G.K., Mayo S.L. Preprocessing of rotamers for protein design calculations. J Comput Chem 2004, 25:1797-1800.
    • (2004) J Comput Chem , vol.25 , pp. 1797-1800
    • Shah, P.S.1    Hom, G.K.2    Mayo, S.L.3
  • 15
    • 34547840252 scopus 로고    scopus 로고
    • Dead-end elimination with backbone flexibility
    • Georgiev I., Donald B.R. Dead-end elimination with backbone flexibility. Bioinformatics 2007, 23:i185-194.
    • (2007) Bioinformatics , vol.23
    • Georgiev, I.1    Donald, B.R.2
  • 16
    • 46449106372 scopus 로고    scopus 로고
    • The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
    • Georgiev I., Lilien R.H., Donald B.R. The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. J Comput Chem 2008, 29:1527-1542.
    • (2008) J Comput Chem , vol.29 , pp. 1527-1542
    • Georgiev, I.1    Lilien, R.H.2    Donald, B.R.3
  • 18
    • 33846102955 scopus 로고    scopus 로고
    • Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function
    • Treynor T.P., Vizcarra C.L., Nedelcu D., Mayo S.L. Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function. Proc Natl Acad Sci USA 2007, 104:48-53.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 48-53
    • Treynor, T.P.1    Vizcarra, C.L.2    Nedelcu, D.3    Mayo, S.L.4
  • 19
    • 77951881215 scopus 로고    scopus 로고
    • Design of multispecific protein sequences using probabilistic graphical modeling
    • Fromer M., Yanover C., Linial M. Design of multispecific protein sequences using probabilistic graphical modeling. Proteins 2009.
    • (2009) Proteins
    • Fromer, M.1    Yanover, C.2    Linial, M.3
  • 21
    • 0036892389 scopus 로고    scopus 로고
    • Thoroughly sampling sequence space: large-scale protein design of structural ensembles
    • Larson S.M., England J.L., Desjarlais J.R., Pande V.S. Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Sci 2002, 11:2804-2813.
    • (2002) Protein Sci , vol.11 , pp. 2804-2813
    • Larson, S.M.1    England, J.L.2    Desjarlais, J.R.3    Pande, V.S.4
  • 22
    • 33746639718 scopus 로고    scopus 로고
    • Emergence of protein fold families through rational design
    • Ding F., Dokholyan N.V. Emergence of protein fold families through rational design. PLoS Comput Biol 2006, 2:e85.
    • (2006) PLoS Comput Biol , vol.2
    • Ding, F.1    Dokholyan, N.V.2
  • 23
    • 70349775833 scopus 로고    scopus 로고
    • Backbone flexibility in computational protein design
    • Mandell D.J., Kortemme T. Backbone flexibility in computational protein design. Curr Opin Biotechnol 2009, 20:420-428.
    • (2009) Curr Opin Biotechnol , vol.20 , pp. 420-428
    • Mandell, D.J.1    Kortemme, T.2
  • 25
    • 34848845491 scopus 로고    scopus 로고
    • Deciphering protein dynamics from NMR data using explicit structure sampling and selection
    • Chen Y., Campbell S.L., Dokholyan N.V. Deciphering protein dynamics from NMR data using explicit structure sampling and selection. Biophys J 2007, 93:2300-2306.
    • (2007) Biophys J , vol.93 , pp. 2300-2306
    • Chen, Y.1    Campbell, S.L.2    Dokholyan, N.V.3
  • 27
    • 12544260150 scopus 로고    scopus 로고
    • Recapitulation of protein family divergence using flexible backbone protein design
    • Saunders C.T., Baker D. Recapitulation of protein family divergence using flexible backbone protein design. J Mol Biol 2005, 346:631-644.
    • (2005) J Mol Biol , vol.346 , pp. 631-644
    • Saunders, C.T.1    Baker, D.2
  • 28
    • 32044456003 scopus 로고    scopus 로고
    • The backrub motion: how protein backbone shrugs when a sidechain dances
    • Davis I.W., Arendall W.B., Richardson D.C., Richardson J.S. The backrub motion: how protein backbone shrugs when a sidechain dances. Structure 2006, 14:265-274.
    • (2006) Structure , vol.14 , pp. 265-274
    • Davis, I.W.1    Arendall, W.B.2    Richardson, D.C.3    Richardson, J.S.4
  • 29
    • 45649084560 scopus 로고    scopus 로고
    • Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction
    • Smith C.A., Kortemme T. Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol 2008, 380:742-756.
    • (2008) J Mol Biol , vol.380 , pp. 742-756
    • Smith, C.A.1    Kortemme, T.2
  • 30
    • 68349104348 scopus 로고    scopus 로고
    • Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
    • Mandell D.J., Coutsias E.A., Kortemme T. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 2009, 6:551-552.
