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Volumn 83, Issue 6, 2002, Pages 3113-3125

Addition of missing loops and domains to protein models by x-ray solution scattering

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PROTEIN;

EID: 0036930752     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)75315-0     Document Type: Article
Times cited : (89)

References (57)
  • 1
    • 0031587295 scopus 로고    scopus 로고
    • Pentameric and decameric structures in solution of serum amyloid P component by X-ray and neutron scattering and molecular modelling analyses
    • Ashton, A. W., M. K. Boehm, J. R. Gallimore, M. B. Pepys, and S. J. Perkins. 1997. Pentameric and decameric structures in solution of serum amyloid P component by X-ray and neutron scattering and molecular modelling analyses. J. Mol. Biol. 272:408-422. Abdom.
    • (1997) J. Mol. Biol. , vol.272 , pp. 408-422
    • Ashton, A.W.1    Boehm, M.K.2    Gallimore, J.R.3    Pepys, M.B.4    Perkins, S.J.5
  • 2
    • 0029097099 scopus 로고
    • Global fold determination from a small number of distance restraints
    • Aszodi, A., M. J. Gradwell, and W. R. Taylor. 1995. Global fold determination from a small number of distance restraints. J. Mol. Biol. 251:308-326.
    • (1995) J. Mol. Biol. , vol.251 , pp. 308-326
    • Aszodi, A.1    Gradwell, M.J.2    Taylor, W.R.3
  • 4
    • 0024033744 scopus 로고
    • Data acquisition systems for linear and area X-ray detectors using delay line readout
    • Boulin, C. J., R. Kempf, A. Gabriel, and M. H. J. Koch. 1988. Data acquisition systems for linear and area X-ray detectors using delay line readout. Nuclear Instrum. Methods A. 269:312-320.
    • (1988) Nuclear Instrum. Methods A , vol.269 , pp. 312-320
    • Boulin, C.J.1    Kempf, R.2    Gabriel, A.3    Koch, M.H.J.4
  • 5
    • 0022787110 scopus 로고
    • Data appraisal, evaluation and display for synchrotron radiation experiments: Hardware and software
    • Boulin, C., R. Kempf, M. H. J. Koch, and S. M. McLaughlin. 1986. Data appraisal, evaluation and display for synchrotron radiation experiments: Hardware and software. Nuclear Instrum. Methods A. 249:399-407.
    • (1986) Nuclear Instrum. Methods A , vol.249 , pp. 399-407
    • Boulin, C.1    Kempf, R.2    Koch, M.H.J.3    McLaughlin, S.M.4
  • 6
    • 0033106244 scopus 로고    scopus 로고
    • Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
    • Cuff, J. A., and G. J. Barton. 1999. Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins. 34:508-519.
    • (1999) Proteins , vol.34 , pp. 508-519
    • Cuff, J.A.1    Barton, G.J.2
  • 7
    • 0034663597 scopus 로고    scopus 로고
    • Application of multiple sequence alignment profiles to improve protein secondary structure prediction
    • Cuff, J. A., and G. J. Barton. 2000. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins. 40:502-511.
    • (2000) Proteins , vol.40 , pp. 502-511
    • Cuff, J.A.1    Barton, G.J.2
  • 9
    • 84908087566 scopus 로고
    • Zerstreuung von roentgenstrahlen
    • Debye, P. 1915. Zerstreuung von roentgenstrahlen. Ann. Phys. 46:809-823.
    • (1915) Ann. Phys. , vol.46 , pp. 809-823
    • Debye, P.1
  • 10
    • 0015994218 scopus 로고
    • Real-space refinement of the structure of hen egg-white lysozyme
    • Diamond, R. 1974. Real-space refinement of the structure of hen egg-white lysozyme. J. Mol. Biol. 82:371-391.
    • (1974) J. Mol. Biol. , vol.82 , pp. 371-391
    • Diamond, R.1
  • 13
  • 15
    • 0029101826 scopus 로고
    • Recognizing native folds by the arrangement of hydrophobic and polar residues
    • Huang, E. S., S. Subbiah, and M. Levitt. 1995. Recognizing native folds by the arrangement of hydrophobic and polar residues. J. Mol. Biol. 252:709-720.
    • (1995) J. Mol. Biol. , vol.252 , pp. 709-720
    • Huang, E.S.1    Subbiah, S.2    Levitt, M.3
  • 16
    • 43949164756 scopus 로고
    • Simulated annealing: Practice versus theory
    • Ingber, L. 1993. Simulated annealing: Practice versus theory. Math. Comput. Model. 18:29-57.
