메뉴 건너뛰기




Volumn 425, Issue 18, 2013, Pages 3563-3575

Computational design of a protein-based enzyme inhibitor

Author keywords

Hot spot; Protein engineering and design; Protein protein interactions; Rosetta molecular modeling program

Indexed keywords

ENZYME INHIBITOR; LYSOZYME;

EID: 84883277095     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.06.035     Document Type: Article
Times cited : (73)

References (40)
  • 4
    • 36448933773 scopus 로고    scopus 로고
    • A de novo designed protein- protein interface
    • Huang PS, Love JJ, Mayo SL. A de novo designed protein- protein interface. Protein Sci 2007;16:2770-4.
    • (2007) Protein Sci , vol.16 , pp. 2770-2774
    • Huang, P.S.1    Love, J.J.2    Mayo, S.L.3
  • 5
    • 79954633234 scopus 로고    scopus 로고
    • A de novo protein binding pair by computational design and directed evolution
    • Karanicolas J, Corn JE, Chen I, Joachimiak LA, Dym O, Peck SH, et al. A de novo protein binding pair by computational design and directed evolution. Mol Cell 2011;42:250-60.
    • (2011) Mol Cell , vol.42 , pp. 250-260
    • Karanicolas, J.1    Corn, J.E.2    Chen, I.3    Joachimiak, L.A.4    Dym, O.5    Peck, S.H.6
  • 7
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol 1998;280:1-9.
    • (1998) J Mol Biol , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 8
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson T, Wells JA. A hot spot of binding energy in a hormone-receptor interface. Science 1995;267:383-6.
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 9
    • 34548779127 scopus 로고    scopus 로고
    • Hot spots - A review of the protein-protein interface determinant amino-acid residues
    • Moreira IS, Fernandes PA, Ramos MJ. Hot spots-a review of the protein-protein interface determinant amino-acid residues. Proteins 2007;68:803-12.
    • (2007) Proteins , vol.68 , pp. 803-812
    • Moreira, I.S.1    Fernandes, P.A.2    Ramos, M.J.3
  • 10
    • 34248335852 scopus 로고    scopus 로고
    • Nonnatural protein-protein interaction-pair design by key residues grafting
    • Liu S, Zhu X, Liang H, Cao A, Chang Z, Lai L. Nonnatural protein-protein interaction-pair design by key residues grafting. Proc Natl Acad Sci USA 2007;104:5330-5.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 5330-5335
    • Liu, S.1    Zhu, X.2    Liang, H.3    Cao, A.4    Chang, Z.5    Lai, L.6
  • 11
    • 79956017135 scopus 로고    scopus 로고
    • Computational design of proteins targeting the conserved stem region of influenza hemagglutinin
    • Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, Strauch EM, et al. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 2011;332:816-21.
    • (2011) Science , vol.332 , pp. 816-821
    • Fleishman, S.J.1    Whitehead, T.A.2    Ekiert, D.C.3    Dreyfus, C.4    Corn, J.E.5    Strauch, E.M.6
  • 12
    • 80054899738 scopus 로고    scopus 로고
    • Community-wide assessment of proteininterface modeling suggests improvements to design methodology
    • Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, et al. Community-wide assessment of proteininterface modeling suggests improvements to design methodology. J Mol Biol 2011;414:289-302.
    • (2011) J Mol Biol , vol.414 , pp. 289-302
    • Fleishman, S.J.1    Whitehead, T.A.2    Strauch, E.M.3    Corn, J.E.4    Qin, S.5    Zhou, H.X.6
  • 13
    • 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. A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds. Protein Sci 2013;22:74-82.
    • (2013) Protein Sci , vol.22 , pp. 74-82
    • Stranges, P.B.1    Kuhlman, B.2
  • 14
    • 0013852463 scopus 로고
    • Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution
    • Blake CC, Koenig DF, Mair GA, North AC, Phillips DC, Sarma VR. Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution. Nature 1965;206:757-61.
    • (1965) Nature , vol.206 , pp. 757-761
    • Blake, C.C.1    Koenig, D.F.2    Mair, G.A.3    North, A.C.4    Phillips, D.C.5    Sarma, V.R.6
  • 15
    • 4544250973 scopus 로고    scopus 로고
    • Crystal structure of a shark single-domain antibody v region in complex with lysozyme
    • Stanfield RL, Dooley H, Flajnik MF, Wilson IA. Crystal structure of a shark single-domain antibody V region in complex with lysozyme. Science 2004;305:1770-3.
    • (2004) Science , vol.305 , pp. 1770-1773
    • Stanfield, R.L.1    Dooley, H.2    Flajnik, M.F.3    Wilson, I.A.4
  • 16
    • 0030040277 scopus 로고    scopus 로고
    • Interactions of protein antigens with antibodies
    • Davies DR, Cohen GH. Interactions of protein antigens with antibodies. Proc Natl Acad Sci USA 1996;93:7-12.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 7-12
    • Davies, D.R.1    Cohen, G.H.2
  • 17
    • 34547549758 scopus 로고    scopus 로고
    • Structure and evolution of the Ivy protein family, unexpected lysozyme inhibitors in Gram-negative bacteria
    • Abergel C, Monchois V, Byrne D, Chenivesse S, Lembo F, Lazzaroni JC, et al. Structure and evolution of the Ivy protein family, unexpected lysozyme inhibitors in Gram-negative bacteria. Proc Natl Acad Sci USA 2007;104:6394-9.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 6394-6399