    • (2009) Nat Methods , vol.6 , pp. 551-552
    • Mandell, D.J.1    Coutsias, E.A.2    Kortemme, T.3
  • 33
    • 65249171530 scopus 로고    scopus 로고
    • Design of protein-interaction specificity gives selective bZIP-binding peptides
    • Grigoryan G., Reinke A.W., Keating A.E. Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature 2009, 458:859-864.
    • (2009) Nature , vol.458 , pp. 859-864
    • Grigoryan, G.1    Reinke, A.W.2    Keating, A.E.3
  • 36
    • 0035838974 scopus 로고    scopus 로고
    • Extending the accuracy limits of prediction for side-chain conformations
    • Xiang Z., Honig B. Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 2001, 311:421-430.
    • (2001) J Mol Biol , vol.311 , pp. 421-430
    • Xiang, Z.1    Honig, B.2
  • 37
    • 0036149564 scopus 로고    scopus 로고
    • Side-chain modeling with an optimized scoring function
    • Liang S., Grishin N.V. Side-chain modeling with an optimized scoring function. Protein Sci 2002, 11:322-331.
    • (2002) Protein Sci , vol.11 , pp. 322-331
    • Liang, S.1    Grishin, N.V.2
  • 38
    • 50049116635 scopus 로고    scopus 로고
    • OPUS-Rota: a fast and accurate method for side-chain modeling
    • Lu M., Dousis A.D., Ma J. OPUS-Rota: a fast and accurate method for side-chain modeling. Protein Sci 2008, 17:1576-1585.
    • (2008) Protein Sci , vol.17 , pp. 1576-1585
    • Lu, M.1    Dousis, A.D.2    Ma, J.3
  • 39
    • 1342310514 scopus 로고    scopus 로고
    • Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library
    • Peterson R.W., Dutton P.L., Wand A.J. Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library. Protein Sci 2004, 13:735-751.
    • (2004) Protein Sci , vol.13 , pp. 735-751
    • Peterson, R.W.1    Dutton, P.L.2    Wand, A.J.3
  • 40
    • 45649083705 scopus 로고    scopus 로고
    • A simple model of backbone flexibility improves modeling of side-chain conformational variability
    • Friedland G.D., Linares A.J., Smith C.A., Kortemme T. A simple model of backbone flexibility improves modeling of side-chain conformational variability. J Mol Biol 2008, 380:757-774.
    • (2008) J Mol Biol , vol.380 , pp. 757-774
    • Friedland, G.D.1    Linares, A.J.2    Smith, C.A.3    Kortemme, T.4
  • 41
    • 67049155677 scopus 로고    scopus 로고
    • A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family
    • Friedland G.D., Lakomek N.A., Griesinger C., Meiler J., Kortemme T. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol 2009, 5:e1000393.
    • (2009) PLoS Comput Biol , vol.5
    • Friedland, G.D.1    Lakomek, N.A.2    Griesinger, C.3    Meiler, J.4    Kortemme, T.5
  • 42
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme T., Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci USA 2002, 99:14116-14121.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 43
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
    • Guerois R., Nielsen J.E., Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002, 320:369-387.
    • (2002) J Mol Biol , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 44
    • 36749018607 scopus 로고    scopus 로고
    • Modeling backbone flexibility improves protein stability estimation
    • Yin S., Ding F., Dokholyan N.V. Modeling backbone flexibility improves protein stability estimation. Structure 2007, 15:1567-1576.
    • (2007) Structure , vol.15 , pp. 1567-1576
    • Yin, S.1    Ding, F.2    Dokholyan, N.V.3
  • 46
    • 57049180165 scopus 로고    scopus 로고
    • Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design
    • Humphris E.L., Kortemme T. Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. Structure 2008, 16:1777-1788.
    • (2008) Structure , vol.16 , pp. 1777-1788
    • Humphris, E.L.1    Kortemme, T.2
  • 47
    • 29444447288 scopus 로고    scopus 로고
    • Structure-based prediction of bZIP partnering specificity
    • Grigoryan G., Keating A.E. Structure-based prediction of bZIP partnering specificity. J Mol Biol 2006, 355:1125-1142.
    • (2006) J Mol Biol , vol.355 , pp. 1125-1142
    • Grigoryan, G.1    Keating, A.E.2
  • 48
    • 27244460904 scopus 로고    scopus 로고
    • Protein-DNA binding specificity predictions with structural models
    • Morozov A.V., Havranek J.J., Baker D., Siggia E.D. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res 2005, 33:5781-5798.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5781-5798
    • Morozov, A.V.1    Havranek, J.J.2    Baker, D.3    Siggia, E.D.4
  • 49
    • 7044239239 scopus 로고    scopus 로고
    • A simple physical model for the prediction and design of protein-DNA interactions
    • Havranek J.J., Duarte C.M., Baker D. A simple physical model for the prediction and design of protein-DNA interactions. J Mol Biol 2004, 344:59-70.
