메뉴 건너뛰기




Volumn 108, Issue 39, 2011, Pages 16247-16252

Accessing protein conformational ensembles using room-temperature X-ray crystallography

Author keywords

Energy landscape; Protein conformational dynamics; qFit; Ringer

Indexed keywords

H RAS PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

EID: 80053626537     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1111325108     Document Type: Article
Times cited : (483)

References (44)
  • 2
    • 36749071554 scopus 로고    scopus 로고
    • Observation of Decreased Radiation Damage at Higher Dose Rates in Room Temperature Protein Crystallography
    • DOI 10.1016/j.str.2007.10.013, PII S0969212607004145
    • Southworth-Davies RJ, Medina MA, Carmichael I, Garman EF (2007) Observation of decreased radiation damage at higher dose rates in room temperature protein crystallography. Structure 15:1531-1541. (Pubitemid 350213411)
    • (2007) Structure , vol.15 , Issue.12 , pp. 1531-1541
    • Southworth-Davies, R.J.1    Medina, M.A.2    Carmichael, I.3    Garman, E.F.4
  • 3
    • 0009528256 scopus 로고
    • Studies of insulin crystals at low temperatures: Effects on mosaic character and radiation sensitivity
    • Low BW, Chen CC, Berger JE, Singman L, Pletcher JF (1966) Studies of insulin crystals at low temperatures: Effects on mosaic character and radiation sensitivity. Proc Natl Acad Sci USA 56:1746-1750.
    • (1966) Proc Natl Acad Sci USA , vol.56 , pp. 1746-1750
    • Low, B.W.1    Chen, C.C.2    Berger, J.E.3    Singman, L.4    Pletcher, J.F.5
  • 4
    • 0001266927 scopus 로고
    • Cryocrystallography of ribosomal particles
    • Hope H, et al. (1989) Cryocrystallography of ribosomal particles. Acta Crystallogr B 45:190-199.
    • (1989) Acta Crystallogr B , vol.45 , pp. 190-199
    • Hope, H.1
  • 5
    • 0141987861 scopus 로고    scopus 로고
    • 'Cool' crystals: Macromolecular cryocrystallography and radiation damage
    • Garman E (2003) 'Cool' crystals: Macromolecular cryocrystallography and radiation damage. Curr Opin Struct Biol 13:545-551.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 545-551
    • Garman, E.1
  • 6
    • 0030877587 scopus 로고    scopus 로고
    • Conformational substates in enzyme mechanism: The 120 K structure of alpha-lytic protease at 1.5 A resolution
    • Rader SD, Agard DA (1997) Conformational substates in enzyme mechanism: The 120 K structure of alpha-lytic protease at 1.5 A resolution. Protein Sci 6:1375-1386.
    • (1997) Protein Sci , vol.6 , pp. 1375-1386
    • Rader, S.D.1    Agard, D.A.2
  • 7
    • 44649131326 scopus 로고    scopus 로고
    • Picometer-Scale Conformational Heterogeneity Separates Functional from Nonfunctional States of a Photoreceptor Protein
    • DOI 10.1016/j.str.2008.02.022, PII S0969212608001469
    • Coureux PD, Fan ZP, Stojanoff V, Genick UK (2008) Picometer-scale conformational heterogeneity separates functional from nonfunctional states of a photoreceptor protein. Structure 16:863-872. (Pubitemid 351778378)
    • (2008) Structure , vol.16 , Issue.6 , pp. 863-872
    • Coureux, P.-D.1    Fan, Z.P.2    Stojanoff, V.3    Genick, U.K.4
  • 8
    • 0023652260 scopus 로고
    • Thermal expansion of a protein
    • Frauenfelder H, et al. (1987) Thermal expansion of a protein. Biochemistry 26:254-261.
    • (1987) Biochemistry , vol.26 , pp. 254-261
    • Frauenfelder, H.1
  • 9
    • 0026606219 scopus 로고
    • Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K
    • Tilton RF, Jr, Dewan JC, Petsko GA (1992) Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K. Biochemistry 31:2469-2481.
    • (1992) Biochemistry , vol.31 , pp. 2469-2481
