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1
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44849107479
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Synchrotron radiation studies of non-crystalline systems
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Koch M.H., and Bras W. Synchrotron radiation studies of non-crystalline systems. Ann Rep Prog Chem, Sect C: Phys Chem 104 (2008) 35-80
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(2008)
Ann Rep Prog Chem, Sect C: Phys Chem
, vol.104
, pp. 35-80
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Koch, M.H.1
Bras, W.2
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2
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43949088521
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High-throughput small angle X-ray scattering from proteins in solution using a microfluidic front-end
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A 200 nl microfluidic chamber has been developed for high-throughput protein characterization using solution X-ray scattering. A fully automated stream of data collection to low-resolution three-dimensional structure modeling is proposed on the basis of machine learning techniques.
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Toft K.N., Vestergaard B., Nielsen S.S., Snakenborg D., Jeppesen M.G., Jacobsen J.K., Arleth L., and Kutter J.P. High-throughput small angle X-ray scattering from proteins in solution using a microfluidic front-end. Anal Chem 80 (2008) 3648-3654. A 200 nl microfluidic chamber has been developed for high-throughput protein characterization using solution X-ray scattering. A fully automated stream of data collection to low-resolution three-dimensional structure modeling is proposed on the basis of machine learning techniques.
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(2008)
Anal Chem
, vol.80
, pp. 3648-3654
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Toft, K.N.1
Vestergaard, B.2
Nielsen, S.S.3
Snakenborg, D.4
Jeppesen, M.G.5
Jacobsen, J.K.6
Arleth, L.7
Kutter, J.P.8
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3
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35748982423
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Analysis of X-ray and neutron scattering from biomacromolecular solutions
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This article reviews computational approaches developed by the authors' group to obtain ab initio three-dimensional models from solution X-ray or neutron scattering data as well as to construct multi-component structures based on known constituent structures. The programs from this group are highly user friendly and currently most widely used by structural biologists. Many of the programs can incorporate complementary information from other structural techniques.
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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. This article reviews computational approaches developed by the authors' group to obtain ab initio three-dimensional models from solution X-ray or neutron scattering data as well as to construct multi-component structures based on known constituent structures. The programs from this group are highly user friendly and currently most widely used by structural biologists. Many of the programs can incorporate complementary information from other structural techniques.
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(2007)
Curr Opin Struct Biol
, vol.17
, pp. 562-571
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Petoukhov, M.V.1
Svergun, D.I.2
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4
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38349097870
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Structural basis of microtubule severing by the hereditary spastic paraplegia protein spastin
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The hexameric structure model deduced from solution X-ray scattering data allowed the authors to interpret the monomeric crystal structure of the ATPase domain of the AAA ATPase spastin in the context of physiologically relevant hexamer assembly, a common oligomeric state in many AAA ATPases. A molecular mechanism is proposed for sepatin-mediated severing of microtubules, based on the three-dimensional structure model and structure-guided mutagenesis.
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Roll-Mecak A., and Vale R.D. Structural basis of microtubule severing by the hereditary spastic paraplegia protein spastin. Nature 451 (2008) 363-367. The hexameric structure model deduced from solution X-ray scattering data allowed the authors to interpret the monomeric crystal structure of the ATPase domain of the AAA ATPase spastin in the context of physiologically relevant hexamer assembly, a common oligomeric state in many AAA ATPases. A molecular mechanism is proposed for sepatin-mediated severing of microtubules, based on the three-dimensional structure model and structure-guided mutagenesis.
