메뉴 건너뛰기




Volumn 8, Issue 8, 2012, Pages

The Role of Local Backrub Motions in Evolved and Designed Mutations

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL ATOMIC STRUCTURE; PEPTIDES;

EID: 84866060981     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002629     Document Type: Article
Times cited : (29)

References (44)
  • 2
    • 77954811495 scopus 로고    scopus 로고
    • Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
    • Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, et al. (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329: 309-313.
    • (2010) Science , vol.329 , pp. 309-313
    • Siegel, J.B.1    Zanghellini, A.2    Lovick, H.M.3    Kiss, G.4    Lambert, A.R.5
  • 4
    • 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, et al. (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332: 816-821.
    • (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
  • 5
    • 0029366730 scopus 로고
    • Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-alpha transforming growth factor
    • Fadel AR, Jin DQ, Montelione GT, Levy RM, (1995) Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-alpha transforming growth factor. J Biomol NMR 6: 221-226.
    • (1995) J Biomol NMR , vol.6 , pp. 221-226
    • Fadel, A.R.1    Jin, D.Q.2    Montelione, G.T.3    Levy, R.M.4
  • 6
    • 0032553587 scopus 로고    scopus 로고
    • High-resolution protein design with backbone freedom
    • Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS, (1998) High-resolution protein design with backbone freedom. Science 282: 1462-1467.
    • (1998) Science , vol.282 , pp. 1462-1467
    • Harbury, P.B.1    Plecs, J.J.2    Tidor, B.3    Alber, T.4    Kim, P.S.5
  • 7
    • 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 JR, Keating AE, (2007) Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL. J Mol Biol 371: 1099-1117.
    • (2007) J Mol Biol , vol.371 , pp. 1099-1117
    • Fu, X.1    Apgar, J.R.2    Keating, A.E.3
  • 8
    • 0345306764 scopus 로고    scopus 로고
    • Design of a novel globular protein fold with atomic-level accuracy
    • Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302: 1364-1368.
    • (2003) Science , vol.302 , pp. 1364-1368
    • Kuhlman, B.1    Dantas, G.2    Ireton, G.C.3    Varani, G.4    Stoddard, B.L.5
  • 12
    • 57049180165 scopus 로고    scopus 로고
    • Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design
    • Humphris EL, Kortemme T, (2008) Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. Structure 16: 1777-1788.
    • (2008) Structure , vol.16 , pp. 1777-1788
    • Humphris, E.L.1    Kortemme, T.2
  • 13
    • 45649083705 scopus 로고    scopus 로고
    • A simple model of backbone flexibility improves modeling of side-chain conformational variability
    • Friedland GD, Linares AJ, Smith CA, Kortemme T, (2008) A simple model of backbone flexibility improves modeling of side-chain conformational variability. J Mol Biol 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
  • 14
    • 45649084560 scopus 로고    scopus 로고
    • Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction
    • Smith CA, Kortemme T, (2008) Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol 380: 742-756.
    • (2008) J Mol Biol , vol.380 , pp. 742-756
    • Smith, C.A.1    Kortemme, T.2
  • 15
    • 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 GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T, (2009) A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol 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
  • 16
    • 79960609097 scopus 로고    scopus 로고
    • Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design
    • Smith CA, Kortemme T, (2011) Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design. PLoS One 6: e20451.
    • (2011) PLoS One , vol.6
    • Smith, C.A.1    Kortemme, T.2
  • 17
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the ends of alpha helices
    • Richardson JS, Richardson DC, (1988) Amino acid preferences for specific locations at the ends of alpha helices. Science 240: 1648-1652.
    • (1988) Science , vol.240 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 18
    • 0024290488 scopus 로고
    • Helix signals in proteins
    • Presta LG, Rose GD, (1988) Helix signals in proteins. Science 240: 1632-1641.
    • (1988) Science , vol.240 , pp. 1632-1641
    • Presta, L.G.1    Rose, G.D.2
  • 19
    • 0024972479 scopus 로고
    • Capping and alpha-helix stability
    • Serrano L, Fersht AR, (1989) Capping and alpha-helix stability. Nature 342: 296-299.
    • (1989) Nature , vol.342 , pp. 296-299
    • Serrano, L.1    Fersht, A.R.2
  • 20
    • 1842591839 scopus 로고    scopus 로고
    • Kinetic role of helix caps in protein folding is context-dependent
    • Kapp GT, Richardson JS, Oas TG, (2004) Kinetic role of helix caps in protein folding is context-dependent. Biochemistry 43: 3814-3823.
    • (2004) Biochemistry , vol.43 , pp. 3814-3823