    • Tilton Jr., R.F.1    Dewan, J.C.2    Petsko, G.A.3
  • 10
    • 0035943379 scopus 로고    scopus 로고
    • Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions
    • DOI 10.1006/jmbi.2001.4891
    • Juers DH, Matthews BW (2001) Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions. J Mol Biol 311:851-862. (Pubitemid 32803740)
    • (2001) Journal of Molecular Biology , vol.311 , Issue.4 , pp. 851-862
    • Juers, D.H.1    Matthews, B.W.2
  • 11
    • 77950847812 scopus 로고    scopus 로고
    • Temperature-dependent macromolecular X-ray crystallography
    • Weik M, Colletier JP (2010) Temperature-dependent macromolecular X-ray crystallography. Acta Crystallogr D Biol Crystallogr 66:437-446.
    • (2010) Acta Crystallogr D Biol Crystallogr , vol.66 , pp. 437-446
    • Weik, M.1    Colletier, J.P.2
  • 12
    • 79958207530 scopus 로고    scopus 로고
    • Mining electron density for functionally relevant protein polysterism in crystal structures
    • Fraser JS, Jackson CJ (2010) Mining electron density for functionally relevant protein polysterism in crystal structures. Cell Mol Life Sci 68:1829-1841.
    • (2010) Cell Mol Life Sci , vol.68 , pp. 1829-1841
    • Fraser, J.S.1    Jackson, C.J.2
  • 13
    • 0018793861 scopus 로고
    • Temperature-dependent X-ray diffraction as a probe of protein structural dynamics
    • Frauenfelder H, Petsko GA, Tsernoglou D (1979) Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature 280:558-563.
    • (1979) Nature , vol.280 , pp. 558-563
    • Frauenfelder, H.1    Petsko, G.A.2    Tsernoglou, D.3
  • 14
    • 0026720247 scopus 로고
    • Crystalline ribonuclease A loses function below the dynamical transition at 220 K
    • Rasmussen BF, Stock AM, Ringe D, Petsko GA (1992) Crystalline ribonuclease A loses function below the dynamical transition at 220 K. Nature 357:423-424.
    • (1992) Nature , vol.357 , pp. 423-424
    • Rasmussen, B.F.1    Stock, A.M.2    Ringe, D.3    Petsko, G.A.4
  • 15
    • 1842687872 scopus 로고    scopus 로고
    • Biomolecular cryocrystallography: Structural changes during flashcooling
    • Halle B (2004) Biomolecular cryocrystallography: structural changes during flashcooling. Proc Natl Acad Sci USA 101:4793-4798.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 4793-4798
    • Halle, B.1
  • 16
    • 71449103005 scopus 로고    scopus 로고
    • Hidden alternative structures of proline isomerase essential for catalysis
    • Fraser JS, et al. (2009) Hidden alternative structures of proline isomerase essential for catalysis. Nature 462:669-673.
    • (2009) Nature , vol.462 , pp. 669-673
    • Fraser, J.S.1
  • 18
    • 77953977241 scopus 로고    scopus 로고
    • Automated electron-density sampling reveals widespread conformational polymorphism in proteins
    • Lang PT, et al. (2010) Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci 19:1420-1431.
    • (2010) Protein Sci , vol.19 , pp. 1420-1431
    • Lang, P.T.1
  • 19
    • 76449098262 scopus 로고    scopus 로고
    • PHENIX: A comprehensive Python-based system for macromolecular structure solution
    • Adams PD, et al. (2010) PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213-221.
    • (2010) Acta Crystallogr D Biol Crystallogr , vol.66 , pp. 213-221
    • Adams, P.D.1
  • 20
    • 20944434880 scopus 로고    scopus 로고
    • Cryo-cooling in macromolecular crystallography: Advantages, disadvantages and optimization
    • DOI 10.1017/S0033583504004007
    • Juers DH, Matthews BW (2004) Cryo-cooling in macromolecular crystallography: Advantages, disadvantages and optimization. Q Rev Biophys 37:105-119. (Pubitemid 40867963)
    • (2004) Quarterly Reviews of Biophysics , vol.37 , Issue.2 , pp. 105-119