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(2008)
Nature
, vol.451
, pp. 363-367
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Roll-Mecak, A.1
Vale, R.D.2
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5
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33750843407
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Monitoring intermediate filament assembly by small-angle X-ray scattering reveals the molecular architecture of assembly intermediates
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Sokolova A.V., Kreplak L., Wedig T., Mucke N., Svergun D.I., Herrmann H., Aebi U., and Strelkov S.V. Monitoring intermediate filament assembly by small-angle X-ray scattering reveals the molecular architecture of assembly intermediates. Proc Natl Acad Sci U S A 103 (2006) 16206-16211
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(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 16206-16211
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Sokolova, A.V.1
Kreplak, L.2
Wedig, T.3
Mucke, N.4
Svergun, D.I.5
Herrmann, H.6
Aebi, U.7
Strelkov, S.V.8
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6
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33846378082
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Structural characterization of beta-sheeted oligomers formed on the pathway of oxidative prion protein aggregation in vitro
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Redecke L., von Bergen M., Clos J., Konarev P.V., Svergun D.I., Fittschen U.E., Broekaert J.A., Bruns O., Georgieva D., Mandelkow E., et al. Structural characterization of beta-sheeted oligomers formed on the pathway of oxidative prion protein aggregation in vitro. J Struct Biol 157 (2007) 308-320
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(2007)
J Struct Biol
, vol.157
, pp. 308-320
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Redecke, L.1
von Bergen, M.2
Clos, J.3
Konarev, P.V.4
Svergun, D.I.5
Fittschen, U.E.6
Broekaert, J.A.7
Bruns, O.8
Georgieva, D.9
Mandelkow, E.10
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7
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3843074353
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Liquid-chromatography-coupled SAXS for accurate sizing of aggregating proteins
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Mathew E., Mirza A., and Menhart N. Liquid-chromatography-coupled SAXS for accurate sizing of aggregating proteins. J Synchrotron Radiat 11 (2004) 314-318
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(2004)
J Synchrotron Radiat
, vol.11
, pp. 314-318
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Mathew, E.1
Mirza, A.2
Menhart, N.3
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8
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45849129440
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Analysis of self-associating proteins by singular value decomposition of solution scattering data
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Williamson T.E., Craig B.A., Kondrashkina E., Bailey-Kellogg C., and Friedman A.M. Analysis of self-associating proteins by singular value decomposition of solution scattering data. Biophys J 12 (2008) 4906-4923
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(2008)
Biophys J
, vol.12
, pp. 4906-4923
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Williamson, T.E.1
Craig, B.A.2
Kondrashkina, E.3
Bailey-Kellogg, C.4
Friedman, A.M.5
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9
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34247891557
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Structural characterization of flexible proteins using small-angle X-ray scattering
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It describes the ensemble optimization method, which uses genetic algorithm to optimize the fit of an ensemble of protein conformations produced by the Monte Carlo method to an experimental scattering curve. The resulting ensemble represents a set of multiple protein conformations that are likely to co-exist.
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Bernado P., Mylonas E., Petoukhov M.V., Blackledge M., and Svergun D.I. Structural characterization of flexible proteins using small-angle X-ray scattering. J Am Chem Soc 129 (2007) 5656-5664. It describes the ensemble optimization method, which uses genetic algorithm to optimize the fit of an ensemble of protein conformations produced by the Monte Carlo method to an experimental scattering curve. The resulting ensemble represents a set of multiple protein conformations that are likely to co-exist.
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(2007)
J Am Chem Soc
, vol.129
, pp. 5656-5664
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Bernado, P.1
Mylonas, E.2
Petoukhov, M.V.3
Blackledge, M.4
Svergun, D.I.5
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10
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38549146411
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Structural characterization of the active and inactive states of Src kinase in solution by small-angle X-ray scattering
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Bernado P., Perez Y., Svergun D.I., and Pons M. Structural characterization of the active and inactive states of Src kinase in solution by small-angle X-ray scattering. J Mol Biol 376 (2008) 492-505
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(2008)
J Mol Biol
, vol.376
, pp. 492-505
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Bernado, P.1
Perez, Y.2
Svergun, D.I.3
Pons, M.4
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11
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34249894142
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Small-angle X-ray scattering from RNA, proteins, and protein complexes
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This article reviews the use of solution X-ray scattering in characterizing nucleic acid folding intermediates and unfolded proteins. It also discusses limitations in three-dimensional reconstruction techniques as well as challenges in dealing with protein-detergent complexes.
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Lipfert J., and Doniach S. Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu Rev Biophys Biomol Struct 36 (2007) 307-327. This article reviews the use of solution X-ray scattering in characterizing nucleic acid folding intermediates and unfolded proteins. It also discusses limitations in three-dimensional reconstruction techniques as well as challenges in dealing with protein-detergent complexes.
