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Tsuruta H., and Irving T.C. Experimental approaches for solution X-ray scattering and fiber diffraction. Curr Opin Struct Biol 18 (2008) 601-608
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This article presents an automated system and data analysis pipeline for SAXS data collection. The results on 50 samples indicate the relatively small amounts of material needed, the robust features of SAXS for efficient throughput, and the high percentage of samples for which structural data can be obtained.
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Hura G.L., Menon A.L., Hammel M., Rambo R.P., Poole II F.L., Tsutakawa S.E., Jenney Jr. F.E., Classen S., Frankel K.A., Hopkins R.C., et al. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods 6 (2009) 606-612. This article presents an automated system and data analysis pipeline for SAXS data collection. The results on 50 samples indicate the relatively small amounts of material needed, the robust features of SAXS for efficient throughput, and the high percentage of samples for which structural data can be obtained.
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Hao, Q.2
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52949149420
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Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair
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SAXS was used to determine the correct crystallographic dimer in solution and to further test the residues involved in the Mre11 dimerization interface. SAXS of the Mre11 mutants demonstrated a mixed monomer-dimer population suggesting disruption of the interface can be achieved by the incorporation of charged residues in the hydrophobic interface.
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Williams R.S., Moncalian G., Williams J.S., Yamada Y., Limbo O., Shin D.S., Groocock L.M., Cahill D., Hitomi C., Guenther G., et al. Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair. Cell 135 (2008) 97-109. SAXS was used to determine the correct crystallographic dimer in solution and to further test the residues involved in the Mre11 dimerization interface. SAXS of the Mre11 mutants demonstrated a mixed monomer-dimer population suggesting disruption of the interface can be achieved by the incorporation of charged residues in the hydrophobic interface.
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Cell
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Williams, R.S.1
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Hitomi, C.9
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13
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45949104681
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Structural basis of guanine nucleotide exchange mediated by the T-cell essential Vav1
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Chrencik J.E., Brooun A., Zhang H., Mathews I.I., Hura G.L., Foster S.A., Perry J.J., Streiff M., Ramage P., Widmer H., et al. Structural basis of guanine nucleotide exchange mediated by the T-cell essential Vav1. J Mol Biol 380 (2008) 828-843
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Chrencik, J.E.1
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Zhang, H.3
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Hura, G.L.5
Foster, S.A.6
Perry, J.J.7
Streiff, M.8
Ramage, P.9
Widmer, H.10
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53049094260
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Crystal structure of the lysine riboswitch regulatory mRNA element
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Garst A.D., Heroux A., Rambo R.P., and Batey R.T. Crystal structure of the lysine riboswitch regulatory mRNA element. J Biol Chem 283 (2008) 22347-22351
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Garst, A.D.1
Heroux, A.2
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71449098436
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Structural mechanism of abscisic acid binding and signaling by dimeric PYR1
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Nishimura N., Hitomi K., Arvai A.S., Rambo R.P., Hitomi C., Cutler S.R., Schroeder J.I., and Getzoff E.D. Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. Science (2009) 1181829
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Science
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Nishimura, N.1
Hitomi, K.2
Arvai, A.S.3
Rambo, R.P.4
Hitomi, C.5
Cutler, S.R.6
Schroeder, J.I.7
Getzoff, E.D.8
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16
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67349137146
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Domain organization of the monomeric form of the Tom70 mitochondrial import receptor
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The X-ray crystal structure of Tom70 crystallized as a dimer where each monomer was composed of discrete N-terminal and C-terminal domains. The linker region between the two domains was missing from the electron density map, which consequently made the assignment of the correct domain topology ambiguous. Comparison of the SAXS profile with the two plausible models resolved the ambiguity and a further ab initio shape reconstruction provided additional support for the correct choice.