    • (1993) Math. Comput. Model. , vol.18 , pp. 29-57
    • Ingber, L.1
  • 17
    • 0000699921 scopus 로고    scopus 로고
    • Local interactions and protein foldig: A three-dimensional off-latice approach
    • Irbaeck, A., C. Peterson, F. Potthast, and O. Sommelius. 1997. Local interactions and protein foldig: A three-dimensional off-latice approach. J. Chem. Phys. 107:273-282.
    • (1997) J. Chem. Phys. , vol.107 , pp. 273-282
    • Irbaeck, A.1    Peterson, C.2    Potthast, F.3    Sommelius, O.4
  • 18
    • 0026460365 scopus 로고
    • The threedimensional structure of a glutathione S-transferase from the mu gene class: Structural analysis of the binary complex of isoenzyme 3-3 and glutathione at 2.2-A resolution
    • Ji, X., P. Zhang, R. N. Armstrong, and G. L. Gilliland. 1992. The threedimensional structure of a glutathione S-transferase from the mu gene class: Structural analysis of the binary complex of isoenzyme 3-3 and glutathione at 2.2-A resolution. Biochemistry. 31:10169-10184.
    • (1992) Biochemistry , vol.31 , pp. 10169-10184
    • Ji, X.1    Zhang, P.2    Armstrong, R.N.3    Gilliland, G.L.4
  • 19
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors
    • Kabsch, W. A. 1978. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A. 34:827-828.
    • (1978) Acta Crystallogr. A , vol.34 , pp. 827-828
    • Kabsch, W.A.1
  • 20
  • 21
    • 0030831667 scopus 로고    scopus 로고
    • Validation of protein models from Ca coordinates alone
    • Kleywegt, G. J. 1997. Validation of protein models from Ca coordinates alone. J. Mol. Biol. 273:371-376.
    • (1997) J. Mol. Biol. , vol.273 , pp. 371-376
    • Kleywegt, G.J.1
  • 22
    • 0020114103 scopus 로고
    • X-ray diffraction and scattering on disordered systems using synchrotron radiation
    • Koch, M. H. J., and J. Bordas. 1983. X-ray diffraction and scattering on disordered systems using synchrotron radiation. Nuclear Instrum. Methods. 208:461-469.
    • (1983) Nuclear Instrum. Methods , vol.208 , pp. 461-469
    • Koch, M.H.J.1    Bordas, J.2
  • 23
    • 0034849689 scopus 로고    scopus 로고
    • MASSHA: A graphic system for rigid body modelling of macromolecular complexes against solution scattering data
    • Konarev, P. V., M. V. Petoukhov, and D. I. Svergun. 2001. MASSHA: A graphic system for rigid body modelling of macromolecular complexes against solution scattering data. J. Appl. Crystallogr. 34:527-532.
    • (2001) J. Appl. Crystallogr. , vol.34 , pp. 527-532
    • Konarev, P.V.1    Petoukhov, M.V.2    Svergun, D.I.3
  • 24
    • 0033571450 scopus 로고    scopus 로고
    • The crystal structure of the minus-end-directed microtubule motor protein ncd reveals variable dimer conformations
    • Kozielski, F., S. De Bonis, W. P. Burmeister, C. Cohen-Addad, and R. H. Wade. 1999. The crystal structure of the minus-end-directed microtubule motor protein ncd reveals variable dimer conformations. Struct. Fold Des. 7:1407-1416.
    • (1999) Struct. Fold Des. , vol.7 , pp. 1407-1416
    • Kozielski, F.1    De Bonis, S.2    Burmeister, W.P.3    Cohen-Addad, C.4    Wade, R.H.5
  • 25
    • 0034503624 scopus 로고    scopus 로고
    • A software system for automated and interactive rigid body modeling of solution scattering data
    • Kozin, M. B., and D. I. Svergun. 2000. A software system for automated and interactive rigid body modeling of solution scattering data. J. Appl. Crystallogr. 33:775-777.
    • (2000) J. Appl. Crystallogr. , vol.33 , pp. 775-777
    • Kozin, M.B.1    Svergun, D.I.2
  • 26
    • 0035124442 scopus 로고    scopus 로고
    • Automated matching of high- and low-resolution structural models
    • Kozin, M. B., and D. I. Svergun. 2001. Automated matching of high- and low-resolution structural models. J. Appl. Crystallogr. 34:33-41.
