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Volumn 7, Issue 3, 2012, Pages

Incorporation of noncanonical amino acids into rosetta and use in computational protein-peptide interface design

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA METHYL TRYPTOPHAN; AMINO ACID; ASPARAGINE; CALPAIN 1; CALPASTATIN; GLYCINE; HOMOSERINE; LEUCINE; NONCANONICAL AMINO ACID; PHENYLALANINE; TRYPTOPHAN; UNCLASSIFIED DRUG; CALCIUM BINDING PROTEIN; CALPAIN; PEPTIDE; PROTEIN;

EID: 84858266350     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032637     Document Type: Article
Times cited : (89)

References (52)
  • 1
    • 0030793767 scopus 로고    scopus 로고
    • De Novo Protein Design: Fully Automated Sequence Selection
    • Dahiyat BI, Mayo SL, (1997) De Novo Protein Design: Fully Automated Sequence Selection. Science 278: 82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 2
    • 33748207212 scopus 로고    scopus 로고
    • Configurational-bias sampling technique for predicting side-chain conformations in proteins
    • Jain T, (2006) Configurational-bias sampling technique for predicting side-chain conformations in proteins. Protein Science 15: 2029-2039.
    • (2006) Protein Science , vol.15 , pp. 2029-2039
    • Jain, T.1
  • 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
    • 0026686436 scopus 로고
    • Total chemical synthesis of a D-enzyme: the enantiomers of HIV-1 protease show reciprocal chiral substrate specificity [corrected]
    • Milton RC, Milton SC, Kent SB, (1992) Total chemical synthesis of a D-enzyme: the enantiomers of HIV-1 protease show reciprocal chiral substrate specificity [corrected]. Science 256: 1445-1448.
    • (1992) Science , vol.256 , pp. 1445-1448
    • Milton, R.C.1    Milton, S.C.2    Kent, S.B.3
  • 6
    • 1842502994 scopus 로고    scopus 로고
    • Enfuvirtide: a fusion inhibitor for the treatment of HIV infection
    • Fung HB, Guo Y, (2004) Enfuvirtide: a fusion inhibitor for the treatment of HIV infection. Clin Ther 26: 352-378.
    • (2004) Clin Ther , vol.26 , pp. 352-378
    • Fung, H.B.1    Guo, Y.2
  • 7
    • 0042208406 scopus 로고    scopus 로고
    • phi-Values beyond the ribosomally encoded amino acids: kinetic and thermodynamic consequences of incorporating trifluoromethyl amino acids in a globular protein
    • Horng JC, Raleigh DP, (2003) phi-Values beyond the ribosomally encoded amino acids: kinetic and thermodynamic consequences of incorporating trifluoromethyl amino acids in a globular protein. J Am Chem Soc 125: 9286-9287.
    • (2003) J Am Chem Soc , vol.125 , pp. 9286-9287
    • Horng, J.C.1    Raleigh, D.P.2
  • 8
    • 0025262173 scopus 로고
    • Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure
    • Hendrickson WA, Horton JR, LeMaster DM, (1990) Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J 9: 1665-1672.
    • (1990) EMBO J , vol.9 , pp. 1665-1672
    • Hendrickson, W.A.1    Horton, J.R.2    LeMaster, D.M.3
  • 9
    • 66249139193 scopus 로고    scopus 로고
    • Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature
    • Banerjee R, Chattopadhyay S, Basu G, (2009) Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature. Proteins 76: 184-200.
    • (2009) Proteins , vol.76 , pp. 184-200
    • Banerjee, R.1    Chattopadhyay, S.2    Basu, G.3
  • 10
    • 79961117960 scopus 로고    scopus 로고
    • Enhanced refoldability and thermoactivity of fluorinated phosphotriesterase
    • Baker PJ, Montclare JK, (2011) Enhanced refoldability and thermoactivity of fluorinated phosphotriesterase. Chembiochem 12: 1845-1848.
    • (2011) Chembiochem , vol.12 , pp. 1845-1848
    • Baker, P.J.1    Montclare, J.K.2
  • 11
    • 2942568222 scopus 로고    scopus 로고
    • Unimod: Protein modifications for mass spectrometry
    • Creasy DM, Cottrell JS, (2004) Unimod: Protein modifications for mass spectrometry. PROTEOMICS 4: 1534-1536.