    • (2004) J Mol Biol , vol.344 , pp. 59-70
    • Havranek, J.J.1    Duarte, C.M.2    Baker, D.3
  • 50
    • 67249103597 scopus 로고    scopus 로고
    • Assessment of the optimization of affinity and specificity at protein-DNA interfaces
    • Ashworth J., Baker D. Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Nucleic Acids Res 2009, 37:e73.
    • (2009) Nucleic Acids Res , vol.37
    • Ashworth, J.1    Baker, D.2
  • 51
    • 73249134379 scopus 로고    scopus 로고
    • Experimental determination of the evolvability of a transcription factor
    • Maerkl S.J., Quake S.R. Experimental determination of the evolvability of a transcription factor. Proc Natl Acad Sci USA 2009, 106:18650-18655.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 18650-18655
    • Maerkl, S.J.1    Quake, S.R.2
  • 53
    • 0023140044 scopus 로고
    • Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin
    • Elber R., Karplus M. Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science 1987, 235:318-321.
    • (1987) Science , vol.235 , pp. 318-321
    • Elber, R.1    Karplus, M.2
  • 55
    • 0037217406 scopus 로고    scopus 로고
    • Automated design of specificity in molecular recognition
    • Havranek J.J., Harbury P.B. Automated design of specificity in molecular recognition. Nat Struct Biol 2003, 10:45-52.
    • (2003) Nat Struct Biol , vol.10 , pp. 45-52
    • Havranek, J.J.1    Harbury, P.B.2
  • 56
    • 31944435091 scopus 로고    scopus 로고
    • Computational design of a single amino acid sequence that can switch between two distinct protein folds
    • Ambroggio X.I., Kuhlman B. Computational design of a single amino acid sequence that can switch between two distinct protein folds. J Am Chem Soc 2006, 128:1154-1161.
    • (2006) J Am Chem Soc , vol.128 , pp. 1154-1161
    • Ambroggio, X.I.1    Kuhlman, B.2
  • 57
    • 34548383489 scopus 로고    scopus 로고
    • Design of multi-specificity in protein interfaces
    • Humphris E.L., Kortemme T. Design of multi-specificity in protein interfaces. PLoS Comput Biol 2007, 3:e164.
    • (2007) PLoS Comput Biol , vol.3
    • Humphris, E.L.1    Kortemme, T.2
  • 60
    • 33746799726 scopus 로고    scopus 로고
    • Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning
    • Pal G., Kouadio J.L., Artis D.R., Kossiakoff A.A., Sidhu S.S. Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning. J Biol Chem 2006, 281:22378-22385.
    • (2006) J Biol Chem , vol.281 , pp. 22378-22385
    • Pal, G.1    Kouadio, J.L.2    Artis, D.R.3    Kossiakoff, A.A.4    Sidhu, S.S.5
  • 61
    • 70349901079 scopus 로고    scopus 로고
    • Stability effects of mutations and protein evolvability
    • Tokuriki N., Tawfik D.S. Stability effects of mutations and protein evolvability. Curr Opin Struct Biol 2009, 19:596-604.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 596-604
    • Tokuriki, N.1    Tawfik, D.S.2
  • 62
    • 33845690052 scopus 로고    scopus 로고
    • Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library
    • Mena M.A., Treynor T.P., Mayo S.L., Daugherty P.S. Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library. Nat Biotechnol 2006, 24:1569-1571.
    • (2006) Nat Biotechnol , vol.24 , pp. 1569-1571
    • Mena, M.A.1    Treynor, T.P.2    Mayo, S.L.3    Daugherty, P.S.4
  • 63
    • 33845624902 scopus 로고    scopus 로고
    • Structure-guided SCHEMA recombination of distantly related beta-lactamases
    • Meyer M.M., Hochrein L., Arnold F.H. Structure-guided SCHEMA recombination of distantly related beta-lactamases. Protein Eng Des Sel 2006, 19:563-570.
    • (2006) Protein Eng Des Sel , vol.19 , pp. 563-570
    • Meyer, M.M.1    Hochrein, L.2    Arnold, F.H.3
  • 66
    • 71449103005 scopus 로고    scopus 로고
    • Hidden alternative structures of proline isomerase essential for catalysis
    • Fraser J.S., Clarkson M.W., Degnan S.C., Erion R., Kern D., Alber T. Hidden alternative structures of proline isomerase essential for catalysis. Nature 2009, 462:669-673.
    • (2009) Nature , vol.462 , pp. 669-673
    • Fraser, J.S.1    Clarkson, M.W.2    Degnan, S.C.3    Erion, R.4    Kern, D.5    Alber, T.6
  • 67


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.