    • Kapp, G.T.1    Richardson, J.S.2    Oas, T.G.3
  • 21
    • 0033229975 scopus 로고    scopus 로고
    • Experimental assessment of differences between related protein crystal structures
    • Kleywegt GJ, (1999) Experimental assessment of differences between related protein crystal structures. Acta Crystallogr D Biol Crystallogr 55: 1878-1884.
    • (1999) Acta Crystallogr D Biol Crystallogr , vol.55 , pp. 1878-1884
    • Kleywegt, G.J.1
  • 24
    • 0029011701 scopus 로고
    • A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
    • Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, et al. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117: 5179-5197.
    • (1995) J Am Chem Soc , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Gould, I.R.4    Merz, K.M.5
  • 25
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T, Karplus M, (1999) Effective energy function for proteins in solution. Proteins 35: 133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 27
    • 0030010605 scopus 로고    scopus 로고
    • Experimentally observed conformation-dependent geometry and hidden strain in proteins
    • Karplus PA, (1996) Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci 5: 1406-1420.
    • (1996) Protein Sci , vol.5 , pp. 1406-1420
    • Karplus, P.A.1
  • 29
    • 0026619394 scopus 로고
    • Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992
    • Richardson JS, Richardson DC, Tweedy NB, Gernert KM, Quinn TP, et al. (1992) Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992. Biophys J 63: 1185-1209.
    • (1992) Biophys J , vol.63 , pp. 1185-1209
    • Richardson, J.S.1    Richardson, D.C.2    Tweedy, N.B.3    Gernert, K.M.4    Quinn, T.P.5
  • 30
    • 0032424128 scopus 로고    scopus 로고
    • Aromatic rescue of glycine in beta sheets
    • Merkel JS, Regan L, (1998) Aromatic rescue of glycine in beta sheets. Fold Des 3: 449-455.
    • (1998) Fold Des , vol.3 , pp. 449-455
    • Merkel, J.S.1    Regan, L.2
  • 31
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder H, Sligar SG, Wolynes PG, (1991) The energy landscapes and motions of proteins. Science 254: 1598-1603.
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 32
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • Tokuriki N, Tawfik DS, (2009) Protein dynamism and evolvability. Science 324: 203-207.
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 33
    • 34548040966 scopus 로고    scopus 로고
    • Crystal structure of an ancient protein: evolution by conformational epistasis
    • Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW, (2007) Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317: 1544-1548.
    • (2007) Science , vol.317 , pp. 1544-1548
    • Ortlund, E.A.1    Bridgham, J.T.2    Redinbo, M.R.3    Thornton, J.W.4
  • 35
    • 0037412183 scopus 로고    scopus 로고
    • Protein design is NP-hard
    • Pierce NA, Winfree E, (2002) Protein design is NP-hard. Protein Eng 15: 779-782.
    • (2002) Protein Eng , vol.15 , pp. 779-782
    • Pierce, N.A.1    Winfree, E.2
  • 38
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word JM, Lovell SC, Richardson JS, Richardson DC, (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285: 1735-1747.
    • (1999) J Mol Biol , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 39
    • 70350509577 scopus 로고    scopus 로고
    • KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program
    • Chen VB, Davis IW, Richardson DC, (2009) KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program. Protein Sci 18: 2403-2409.
    • (2009) Protein Sci , vol.18 , pp. 2403-2409
    • Chen, V.B.1    Davis, I.W.2    Richardson, D.C.3
  • 40
    • 0026696173 scopus 로고
    • Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59
    • Bell JA, Becktel WJ, Sauer U, Baase WA, Matthews BW, (1992) Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59. Biochemistry 31: 3590-3596.
    • (1992) Biochemistry , vol.31 , pp. 3590-3596
    • Bell, J.A.1    Becktel, W.J.2    Sauer, U.3    Baase, W.A.4    Matthews, B.W.5
  • 41
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 42
    • 0033582329 scopus 로고    scopus 로고
    • Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering
    • Lovell SC, Word JM, Richardson JS, Richardson DC, (1999) Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proc Natl Acad Sci U S A 96: 400-405.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 400-405
    • Lovell, S.C.1    Word, J.M.2    Richardson, J.S.3    Richardson, D.C.4
  • 44
    • 0033613812 scopus 로고    scopus 로고
    • Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms
    • Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, et al. (1999) Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 285: 1711-1733.
    • (1999) J Mol Biol , vol.285 , pp. 1711-1733
    • Word, J.M.1    Lovell, S.C.2    LaBean, T.H.3    Taylor, H.C.4    Zalis, M.E.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.