    • (2004) PROTEOMICS , vol.4 , pp. 1534-1536
    • Creasy, D.M.1    Cottrell, J.S.2
  • 12
    • 2942564448 scopus 로고    scopus 로고
    • The RESID Database of Protein Modifications as a resource and annotation tool
    • Garavelli JS, (2004) The RESID Database of Protein Modifications as a resource and annotation tool. PROTEOMICS 4: 1527-1533.
    • (2004) PROTEOMICS , vol.4 , pp. 1527-1533
    • Garavelli, J.S.1
  • 13
    • 2942598149 scopus 로고    scopus 로고
    • PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation
    • Hornbeck PV, Chabra I, Kornhauser JM, Skrzypek E, Zhang B, (2004) PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. PROTEOMICS 4: 1551-1561.
    • (2004) PROTEOMICS , vol.4 , pp. 1551-1561
    • Hornbeck, P.V.1    Chabra, I.2    Kornhauser, J.M.3    Skrzypek, E.4    Zhang, B.5
  • 15
    • 0037166006 scopus 로고    scopus 로고
    • Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA
    • Srinivasan G, James CM, Krzycki JA, (2002) Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296: 1459-1462.
    • (2002) Science , vol.296 , pp. 1459-1462
    • Srinivasan, G.1    James, C.M.2    Krzycki, J.A.3
  • 17
    • 44349127313 scopus 로고    scopus 로고
    • Using quantum mechanics to improve estimates of amino acid side chain rotamer energies
    • Renfrew PD, Butterfoss GL, Kuhlman B, (2008) Using quantum mechanics to improve estimates of amino acid side chain rotamer energies. Proteins 71: 1637-1646.
    • (2008) Proteins , vol.71 , pp. 1637-1646
    • Renfrew, P.D.1    Butterfoss, G.L.2    Kuhlman, B.3
  • 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, et al. (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487: 545-574.
    • (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
  • 20
  • 21
    • 68349104348 scopus 로고    scopus 로고
    • Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
    • Mandell DJ, Coutsias EA, Kortemme T, (2009) Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Meth 6: 551-552.
    • (2009) Nat Meth , vol.6 , pp. 551-552
    • Mandell, D.J.1    Coutsias, E.A.2    Kortemme, T.3
  • 23
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray protein structure refinement
    • Engh RA, Huber R, (1991) Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallographica Section A 47: 392-400.
    • (1991) Acta Crystallographica Section A , vol.47 , pp. 392-400
    • Engh, R.A.1    Huber, R.2
  • 26
    • 33644897573 scopus 로고    scopus 로고
    • Calpain inhibition: a therapeutic strategy targeting multiple disease states
    • Carragher NO, (2006) Calpain inhibition: a therapeutic strategy targeting multiple disease states. Curr Pharm Des 12: 615-638.
    • (2006) Curr Pharm Des , vol.12 , pp. 615-638
    • Carragher, N.O.1
  • 29
    • 56749172400 scopus 로고    scopus 로고
    • Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin
    • Hanna RA, Campbell RL, Davies PL, (2008) Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin. Nature 456: 409-412.
    • (2008) Nature , vol.456 , pp. 409-412
    • Hanna, R.A.1    Campbell, R.L.2    Davies, P.L.3
  • 30
    • 56749143763 scopus 로고    scopus 로고
    • Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains
    • Moldoveanu T, Gehring K, Green DR, (2008) Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains. Nature 456: 404-408.
    • (2008) Nature , vol.456 , pp. 404-408
    • Moldoveanu, T.1    Gehring, K.2    Green, D.R.3
  • 31
    • 0037453230 scopus 로고    scopus 로고
    • A Structural Model for the Inhibition of Calpain by Calpastatin: Crystal Structures of the Native Domain VI of Calpain and its Complexes with Calpastatin Peptide and a Small Molecule Inhibitor
    • Todd B, Moore D, Deivanayagam CCS, Lin G-d, Chattopadhyay D, et al. (2003) A Structural Model for the Inhibition of Calpain by Calpastatin: Crystal Structures of the Native Domain VI of Calpain and its Complexes with Calpastatin Peptide and a Small Molecule Inhibitor. Journal of Molecular Biology 328: 131-146.