    • (2001) J. Appl. Crystallogr. , vol.34 , pp. 33-41
    • Kozin, M.B.1    Svergun, D.I.2
  • 27
    • 0031007335 scopus 로고    scopus 로고
    • Structures of calmodulin and a functional myosin light chain kinase in the activated complex: A neutron scattering study
    • Krueger, J. K., G. A. Olah, S. E. Rokop, G. Zhi, J. T. Stull, and J. Trewhella. 1997. Structures of calmodulin and a functional myosin light chain kinase in the activated complex: A neutron scattering study. Biochemistry. 36:6017-6023.
    • (1997) Biochemistry , vol.36 , pp. 6017-6023
    • Krueger, J.K.1    Olah, G.A.2    Rokop, S.E.3    Zhi, G.4    Stull, J.T.5    Trewhella, J.6
  • 28
    • 0017157584 scopus 로고
    • A simplified representation of protein conformations for rapid simulation of protein folding
    • Levitt, M. 1976. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104:59-107.
    • (1976) J. Mol. Biol. , vol.104 , pp. 59-107
    • Levitt, M.1
  • 29
    • 0028593398 scopus 로고
    • Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV
    • Lim, K., J. X. Ho, K. Keeling, G. L. Gilliland, X. Ji, F. Ruker, and D. C. Carter. 1994. Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV. Protein Sci. 3:2233-2244.
    • (1994) Protein Sci. , vol.3 , pp. 2233-2244
    • Lim, K.1    Ho, J.X.2    Keeling, K.3    Gilliland, G.L.4    Ji, X.5    Ruker, F.6    Carter, D.C.7
  • 30
    • 0030587599 scopus 로고    scopus 로고
    • Crystal structure of reduced protein R2 of ribonucleotide reductase: The structural basis for oxygen activation at a dinuclear iron site
    • Logan, D. T., X. D. Su, A. Aberg, K. Regnstrom, J. Hajdu, H. Eklund, and P. Nordlund. 1996. Crystal structure of reduced protein R2 of ribonucleotide reductase: The structural basis for oxygen activation at a dinuclear iron site. Structure. 4:1053-1064.
    • (1996) Structure , vol.4 , pp. 1053-1064
    • Logan, D.T.1    Su, X.D.2    Aberg, A.3    Regnstrom, K.4    Hajdu, J.5    Eklund, H.6    Nordlund, P.7
  • 31
    • 84977303841 scopus 로고
    • The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complex with inhibitors
    • Marquart, M., J. Walter, J. Deisenhofer, W. Bode, and R. Huber. 1983. The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complex with inhibitors. Acta Crystallogr. B. 39:480-490.
    • (1983) Acta Crystallogr. B , vol.39 , pp. 480-490
    • Marquart, M.1    Walter, J.2    Deisenhofer, J.3    Bode, W.4    Huber, R.5
  • 32
    • 0028931691 scopus 로고
    • Crystal structures of a schistosomal drug and vaccine target: Glutathione S-transferase from Schistosomajaponica and its complex with the leading antischistosomal drug praziquantel
    • McTigue, M. A., D. R. Williams, and J. A. Tainer. 1995. Crystal structures of a schistosomal drug and vaccine target: Glutathione S-transferase from Schistosomajaponica and its complex with the leading antischistosomal drug praziquantel. J. Mol. Biol. 246:21-27.
    • (1995) J. Mol. Biol. , vol.246 , pp. 21-27
    • McTigue, M.A.1    Williams, D.R.2    Tainer, J.A.3
  • 33
    • 0030832286 scopus 로고    scopus 로고
    • The structure of the acto-myosin subfragment I complex: Results of searches using data from electron microscopy and x-ray crystallography
    • Mendelson, R., and E. P. Morris. 1997. The structure of the acto-myosin subfragment I complex: Results of searches using data from electron microscopy and x-ray crystallography. Proc. Natl. Acad. Sci. U.S.A. 94:8533-8538.
    • (1997) Proc. Natl. Acad. Sci. U.S.A. , vol.94 , pp. 8533-8538
    • Mendelson, R.1    Morris, E.P.2
  • 34
    • 0032960853 scopus 로고    scopus 로고
    • Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues
    • Miyazawa, S., and R. L. Jernigan. 1999. Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues. Proteins Struct. Funct. Genet. 34:49-68.
    • (1999) Proteins Struct. Funct. Genet. , vol.34 , pp. 49-68
    • Miyazawa, S.1    Jernigan, R.L.2
  • 35
    • 0021153567 scopus 로고
    • Generation of β-globin by sequence-specific proteolysis of a hybrid protein produced in Escherichia coli
    • Nagai, K., and H. C. Thogersen. 1984. Generation of β-globin by sequence-specific proteolysis of a hybrid protein produced in Escherichia coli. Nature. 309:810-812.
