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Volumn 1, Issue SUPPL.70, 2012, Pages

Sample preparation, data collection, and preliminary data analysis in biomolecular solution X-ray scattering

Author keywords

Aggregation; Protein and RNA structure; Radiation damage; Sample preparation; SAXS; Solution X ray scattering; Structural biology; WAXS

Indexed keywords

BUFFER; PROTEIN;

EID: 84875605901     PISSN: 19343655     EISSN: 19343663     Source Type: Journal    
DOI: 10.1002/0471140864.ps1714s70     Document Type: Article
Times cited : (27)

References (31)
  • 1
    • 34247891557 scopus 로고    scopus 로고
    • Structural characterization of flexible proteins using small-angle x-ray scattering.
    • Bernado, P., Mylonas, E., Petoukhov, M.V., Blackledge, M., and Svergun, D.I. 2007. Structural characterization of flexible proteins using small-angle x-ray scattering. J. Am. Chem. Soc. 129:5656-5664.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 5656-5664
    • Bernado, P.1    Mylonas, E.2    Petoukhov, M.V.3    Blackledge, M.4    Svergun, D.I.5
  • 2
    • 0031807272 scopus 로고    scopus 로고
    • Low-resolution structures of proteins in solution retrieved from x-ray scattering with a genetic algorithm
    • Chacon, P., Moran, F., Diaz, J.F., Pantos, E., and Andreu, J.M. 1998. Low-resolution structures of proteins in solution retrieved from x-ray scattering with a genetic algorithm. Biophys. J. 74:2760-2775.
    • (1998) Biophys. J. , vol.74 , pp. 2760-2775
    • Chacon, P.1    Moran, F.2    Diaz, J.F.3    Pantos, E.4    Andreu, J.M.5
  • 3
    • 0034511609 scopus 로고    scopus 로고
    • Evaluation of small-angle scattering data of charged particles using the generalized indirect Fourier transformation technique
    • Fritz, G., Bergmann, A., and Glatter, O. 2000. Evaluation of small-angle scattering data of charged particles using the generalized indirect Fourier transformation technique. J. Chem. Phys. 113:9733-9740.
    • (2000) J. Chem. Phys. , vol.113 , pp. 9733-9740
    • Fritz, G.1    Bergmann, A.2    Glatter, O.3
  • 4
    • 28444453002 scopus 로고    scopus 로고
    • Refinement of multidomain protein structures by combination of solution small-angle x-ray scattering andNMRdata
    • Grishaev, A., Wu, J., Trewhella, J., and Bax, A. 2005. Refinement of multidomain protein structures by combination of solution small-angle x-ray scattering andNMRdata. J. Am.Chem. Soc. 127:16621-16628.
    • (2005) J. Am.Chem. Soc. , vol.127 , pp. 16621-16628
    • Grishaev, A.1    Wu, J.2    Trewhella, J.3    Bax, A.4
  • 5
    • 38349018735 scopus 로고    scopus 로고
    • Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints
    • Grishaev, A., Tugarinov, V., Kay, L.E., Trewhella, J., and Bax, A. 2008a. Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints. J. Biomol. NMR 40:95-106.
    • (2008) J. Biomol. NMR , vol.40 , pp. 95-106
    • Grishaev, A.1    Tugarinov, V.2    Kay, L.E.3    Trewhella, J.4    Bax, A.5
  • 6
    • 54049155019 scopus 로고    scopus 로고
    • Solution structure of tRNA(Val) from refinement of homology model against residual dipolar couplings and SAXS data
    • Grishaev, A., Ying, J., Canny, M., Pardi, A., and Bax, A. 2008b. Solution structure of tRNA(Val) from refinement of homology model against residual dipolar couplings and SAXS data. J. Biomol. NMR 42:99-109.
    • (2008) J. Biomol. NMR , vol.42 , pp. 99-109
    • Grishaev, A.1    Ying, J.2    Canny, M.3    Pardi, A.4    Bax, A.5
  • 7
    • 78149240323 scopus 로고    scopus 로고
    • Improved fitting of solution x-ray scattering data to macromolecular structural ensembles by explicit water modeling
    • Grishaev, A., Guo, L., Irving, T., and Bax, A. 2010. Improved fitting of solution x-ray scattering data to macromolecular structural ensembles by explicit water modeling. J. Am. Chem. Soc. 132:15484-15486.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 15484-15486
    • Grishaev, A.1    Guo, L.2    Irving, T.3    Bax, A.4
  • 8
    • 77950223101 scopus 로고    scopus 로고
    • Small-angle scattering for structural biology expanding the frontier while avoiding the pitfalls
    • Jacques, D.A. and Trewhella, J. 2010. Small-angle scattering for structural biology expanding the frontier while avoiding the pitfalls. Prot. Sci. 19:642-657.
    • (2010) Prot. Sci. , vol.19 , pp. 642-657
    • Jacques, D.A.1    Trewhella, J.2
  • 9
    • 0345169163 scopus 로고    scopus 로고
    • Small-angle scattering: A view on the properties, structures and structural changes of biological macromolecules in solution