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Mills R.D., Trewhella J., Qiu T.W., Welte T., Ryan T.M., Hanley T., Knott R.B., Lithgow T., and Mulhern T.D. Domain organization of the monomeric form of the Tom70 mitochondrial import receptor. J Mol Biol 388 (2009) 1043-1058. The X-ray crystal structure of Tom70 crystallized as a dimer where each monomer was composed of discrete N-terminal and C-terminal domains. The linker region between the two domains was missing from the electron density map, which consequently made the assignment of the correct domain topology ambiguous. Comparison of the SAXS profile with the two plausible models resolved the ambiguity and a further ab initio shape reconstruction provided additional support for the correct choice.
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(2009)
J Mol Biol
, vol.388
, pp. 1043-1058
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Mills, R.D.1
Trewhella, J.2
Qiu, T.W.3
Welte, T.4
Ryan, T.M.5
Hanley, T.6
Knott, R.B.7
Lithgow, T.8
Mulhern, T.D.9
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17
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70350690563
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Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase
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SAXS combined with advanced computational approaches were employed to characterize the SAXS to define the shapes and conformations of mPNK complexes including their functional flexibility. On the basis of several thousand conformations of mPNK and their calculated SAXS profiles, the SAXS validated best-fitting model had the FHA linker in an extended conformation. To test the position of DNA predicted from SAXS envelopes, the authors performed an exhaustive search of the protein-DNA interfaces by an EMAP docking approach, an algorithm that searches for the minimal ensemble (MES) of the conformations from the pool of all generated conformations in MD simulations. The combined envelopes for DNA complexes and flexible attachment of the FHA domain to the catalytic segment, elucidated by SAXS, suggests how flexibility enables the interactions of mPNK with diverse DNA substrates and protein partners required for effective orchestration of DNA-end repair.
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Bernstein N.K., Hammel M., Mani R.S., Weinfeld M., Pelikan M., Tainer J.A., and Glover J.N. Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase. Nucleic Acids Res 37 (2009) 6161-6173. SAXS combined with advanced computational approaches were employed to characterize the SAXS to define the shapes and conformations of mPNK complexes including their functional flexibility. On the basis of several thousand conformations of mPNK and their calculated SAXS profiles, the SAXS validated best-fitting model had the FHA linker in an extended conformation. To test the position of DNA predicted from SAXS envelopes, the authors performed an exhaustive search of the protein-DNA interfaces by an EMAP docking approach, an algorithm that searches for the minimal ensemble (MES) of the conformations from the pool of all generated conformations in MD simulations. The combined envelopes for DNA complexes and flexible attachment of the FHA domain to the catalytic segment, elucidated by SAXS, suggests how flexibility enables the interactions of mPNK with diverse DNA substrates and protein partners required for effective orchestration of DNA-end repair.
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(2009)
Nucleic Acids Res
, vol.37
, pp. 6161-6173
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Bernstein, N.K.1
Hammel, M.2
Mani, R.S.3
Weinfeld, M.4
Pelikan, M.5
Tainer, J.A.6
Glover, J.N.7
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18
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44149094083
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XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations
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Fan L., Fuss J.O., Cheng Q.J., Arvai A.S., Hammel M., Roberts V.A., Cooper P.K., and Tainer J.A. XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations. Cell 133 (2008) 789-800
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Cell
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Fan, L.1
Fuss, J.O.2
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Arvai, A.S.4
Hammel, M.5
Roberts, V.A.6
Cooper, P.K.7
Tainer, J.A.8
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19
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70349472553
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Nbs1 flexibly tethers Ctp1 and Mre11-Rad50 to coordinate DNA double-strand break processing and repair
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Nbs1 links the Mre11 nuclease at a DNA double strand break to the CTIP protein that opens DNA surrounding the break. MX, SAXS, and proteolysis results show that the Nbs1 folded core is conserved from pombe to human Nbs1 and that disease-associated Nbs1 mutations fall into the folded and extended N-terminal FHA-BRCT1-BRCT2 domains defined by SAXS and MX. As all parts of a structure contribute to the experimental X-ray scattering, SAXS was used to provide an objective, quantitative measure of structural similarity for pombe and human Nbs1 and to provide molecular insights into the consequences of patient-derived NBS mutations. SAXS shows that the fused, extended, FHA-BRCT1-BRCT2 domains are flexibly linked to C-terminal Mre11-binding and ATM-binding motifs. With the SAXS results, Nbs1 emerges as an extended, flexible binding nexus coordinating interactions of the Mre11-Rad50 core, the checkpoint kinase ATM/Tel1, and the DNA-end-processing factor CTIP.