    • (1984) Nature , vol.309 , pp. 810-812
    • Nagai, K.1    Thogersen, H.C.2
  • 36
    • 0025369904 scopus 로고
    • Crystallization of glutathione S-transferase from human placenta
    • Parker, M. W., M. Lo Bello, and G. Federici. 1990. Crystallization of glutathione S-transferase from human placenta. J. Mol. Biol. 213:221-222.
    • (1990) J. Mol. Biol. , vol.213 , pp. 221-222
    • Parker, M.W.1    Lo Bello, M.2    Federici, G.3
  • 39
    • 0031015737 scopus 로고    scopus 로고
    • Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence
    • Sawaya, M. R., and J. Kraut. 1997. Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence. Biochemistry. 36:586-603.
    • (1997) Biochemistry , vol.36 , pp. 586-603
    • Sawaya, M.R.1    Kraut, J.2
  • 40
    • 0033564015 scopus 로고    scopus 로고
    • Biochemical and structural characterization of recombinant copper-metallothionein from Saccharomyces cerevisiae
    • Sayers, Z., P. Brouillon, D. I. Svergun, P. Zielenkiewicz, and M. H. J. Koch. 1999. Biochemical and structural characterization of recombinant copper-metallothionein from Saccharomyces cerevisiae. Eur. J. Biochem. 262:858-865.
    • (1999) Eur. J. Biochem. , vol.262 , pp. 858-865
    • Sayers, Z.1    Brouillon, P.2    Svergun, D.I.3    Zielenkiewicz, P.4    Koch, M.H.J.5
  • 41
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl, M. J. 1990. Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213:859-883.
    • (1990) J. Mol. Biol. , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 42
    • 0023806075 scopus 로고
    • Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione Stransferase
    • Smith, D. B., and K. S. Johnson. 1988. Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione Stransferase. Gene. 67:31-40.
    • (1988) Gene , vol.67 , pp. 31-40
    • Smith, D.B.1    Johnson, K.S.2
  • 43
    • 0027578071 scopus 로고
    • A direct indirect method of small-angle scattering data treatment
    • Svergun, D. I. 1993. A direct indirect method of small-angle scattering data treatment. J. Appl. Crystallogr. 26:258-267.
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 258-267
    • Svergun, D.I.1
  • 44
    • 0001540719 scopus 로고
    • Solution scattering from biopolymers: Advanced contrast variation data analysis
    • Svergun, D. I. 1994. Solution scattering from biopolymers: Advanced contrast variation data analysis. Acta Crystallogr. A. 50:391-402.
    • (1994) Acta Crystallogr. A , vol.50 , pp. 391-402
    • Svergun, D.I.1
  • 45
    • 0033001996 scopus 로고    scopus 로고
    • Restoring low-resolution structure of biological macromolecules from solution scattering using simulated annealing
    • Svergun, D. I. 1999. Restoring low-resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76:2879-2886.
    • (1999) Biophys. J. , vol.76 , pp. 2879-2886
    • Svergun, D.I.1
  • 46
    • 0031751233 scopus 로고    scopus 로고
    • A model of the quaternary structure of the Escherichia coli F1 ATPase from x-ray solution scattering and evidence for structural changes in the delta subunit during ATP hydrolysis
    • Svergun, D. I., I. Aldag, T. Sieck, K. Altendorf, M. H. J. Koch, D. J. Kane, M. B. Kozin, and G. Grueber. 1998a. A model of the quaternary structure of the Escherichia coli F1 ATPase from x-ray solution scattering and evidence for structural changes in the delta subunit during ATP hydrolysis. Biophys. J. 75:2212-2219.
    • (1998) Biophys. J. , vol.75 , pp. 2212-2219
    • Svergun, D.I.1    Aldag, I.2    Sieck, T.3    Altendorf, K.4    Koch, M.H.J.5    Kane, D.J.6    Kozin, M.B.7    Grueber, G.8
  • 47
    • 0029185933 scopus 로고
    • CRYSOL: A program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates
    • Svergun, D. I., C. Barberato, and M. H. J. Koch. 1995. CRYSOL: A program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28:768-773.
    • (1995) J. Appl. Crystallogr. , vol.28 , pp. 768-773
    • Svergun, D.I.1    Barberato, C.2    Koch, M.H.J.3
  • 48
    • 0031027047 scopus 로고    scopus 로고
    • Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R state
    • Svergun, D. I., C. Barberato, M. H. J. Koch, L. Fetler, and P. Vachette. 1997. Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R state. Proteins. 27:110-117.