    • Juers, D.H.1    Matthews, B.W.2
  • 21
    • 77957296071 scopus 로고    scopus 로고
    • RosettaHoles2: A volumetric packing measure for protein structure refinement and validation
    • Sheffler W, Baker D (2010) RosettaHoles2: A volumetric packing measure for protein structure refinement and validation. Protein Sci 19:1991-1995.
    • (2010) Protein Sci , vol.19 , pp. 1991-1995
    • Sheffler, W.1    Baker, D.2
  • 22
    • 77952040164 scopus 로고    scopus 로고
    • Unambiguous determination of H-atom positions: Comparing results from neutron and high-resolution X-ray crystallography
    • Gardberg AS, et al. (2010) Unambiguous determination of H-atom positions: Comparing results from neutron and high-resolution X-ray crystallography. Acta Crystallogr D Biol Crystallogr 66:558-567.
    • (2010) Acta Crystallogr D Biol Crystallogr , vol.66 , pp. 558-567
    • Gardberg, A.S.1
  • 24
    • 70349807596 scopus 로고    scopus 로고
    • Active site remodeling switches HIV specificity of antiretroviral TRIMCyp
    • Price AJ, et al. (2009) Active site remodeling switches HIV specificity of antiretroviral TRIMCyp. Nat Struct Mol Biol 16:1036-1042.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 1036-1042
    • Price, A.J.1
  • 25
    • 0033571343 scopus 로고    scopus 로고
    • The pre-hydrolysis state of p21(ras) in complex with GTP: New insights into the role of water molecules in the GTP hydrolysis reaction of ras-like proteins
    • DOI 10.1016/S0969-2126(00)80021-0
    • Scheidig AJ, Burmester C, Goody RS (1999) The pre-hydrolysis state of p21(ras) in complex with GTP: New insights into the role of water molecules in the GTP hydrolysis reaction of ras-like proteins. Structure 7:1311-1324. (Pubitemid 29529872)
    • (1999) Structure , vol.7 , Issue.11 , pp. 1311-1324
    • Scheidig, A.J.1    Burmester, C.2    Goody, R.S.3
  • 26
    • 52949089338 scopus 로고    scopus 로고
    • Global conformational dynamics in ras
    • O'Connor C, Kovrigin EL (2008) Global conformational dynamics in ras. Biochemistry 47:10244-10246.
    • (2008) Biochemistry , vol.47 , pp. 10244-10246
    • O'Connor, C.1    Kovrigin, E.L.2
  • 27
    • 63549096871 scopus 로고    scopus 로고
    • Ras conformational switching: Simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics
    • Grant BJ, Gorfe AA, McCammon JA (2009) Ras conformational switching: Simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comput Biol 5:e1000325.
    • (2009) PLoS Comput Biol , vol.5
    • Grant, B.J.1    Gorfe, A.A.2    McCammon, J.A.3
  • 28
    • 0031687777 scopus 로고    scopus 로고
    • Signal transduction via Ras
    • Wittinghofer A (1998) Signal transduction via Ras. Biol Chem 379:933-937.
    • (1998) Biol Chem , vol.379 , pp. 933-937
    • Wittinghofer, A.1
  • 29
    • 0043123344 scopus 로고    scopus 로고
    • GTPase catalysis by Ras and other G-proteins: Insights from substrate directed superimposition
    • DOI 10.1016/S0022-2836(03)00847-7
    • Kosloff M, Selinger Z (2003) GTPase catalysis by Ras and other G-proteins: Insights from Substrate Directed SuperImposition. J Mol Biol 331:1157-1170. (Pubitemid 36969972)
    • (2003) Journal of Molecular Biology , vol.331 , Issue.5 , pp. 1157-1170
    • Kosloff, M.1    Selinger, Z.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. (Pubitemid 21917496)
    • (1991) Science , vol.254 , Issue.5038 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 34
    • 77950397231 scopus 로고    scopus 로고
    • Allosteric modulation of Ras positions Q61 for a direct role in catalysis