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Williams R.S., Dodson G.E., Limbo O., Yamada Y., Williams J.S., Guenther G., Classen S., Glover J.N., Iwasaki H., Russell P., et al. Nbs1 flexibly tethers Ctp1 and Mre11-Rad50 to coordinate DNA double-strand break processing and repair. Cell 139 (2009) 87-99. Nbs1 links the Mre11 nuclease at a DNA double strand break to the CTIP protein that opens DNA surrounding the break. MX, SAXS, and proteolysis results show that the Nbs1 folded core is conserved from pombe to human Nbs1 and that disease-associated Nbs1 mutations fall into the folded and extended N-terminal FHA-BRCT1-BRCT2 domains defined by SAXS and MX. As all parts of a structure contribute to the experimental X-ray scattering, SAXS was used to provide an objective, quantitative measure of structural similarity for pombe and human Nbs1 and to provide molecular insights into the consequences of patient-derived NBS mutations. SAXS shows that the fused, extended, FHA-BRCT1-BRCT2 domains are flexibly linked to C-terminal Mre11-binding and ATM-binding motifs. With the SAXS results, Nbs1 emerges as an extended, flexible binding nexus coordinating interactions of the Mre11-Rad50 core, the checkpoint kinase ATM/Tel1, and the DNA-end-processing factor CTIP.
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(2009)
Cell
, vol.139
, pp. 87-99
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Williams, R.S.1
Dodson, G.E.2
Limbo, O.3
Yamada, Y.4
Williams, J.S.5
Guenther, G.6
Classen, S.7
Glover, J.N.8
Iwasaki, H.9
Russell, P.10
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20
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35748982423
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Analysis of X-ray and neutron scattering from biomacromolecular solutions
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Petoukhov M.V., and Svergun D.I. Analysis of X-ray and neutron scattering from biomacromolecular solutions. Curr Opin Struct Biol 17 (2007) 562-571
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Petoukhov, M.V.1
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21
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50649108803
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The complete VS ribozyme in solution studied by small-angle X-ray scattering
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Building structural models into electron density usually occurs by interpreting an electron density map in terms of the amino or nucleic acid building blocks. Here, the authors interpret a density map in terms of larger helical building blocks and build the entire ribozyme using an ab initio SAXS model.
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Lipfert J., Ouellet J., Norman D.G., Doniach S., and Lilley D.M. The complete VS ribozyme in solution studied by small-angle X-ray scattering. Structure 16 (2008) 1357-1367. Building structural models into electron density usually occurs by interpreting an electron density map in terms of the amino or nucleic acid building blocks. Here, the authors interpret a density map in terms of larger helical building blocks and build the entire ribozyme using an ab initio SAXS model.