    • (1997) Proteins , vol.27 , pp. 110-117
    • Svergun, D.I.1    Barberato, C.2    Koch, M.H.J.3    Fetler, L.4    Vachette, P.5
  • 49
    • 0034640267 scopus 로고    scopus 로고
    • A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome
    • Svergun, D. I., and K. H. Nierhaus. 2000. A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome. J. Biol. Chem. 275:14432-14439.
    • (2000) J. Biol. Chem. , vol.275 , pp. 14432-14439
    • Svergun, D.I.1    Nierhaus, K.H.2
  • 50
    • 0035010533 scopus 로고    scopus 로고
    • Determination of domain structure of proteins from x-ray solution scattering
    • Svergun, D. I., M. V. Petoukhov, and M. H. J. Koch. 2001a. Determination of domain structure of proteins from x-ray solution scattering. Biophys. J. 80:2946-2953.
    • (2001) Biophys. J. , vol.80 , pp. 2946-2953
    • Svergun, D.I.1    Petoukhov, M.V.2    Koch, M.H.J.3
  • 51
    • 0034614372 scopus 로고    scopus 로고
    • Crystal versus solution structures of thiamine diphosphate-dependent enzymes
    • Svergun, D. I., M. V. Petoukhov, M. H. J. Koch, and S. Koenig. 2000. Crystal versus solution structures of thiamine diphosphate-dependent enzymes. J. Biol. Chem. 275:297-302.
    • (2000) J. Biol. Chem , vol.275 , pp. 297-302
    • Svergun, D.I.1    Petoukhov, M.V.2    Koch, M.H.J.3    Koenig, S.4
  • 53
    • 0035816674 scopus 로고    scopus 로고
    • Conformation of the Drosophila motor protein nonclaret disjunctional in solution from x-ray and neutron scattering
    • Svergun, D. I., G. Zaccai, M. Malfois, R. H. Wade, M. H. J. Koch, and F. Kozielski. 2001b. Conformation of the Drosophila motor protein nonclaret disjunctional in solution from x-ray and neutron scattering. J. Biol. Chem. 276:24826-24832.
    • (2001) J. Biol. Chem. , vol.276 , pp. 24826-24832
    • Svergun, D.I.1    Zaccai, G.2    Malfois, M.3    Wade, R.H.4    Koch, M.H.J.5    Kozielski, F.6
  • 54
    • 0029909384 scopus 로고    scopus 로고
    • An iterative method for extracting energy-like quantities from protein structures
    • Thomas, P. D., and K. A. Dill. 1996. An iterative method for extracting energy-like quantities from protein structures. Proc. Natl. Acad. Sci. U.S.A. 93:11628-11633.
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 11628-11633
    • Thomas, P.D.1    Dill, K.A.2
  • 55
    • 0033458848 scopus 로고    scopus 로고
    • Structure of the fibrinogen γ-chain integrin binding and factor XIIIa cross-linking sites obtained through carrier protein driven crystallization
    • Ware, S., J. P. Donahue, J. Hawiger, and W. F. Anderson. 1999. Structure of the fibrinogen γ-chain integrin binding and factor XIIIa cross-linking sites obtained through carrier protein driven crystallization. Protein Sci. 8:2663-2671.
    • (1999) Protein Sci. , vol.8 , pp. 2663-2671
    • Ware, S.1    Donahue, J.P.2    Hawiger, J.3    Anderson, W.F.4
  • 56
    • 0032563192 scopus 로고    scopus 로고
    • Structure of the ankyrin-binding domain of α-Na,K-ATPase
    • Zhang, Z., P. Devarajan, A. L. Dorfman, and J. S. Morrow. 1998. Structure of the ankyrin-binding domain of α-Na,K-ATPase. J. Biol. Chem. 273:18681-18684.
    • (1998) J. Biol. Chem. , vol.273 , pp. 18681-18684
    • Zhang, Z.1    Devarajan, P.2    Dorfman, A.L.3    Morrow, J.S.4
  • 57
    • 0036300912 scopus 로고    scopus 로고
    • Protein structure prediction constrained by solution x-ray scattering data and structural homology identification
    • Zheng, W., and S. Doniach. 2002. Protein structure prediction constrained by solution x-ray scattering data and structural homology identification. J. Mol. Biol. 316:173-187.
    • (2002) J. Mol. Biol. , vol.316 , pp. 173-187
    • Zheng, W.1    Doniach, S.2


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