    • Buhrman G, Holzapfel G, Fetics S, Mattos C (2010) Allosteric modulation of Ras positions Q61 for a direct role in catalysis. Proc Natl Acad Sci USA 107:4931-4936.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 4931-4936
    • Buhrman, G.1    Holzapfel, G.2    Fetics, S.3    Mattos, C.4
  • 35
    • 0038737044 scopus 로고    scopus 로고
    • Switch-of-function mutants based on morphology classification of ras superfamily small GTPases
    • DOI 10.1016/S0092-8674(03)00315-5
    • Heo WD, Meyer T (2003) Switch-of-function mutants based on morphology classification of Ras superfamily small GTPases. Cell 113:315-328. (Pubitemid 36556114)
    • (2003) Cell , vol.113 , Issue.3 , pp. 315-328
    • Heo, W.D.1    Meyer, T.2
  • 36
    • 79955366474 scopus 로고    scopus 로고
    • Critical roles of interactions among switch I-preceding residues and between switch II and its neighboring alpha-helix in conformational dynamics of the GTP-bound Ras family small GTPases
    • Matsumoto K, et al. (2011) Critical roles of interactions among switch I-preceding residues and between switch II and its neighboring alpha-helix in conformational dynamics of the GTP-bound Ras family small GTPases. J Biol Chem 286:15403-15412.
    • (2011) J Biol Chem , vol.286 , pp. 15403-15412
    • Matsumoto, K.1
  • 37
    • 78651330430 scopus 로고    scopus 로고
    • COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
    • Forbes SA, et al. (2011) COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 39:D945-950.
    • (2011) Nucleic Acids Res , vol.39
    • Forbes, S.A.1
  • 38
    • 77957937199 scopus 로고    scopus 로고
    • Atomic-level characterization of the structural dynamics of proteins
    • Shaw DE, et al. (2010) Atomic-level characterization of the structural dynamics of proteins. Science 330:341-346.
    • (2010) Science , vol.330 , pp. 341-346
    • Shaw, D.E.1
  • 39
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • DOI 10.1126/science.286.5438.295
    • Lockless SW, Ranganathan R (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286:295-299. (Pubitemid 29484693)
    • (1999) Science , vol.286 , Issue.5438 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 40
    • 33645834303 scopus 로고    scopus 로고
    • New tools provide new insights in NMR studies of protein dynamics
    • Mittermaier A, Kay LE (2006) New tools provide new insights in NMR studies of protein dynamics. Science 312:224-228.
    • (2006) Science , vol.312 , pp. 224-228
    • Mittermaier, A.1    Kay, L.E.2
  • 41
    • 0042011224 scopus 로고    scopus 로고
    • Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals
    • DOI 10.1110/ps.0350503
    • Kantardjieff KA, Rupp B (2003) Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci 12:1865-1871. (Pubitemid 37022809)
    • (2003) Protein Science , vol.12 , Issue.9 , pp. 1865-1871
    • Kantardjieff, K.A.1    Rupp, B.2
  • 42
    • 33745628037 scopus 로고    scopus 로고
    • The Geometry of the Ribosomal Polypeptide Exit Tunnel
    • DOI 10.1016/j.jmb.2006.05.023, PII S002228360600605X
    • Voss NR, Gerstein M, Steitz TA, Moore PB (2006) The geometry of the ribosomal polypeptide exit tunnel. J Mol Biol 360:893-906. (Pubitemid 43993916)
    • (2006) Journal of Molecular Biology , vol.360 , Issue.4 , pp. 893-906
    • Voss, N.R.1    Gerstein, M.2    Steitz, T.A.3    Moore, P.B.4
  • 43
    • 14644400399 scopus 로고    scopus 로고
    • An amino acid has two sides: A new 2D measure provides a different view of solvent exposure
    • Hamelryck T (2005) An amino acid has two sides: a new 2D measure provides a different view of solvent exposure. Proteins 59:38-48.
    • (2005) Proteins , vol.59 , pp. 38-48
    • Hamelryck, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.