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(2008)
Structure
, vol.16
, pp. 1357-1367
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Lipfert, J.1
Ouellet, J.2
Norman, D.G.3
Doniach, S.4
Lilley, D.M.5
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22
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65149091065
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Structure of the noncatalytic domains and global fold of the protein disulfide isomerase ERp72
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Kozlov G., Maattanen P., Schrag J.D., Hura G.L., Gabrielli L., Cygler M., Thomas D.Y., and Gehring K. Structure of the noncatalytic domains and global fold of the protein disulfide isomerase ERp72. Structure 17 (2009) 651-659
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Structure
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Kozlov, G.1
Maattanen, P.2
Schrag, J.D.3
Hura, G.L.4
Gabrielli, L.5
Cygler, M.6
Thomas, D.Y.7
Gehring, K.8
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23
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36448958312
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The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution
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Hammel M., Nemecek D., Keightley J.A., Thomas Jr. G.J., and Geisbrecht B.V. The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution. Protein Sci 16 (2007) 2605-2617
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Hammel, M.1
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24
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67349185014
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A picornaviral loop-to-loop replication complex
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Claridge J.K., Headey S.J., Chow J.Y., Schwalbe M., Edwards P.J., Jeffries C.M., Venugopal H., Trewhella J., and Pascal S.M. A picornaviral loop-to-loop replication complex. J Struct Biol 166 (2009) 251-262
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Claridge, J.K.1
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Venugopal, H.7
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Pascal, S.M.9
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25
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37049001482
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Small-angle X-ray scattering and NMR studies of the conformation of the PDZ region of SAP97 and its interactions with Kir2.1
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Goult B.T., Rapley J.D., Dart C., Kitmitto A., Grossmann J.G., Leyland M.L., and Lian L.Y. Small-angle X-ray scattering and NMR studies of the conformation of the PDZ region of SAP97 and its interactions with Kir2.1. Biochemistry 46 (2007) 14117-14128
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Goult, B.T.1
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Lian, L.Y.7
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26
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69949149572
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The molecular basis for the regulation of the cap-binding complex by the importins
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Dias S.M., Wilson K.F., Rojas K.S., Ambrosio A.L., and Cerione R.A. The molecular basis for the regulation of the cap-binding complex by the importins. Nat Struct Mol Biol 16 (2009) 930-937
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Dias, S.M.1
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27
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54049155019
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Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data
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val. The authors present a general strategy for future combined investigation utilizing both SAXS and RDCs.
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val. The authors present a general strategy for future combined investigation utilizing both SAXS and RDCs.
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(2008)
J Biomol NMR
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Grishaev, A.1
Ying, J.2
Canny, M.D.3
Pardi, A.4
Bax, A.5
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28
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68049084850
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Determination of multicomponent protein structures in solution using global orientation and shape restraints
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Correct placement and orientation of individual protein components in a large complex is a challenging problem in folding and EM maps. The authors combine RDCs and SAXS data to develop a straightforward approach for assembling multicomponent structures.
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Wang J., Zuo X., Yu P., Byeon I.J., Jung J., Wang X., Dyba M., Seifert S., Schwieters C.D., Qin J., et al. Determination of multicomponent protein structures in solution using global orientation and shape restraints. J Am Chem Soc 131 (2009) 10507-10515. Correct placement and orientation of individual protein components in a large complex is a challenging problem in folding and EM maps. The authors combine RDCs and SAXS data to develop a straightforward approach for assembling multicomponent structures.
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J Am Chem Soc
, vol.131
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Wang, J.1
Zuo, X.2
Yu, P.3
Byeon, I.J.4
Jung, J.5
Wang, X.6
Dyba, M.7
Seifert, S.8
Schwieters, C.D.9
Qin, J.10
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29
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70349783815
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A method for helical RNA global structure determination in solution using small-angle X-ray scattering and NMR measurements
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Determining the global architecture of a folded RNA in terms of its helical building blocks can be readily achieved in a combined approach integrating both SAXS and NMR based residual dipolar coupling measurements. The structural periodicity of the RNA helical backbone provides unique RDC measurements for orienting helices. However, an ambiguity arises when measurements are made in one alignment medium. Here, SAXS resolves the ambiguity and provides additional independent data for refining a family of structures.