    • Abergel, C.1    Monchois, V.2    Byrne, D.3    Chenivesse, S.4    Lembo, F.5    Lazzaroni, J.C.6
  • 18
    • 78650905964 scopus 로고    scopus 로고
    • ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
    • Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 2011;487:545-74.
    • (2011) Methods Enzymol , vol.487 , pp. 545-574
    • Leaver-Fay, A.1    Tyka, M.2    Lewis, S.M.3    Lange, O.F.4    Thompson, J.5    Jacak, R.6
  • 19
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, et al. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-99.
    • (2003) J Mol Biol , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6
  • 22
    • 48749101428 scopus 로고    scopus 로고
    • Picomolar affinity fibronectin domains engineered utilizing loop length diversity, recursive mutagenesis, and loop shuffling
    • Hackel BJ, Kapila A, Wittrup KD. Picomolar affinity fibronectin domains engineered utilizing loop length diversity, recursive mutagenesis, and loop shuffling. J Mol Biol 2008;381:1238-52.
    • (2008) J Mol Biol , vol.381 , pp. 1238-1252
    • Hackel, B.J.1    Kapila, A.2    Wittrup, K.D.3
  • 25
    • 77951443560 scopus 로고    scopus 로고
    • ORF157 from the archaeal virus Acidianus filamentous virus 1 defines a new class of nuclease
    • Goulet A, Pina M, Redder P, Prangishvili D, Vera L, Lichiere J, et al. ORF157 from the archaeal virus Acidianus filamentous virus 1 defines a new class of nuclease. J Virol 2010;84:5025-31.
    • (2010) J Virol , vol.84 , pp. 5025-5031
    • Goulet, A.1    Pina, M.2    Redder, P.3    Prangishvili, D.4    Vera, L.5    Lichiere, J.6
  • 26
    • 0030994634 scopus 로고    scopus 로고
    • Yeast surface display for screening combinatorial polypeptide libraries
    • Boder ET, Wittrup KD. Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 1997;15: 553-7.
    • (1997) Nat Biotechnol , vol.15 , pp. 553-557
    • Boder, E.T.1    Wittrup, K.D.2
  • 27
    • 33947484782 scopus 로고
    • Determination of molecular weights of proteins by gel filtration on Sephadex
    • Whitaker Jr. Determination of molecular weights of proteins by gel filtration on Sephadex. Anal Chem 1963;35:1950-3.
    • (1963) Anal Chem , vol.35 , pp. 1950-1953
    • Whitaker, J.R.1
  • 28
    • 79953169868 scopus 로고    scopus 로고
    • Restricted sidechain plasticity in the structures of native proteins and complexes
    • Fleishman SJ, Khare SD, Koga N, Baker D. Restricted sidechain plasticity in the structures of native proteins and complexes. Protein Sci 2011;20:753-7.
    • (2011) Protein Sci , vol.20 , pp. 753-757
    • Fleishman, S.J.1    Khare, S.D.2    Koga, N.3    Baker, D.4
  • 31
    • 84862025262 scopus 로고    scopus 로고
    • Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing
    • Whitehead TA, Chevalier A, Song Y, Dreyfus C, Fleishman SJ, De Mattos C, et al. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat Biotechnol 2012;30:543-8.
    • (2012) Nat Biotechnol , vol.30 , pp. 543-548
    • Whitehead, T.A.1    Chevalier, A.2    Song, Y.3    Dreyfus, C.4    Fleishman, S.J.5    De Mattos, C.6
  • 33
    • 84861676223 scopus 로고    scopus 로고
    • Computational design of self-assembling protein nanomaterials with atomic level accuracy
    • King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, Andre I, et al. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 2012;336:1171-4.
    • (2012) Science , vol.336 , pp. 1171-1174
    • King, N.P.1    Sheffler, W.2    Sawaya, M.R.3    Vollmar, B.S.4    Sumida, J.P.5    Andre, I.6
  • 34
  • 35
    • 68349104348 scopus 로고    scopus 로고
    • Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
    • Mandell DJ, Coutsias EA, Kortemme T. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 2009;6:551-2.
    • (2009) Nat Methods , vol.6 , pp. 551-552
    • Mandell, D.J.1    Coutsias, E.A.2    Kortemme, T.3
  • 36
  • 37
    • 83355174920 scopus 로고    scopus 로고
    • Enrich: Software for analysis of protein function by enrichment and depletion of variants
    • Fowler DM, Araya CL, Gerard W, Fields S. Enrich: software for analysis of protein function by enrichment and depletion of variants. Bioinformatics 2011;27:3430-1.
    • (2011) Bioinformatics , vol.27 , pp. 3430-3431
    • Fowler, D.M.1    Araya, C.L.2    Gerard, W.3    Fields, S.4
  • 38
    • 79952411326 scopus 로고    scopus 로고
    • Preparation of protein samples for NMR structure, function, and small-molecule screening studies
    • Acton TB, Xiao R, Anderson S, Aramini J, Buchwald WA, Ciccosanti C, et al. Preparation of protein samples for NMR structure, function, and small-molecule screening studies. Methods Enzymol 2011;493:21-60.
    • (2011) Methods Enzymol , vol.493 , pp. 21-60
    • Acton, T.B.1    Xiao, R.2    Anderson, S.3    Aramini, J.4    Buchwald, W.A.5    Ciccosanti, C.6
  • 39
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: An automated program for molecular replacement
    • Vagin A, Teplyakov A. MOLREP: an automated program for molecular replacement. J Appl Crystallogr 1997;30: 1022-5.
    • (1997) J Appl Crystallogr , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.