    • Koch, M.H.J., Vachette, P., and Svergun, D.I. 2003. Small-angle scattering: A view on the properties, structures and structural changes of biological macromolecules in solution. Q. Rev. Biophys. 36:147-227.
    • (2003) Q. Rev. Biophys. , vol.36 , pp. 147-227
    • Koch, M.H.J.1    Vachette, P.2    Svergun, D.I.3
  • 12
    • 77951631601 scopus 로고    scopus 로고
    • Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase
    • Mittag, T., Marsh, J., Grishaev, A., Orlicky, S., Lin, H., Sicheri, F., Tyers, M., and Forman-Kay, J. 2010. Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure 18:494-506.
    • (2010) Structure , vol.18 , pp. 494-506
    • Mittag, T.1    Marsh, J.2    Grishaev, A.3    Orlicky, S.4    Lin, H.5    Sicheri, F.6    Tyers, M.7    Forman-Kay, J.8
  • 13
    • 34248397195 scopus 로고    scopus 로고
    • Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering
    • Mylonas, E. and Svergun, D.I. 2007. Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering. J. Appl. Crystallogr. 40:s245-s249.
    • (2007) J. Appl. Crystallogr. , vol.40
    • Mylonas, E.1    Svergun, D.I.2
  • 14
    • 0034484513 scopus 로고    scopus 로고
    • SAXS experiments on absolute scale with Kratky systems using water as a secondary standard
    • Orthaber, D., Bergmann, A., and Glatter, O. 2000. SAXS experiments on absolute scale with Kratky systems using water as a secondary standard. J. Appl. Crystallogr. 33:218-225.
    • (2000) J. Appl. Crystallogr. , vol.33 , pp. 218-225
    • Orthaber, D.1    Bergmann, A.2    Glatter, O.3
  • 15
    • 67650992092 scopus 로고    scopus 로고
    • Structure and flexibility within proteins identified through small-angle X-ray scattering
    • Pelikan, M., Hura, G.L., Hammel, M. 2009. Structure and flexibility within proteins identified through small-angle X-ray scattering. Gen. Physiol. Biophys. 28:174-189.
    • (2009) Gen. Physiol. Biophys. , vol.28 , pp. 174-189
    • Pelikan, M.1    Hura, G.L.2    Hammel, M.3
  • 16
    • 23244455562 scopus 로고    scopus 로고
    • Global rigid body modeling of macromolecular complexes against small-angle scattering data
    • Petoukhov, M.V. and Svergun, D.I. 2005. Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys. J. 89, 1237-1250.
    • (2005) Biophys. J , vol.89 , pp. 1237-1250
    • Petoukhov, M.V.1    Svergun, D.I.2
  • 17
    • 35748982423 scopus 로고    scopus 로고
    • Analysis of X-ray and neutron scattering from biomacromolecular solutions
    • Petoukhov, M.V. and Svergun, D.I. 2007. Analysis of X-ray and neutron scattering from biomacromolecular solutions. Curr. Opin. Struct. Biol. 17:562-571.
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 562-571
    • Petoukhov, M.V.1    Svergun, D.I.2
  • 18
    • 79960029952 scopus 로고    scopus 로고
    • AquaSAXS: A web server for computation and fitting of SAXS profiles with non-uniformly hydrated atomic models
    • Poitevin, F., Orland, H., Doniach, S., Koehl, P., and Delarue, M. 2011. AquaSAXS: A web server for computation and fitting of SAXS profiles with non-uniformly hydrated atomic models. Nucl. Acids Res. 39:W184-W189.
    • (2011) Nucl. Acids Res. , vol.39
    • Poitevin, F.1    Orland, H.2    Doniach, S.3    Koehl, P.4    Delarue, M.5
  • 19
    • 37149049312 scopus 로고    scopus 로고
    • X-ray solution scattering (SAXS) combined with crystallography and computation: Defining accurate macromolecular structures, conformations and assemblies in solution
    • Putnam, C.D., Hammel, M., Hura, G., and Tainer, J.A. 2007. X-ray solution scattering (SAXS) combined with crystallography and computation: Defining accurate macromolecular structures, conformations and assemblies in solution. Q. Rev. Biophys. 40:191-285.
    • (2007) Q. Rev. Biophys. , vol.40 , pp. 191-285
    • Putnam, C.D.1    Hammel, M.2    Hura, G.3    Tainer, J.A.4
  • 20
    • 77954280480 scopus 로고    scopus 로고
    • FoXS: A web server for rapid computation and fitting of SAXS profiles
    • Schneiderman-Duhovny, D., Hammel, M., and Sali, A. 2010. FoXS: A web server for rapid computation and fitting of SAXS profiles. Nucl. Acids Res. 28:W540-W544.
    • (2010) Nucl. Acids Res. , vol.28
    • Schneiderman-Duhovny, D.1    Hammel, M.2    Sali, A.3
  • 21
    • 33846839463 scopus 로고    scopus 로고
    • A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle x-ray scattering data
    • Schwieters, C.D. and Clore, G.M. 2007. A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle x-ray scattering data. Biochemistry 46:1152-1166.