    • (2003) Journal of Molecular Biology , vol.328 , pp. 131-146
    • Todd, B.1    Moore, D.2    Deivanayagam, C.C.S.3    Lin, G.-d.4    Chattopadhyay, D.5
  • 32
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • Neria E, Fischer S, Karplus M, (1996) Simulation of activation free energies in molecular systems. The Journal of Chemical Physics 105: 1902-1921.
    • (1996) The Journal of Chemical Physics , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 34
    • 0037470581 scopus 로고    scopus 로고
    • An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes
    • Kortemme T, Morozov AV, Baker D, (2003) An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes. Journal of Molecular Biology 326: 1239-1259.
    • (2003) Journal of Molecular Biology , vol.326 , pp. 1239-1259
    • Kortemme, T.1    Morozov, A.V.2    Baker, D.3
  • 35
    • 24944493938 scopus 로고    scopus 로고
    • Toward High-Resolution de Novo Structure Prediction for Small Proteins
    • Bradley P, Misura KMS, Baker D, (2005) Toward High-Resolution de Novo Structure Prediction for Small Proteins. Science 309: 1868-1871.
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.S.2    Baker, D.3
  • 36
    • 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
  • 37
    • 0031727544 scopus 로고    scopus 로고
    • Protein sidechain conformer prediction: a test of the energy function
    • Petrella RJ, Lazaridis T, Karplus M, (1998) Protein sidechain conformer prediction: a test of the energy function. Folding and Design 3: 353-377.
    • (1998) Folding and Design , vol.3 , pp. 353-377
    • Petrella, R.J.1    Lazaridis, T.2    Karplus, M.3
  • 39
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang G, Dunbrack RL Jr, (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 43
    • 0035845509 scopus 로고    scopus 로고
    • Conversion of monomeric protein L to an obligate dimer by computational protein design
    • Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D, (2001) Conversion of monomeric protein L to an obligate dimer by computational protein design. Proc Natl Acad Sci U S A 98: 10687-10691.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 10687-10691
    • Kuhlman, B.1    O'Neill, J.W.2    Kim, D.E.3    Zhang, K.Y.4    Baker, D.5
  • 46
    • 0034789373 scopus 로고    scopus 로고
    • Labelled alpha-methyl-L-tryptophan as a tracer for the study of the brain serotonergic system
    • Diksic M, (2001) Labelled alpha-methyl-L-tryptophan as a tracer for the study of the brain serotonergic system. J Psychiatry Neurosci 26: 293-303.
    • (2001) J Psychiatry Neurosci , vol.26 , pp. 293-303
    • Diksic, M.1
  • 47
    • 69249158062 scopus 로고    scopus 로고
    • Computational design of affinity and specificity at protein-protein interfaces
    • Karanicolas J, Kuhlman B, (2009) Computational design of affinity and specificity at protein-protein interfaces. Curr Opin Struct Biol 19: 458-463.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 458-463
    • Karanicolas, J.1    Kuhlman, B.2
  • 50
    • 54049086941 scopus 로고    scopus 로고
    • Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms
    • Ho B, Agard D, (2008) Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms. BMC Structural Biology 8: 41-41.
    • (2008) BMC Structural Biology , vol.8 , pp. 41
    • Ho, B.1    Agard, D.2
  • 52
    • 0029894733 scopus 로고    scopus 로고
    • Alpha-mercaptoacrylic acid derivatives as novel selective calpain inhibitors
    • Wang KK, Posner A, Raser KJ, Buroker-Kilgore M, Nath R, et al. (1996) Alpha-mercaptoacrylic acid derivatives as novel selective calpain inhibitors. Adv Exp Med Biol 389: 95-101.
    • (1996) Adv Exp Med Biol , vol.389 , pp. 95-101
    • Wang, K.K.1    Posner, A.2    Raser, K.J.3    Buroker-Kilgore, M.4    Nath, R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.