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Wang J., Zuo X., Yu P., Xu H., Starich M.R., Tiede D.M., Shapiro B.A., Schwieters C.D., and Wang Y.X. A method for helical RNA global structure determination in solution using small-angle X-ray scattering and NMR measurements. J Mol Biol 393 (2009) 717-734. Determining the global architecture of a folded RNA in terms of its helical building blocks can be readily achieved in a combined approach integrating both SAXS and NMR based residual dipolar coupling measurements. The structural periodicity of the RNA helical backbone provides unique RDC measurements for orienting helices. However, an ambiguity arises when measurements are made in one alignment medium. Here, SAXS resolves the ambiguity and provides additional independent data for refining a family of structures.
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(2009)
J Mol Biol
, vol.393
, pp. 717-734
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Wang, J.1
Zuo, X.2
Yu, P.3
Xu, H.4
Starich, M.R.5
Tiede, D.M.6
Shapiro, B.A.7
Schwieters, C.D.8
Wang, Y.X.9
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30
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40549143036
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The periplasmic domain of TolR from Haemophilus influenzae forms a dimer with a large hydrophobic groove: NMR solution structure and comparison to SAXS data
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NMR measurements encompassing both NOEs and RDCs were used to determine the solution structure of the periplasmic domain of TolR. Additional SAXS studies were used to confirm the correct dimer model derived by the NMR studies, providing an independent assessment of the model in solution.
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Parsons L.M., Grishaev A., and Bax A. The periplasmic domain of TolR from Haemophilus influenzae forms a dimer with a large hydrophobic groove: NMR solution structure and comparison to SAXS data. Biochemistry 47 (2008) 3131-3142. NMR measurements encompassing both NOEs and RDCs were used to determine the solution structure of the periplasmic domain of TolR. Additional SAXS studies were used to confirm the correct dimer model derived by the NMR studies, providing an independent assessment of the model in solution.
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(2008)
Biochemistry
, vol.47
, pp. 3131-3142
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Parsons, L.M.1
Grishaev, A.2
Bax, A.3
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31
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44449116120
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Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain
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The authors use a combined approach of NMR, X-ray crystallography, and SAXS to develop a structural model of p53 in complex with DNA. They reconcile a previous EM structure of the p53-DNA complex and show a remarkable agreement with the SAXS-based model derived from rigid-body modeling. More importantly, the authors demonstrate by SAXS that the tetramerization of p53 does not occur explicitly through C-terminal or N-terminal domains. Systematic truncations of p53 were explored to define the requirements for quaternary structure formation.
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Wells M., Tidow H., Rutherford T.J., Markwick P., Jensen M.R., Mylonas E., Svergun D.I., Blackledge M., and Fersht A.R. Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. Proc Natl Acad Sci U S A 105 (2008) 5762-5767. The authors use a combined approach of NMR, X-ray crystallography, and SAXS to develop a structural model of p53 in complex with DNA. They reconcile a previous EM structure of the p53-DNA complex and show a remarkable agreement with the SAXS-based model derived from rigid-body modeling. More importantly, the authors demonstrate by SAXS that the tetramerization of p53 does not occur explicitly through C-terminal or N-terminal domains. Systematic truncations of p53 were explored to define the requirements for quaternary structure formation.
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(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 5762-5767
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Wells, M.1
Tidow, H.2
Rutherford, T.J.3
Markwick, P.4
Jensen, M.R.5
Mylonas, E.6
Svergun, D.I.7
Blackledge, M.8
Fersht, A.R.9
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32
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34547634446
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Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex
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Tidow H., Melero R., Mylonas E., Freund S.M., Grossmann J.G., Carazo J.M., Svergun D.I., Valle M., and Fersht A.R. Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex. Proc Natl Acad Sci U S A 104 (2007) 12324-12329
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Proc Natl Acad Sci U S A
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Tidow, H.1
Melero, R.2
Mylonas, E.3
Freund, S.M.4
Grossmann, J.G.5
Carazo, J.M.6
Svergun, D.I.7
Valle, M.8
Fersht, A.R.9
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33
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74049134920
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Ku and DNA-dependent protein kinase (DNA-PK) dynamic conformations and assembly regulate DNA binding and the initial nonhomologous end joining complex
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