    • (2007) Biochemistry , vol.46 , pp. 1152-1166
    • Schwieters, C.D.1    Clore, G.M.2
  • 22
    • 77956641793 scopus 로고    scopus 로고
    • Solution structure of the 128 kDa Enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small- and wide angle x-ray scattering
    • Schwieters, C.D., Suh, J-Y., Grishaev, A., Ghirlando, R., Takayama, Y., and Clore, G.M. 2010. Solution structure of the 128 kDa Enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small- and wide angle x-ray scattering. J. Am. Chem. Soc. 132:13026- 13045.
    • (2010) J. Am. Chem. Soc. , vol.132
    • Schwieters, C.D.1    Suh, J-Y.2    Grishaev, A.3    Ghirlando, R.4    Takayama, Y.5    Clore, G.M.6
  • 23
    • 0026910457 scopus 로고
    • Determination of the regularization parameter in indirect-transform methods using perceptual criteria
    • Svergun, D.I. 1992. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25:495-503.
    • (1992) J. Appl. Crystallogr. , vol.25 , pp. 495-503
    • Svergun, D.I.1
  • 24
    • 0029185933 scopus 로고
    • CRYSOL a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates
    • Svergun, D., Barberato, C., and Koch, M.H.J. 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.1    Barberato, C.2    Koch, M.H.J.3
  • 25
    • 0033001996 scopus 로고    scopus 로고
    • Restoring lowresolution structure of biological macromolecules from solution scattering using simulated annealing
    • Svergun, D.I. 1999. Restoring lowresolution 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
  • 26
    • 0035010533 scopus 로고    scopus 로고
    • Determination of domain structure of proteins from x-ray solution scattering
    • Svergun, D.I., Petoukhov, M.V., and Koch, M.H.J. 2001. Determination of domain structure of proteins from x-ray solution scattering. Biophys. J. 80:2001.
    • (2001) Biophys. J. , vol.80 , pp. 2001
    • Svergun, D.I.1    Petoukhov, M.V.2    Koch, M.H.J.3
  • 27
    • 0038715974 scopus 로고    scopus 로고
    • Evaluation of three algorithms for ab initio determination of three-dimensional shape from one-dimensional solution scattering profiles
    • Takahashi, Y., Nishikawa, Y., and Fujisawa, T. 2003. Evaluation of three algorithms for ab initio determination of three-dimensional shape from one-dimensional solution scattering profiles. J. Appl. Crystallogr. 36:549-552.
    • (2003) J. Appl. Crystallogr. , vol.36 , pp. 549-552
    • Takahashi, Y.1    Nishikawa, Y.2    Fujisawa, T.3
  • 28
    • 79851489016 scopus 로고    scopus 로고
    • Combined use of residual dipolar couplings and solution x-ray scattering to rapidly probe rigid-body conformational transitions in a non-phosphorylatable active-site Mutant of the 128 kDa Enzyme I dimer
    • Takayama, Y., Schwieters, C.D., Grishaev, A., Ghirlando, R., and Clore, G.M. 2011. Combined use of residual dipolar couplings and solution x-ray scattering to rapidly probe rigid-body conformational transitions in a non-phosphorylatable active-site Mutant of the 128 kDa Enzyme I dimer. J. Am. Chem. Soc. 133:424-427.
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 424-427
    • Takayama, Y.1    Schwieters, C.D.2    Grishaev, A.3    Ghirlando, R.4    Clore, G.M.5
  • 29
    • 0037701585 scopus 로고    scopus 로고
    • Uniqueness of ab initio shape determination in small-angle scattering
    • Volkov, V.V. and Svergun, D.I. 2003. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 36:860-864.
    • (2003) J. Appl. Crystallogr. , vol.36 , pp. 860-864
    • Volkov, V.V.1    Svergun, D.I.2
  • 30
    • 0034484041 scopus 로고    scopus 로고
    • Reconstruction of low-resolution three-dimensional density maps from one-dimensional small-angle X-ray scattering data for biomolecules
    • Walther, D., Cohen, F.E., and Doniach, S. 2000. Reconstruction of low-resolution three-dimensional density maps from one-dimensional small-angle X-ray scattering data for biomolecules. J. Appl. Crystallogr. 33:350-363.
    • (2000) J. Appl. Crystallogr. , vol.33 , pp. 350-363
    • Walther, D.1    Cohen, F.E.2    Doniach, S.3
  • 31
    • 68949116065 scopus 로고    scopus 로고
    • A rapid coarse residue-based computational method for X-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes
    • Yang, S., Park, S., Makowski, L., and Roux, B. 2009. A rapid coarse residue-based computational method for X-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes. Biophys. J. 96:4449-4463.
    • (2009) Biophys. J. , vol.96 , pp. 4449-4463
    • Yang, S.1    Park, S.2    Makowski, L.3    Roux, B.4


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