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(2007)
Annu Rev Biophys Biomol Struct
, vol.36
, pp. 307-327
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Lipfert, J.1
Doniach, S.2
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12
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33845562408
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Conformational preference of polyglycine in solution to elongated structure
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Ohnishi S., Kamikubo H., Onitsuka M., Kataoka M., and Shortle D. Conformational preference of polyglycine in solution to elongated structure. J Am Chem Soc 128 (2006) 16338-16344
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J Am Chem Soc
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, pp. 16338-16344
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Ohnishi, S.1
Kamikubo, H.2
Onitsuka, M.3
Kataoka, M.4
Shortle, D.5
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13
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53249149553
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Lee KK, Gan L, Tsuruta H, Moyer C, Conway JF, Duda RL, Hendrix RW, Steven AC, Johnson JE: Global capsid expansion during virus maturation is driven by the local capture of dynamic surface loops. Structure 2008, in press.
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Lee KK, Gan L, Tsuruta H, Moyer C, Conway JF, Duda RL, Hendrix RW, Steven AC, Johnson JE: Global capsid expansion during virus maturation is driven by the local capture of dynamic surface loops. Structure 2008, in press. The combination of time-resolved X-ray scattering and the kinetics of auto-catalytic inter-subunit crosslinking revealed the molecular mechanism of bacterophage HK97 maturation, based on the cryo-electron microscopy and crystallographic structures of the initial and final maturation states of HK97. The remarkably cooperative structural transition points to the crucial role of E-loop which transverse from an initial 'up' position to a cross-link ready 'down' position while maintaining the global icosahedral subunit symmetry.
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14
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40849145295
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Assembly and disassembly dynamics of the cyanobacterial periodosome
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The key protein complexes in circadian clocks of a cyanobacterium have recently been studied in time-resolved fashion. Mixing of two or three Kai protein components exhibits oscillations between two binary complexes of different sizes in exact 24 h periodicity. The observed phase shift between the assembly oscillation and protein phosphorylation is ascribed to the oscillation between a kinetically favored binary complex and a thermodynamically favored one. X-ray scattering profiles of the binary protein complexes have been numerically extracted from X-ray scattering of mixed populations and binary complex structure models are proposed, which are consistent with component crystal structures as well as biochemical data.
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Akiyama S., Nohara A., Ito K., and Maeda Y. Assembly and disassembly dynamics of the cyanobacterial periodosome. Mol Cell 29 (2008) 703-716. The key protein complexes in circadian clocks of a cyanobacterium have recently been studied in time-resolved fashion. Mixing of two or three Kai protein components exhibits oscillations between two binary complexes of different sizes in exact 24 h periodicity. The observed phase shift between the assembly oscillation and protein phosphorylation is ascribed to the oscillation between a kinetically favored binary complex and a thermodynamically favored one. X-ray scattering profiles of the binary protein complexes have been numerically extracted from X-ray scattering of mixed populations and binary complex structure models are proposed, which are consistent with component crystal structures as well as biochemical data.
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(2008)
Mol Cell
, vol.29
, pp. 703-716
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Akiyama, S.1
Nohara, A.2
Ito, K.3
Maeda, Y.4
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15
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33845218265
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Probing fast kinetics in complex fluids by combined rapid mixing and small-angle X-ray scattering
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Panine P., Finet S., Weiss T.M., and Narayanan T. Probing fast kinetics in complex fluids by combined rapid mixing and small-angle X-ray scattering. Adv Colloid Interface Sci 127 (2006) 9-18
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(2006)
Adv Colloid Interface Sci
, vol.127
, pp. 9-18
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Panine, P.1
Finet, S.2
Weiss, T.M.3
Narayanan, T.4
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16
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54249099898
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West JM, Xia J, Tsuruta H, Guo W, O'Day EM, Kantrowitz ER: Time Evolution of the Quaternary Structure of Escherichia coli Aspartate Transcarbamoylase upon Reaction with the Natural Substrates and a Slow Tight Bindign Inhibitor. J Mol Biol 2008, in press.
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West JM, Xia J, Tsuruta H, Guo W, O'Day EM, Kantrowitz ER: Time Evolution of the Quaternary Structure of Escherichia coli Aspartate Transcarbamoylase upon Reaction with the Natural Substrates and a Slow Tight Bindign Inhibitor. J Mol Biol 2008, in press.
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17
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32344442512
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Molecular dimensions and their distributions in early folding intermediates
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This is a comprehensive review of the use of solution X-ray scattering, in particular time-resolved experiments, and other complementary physical methods in the studies on early protein folding intermediates.
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Bilsel O., and Matthews C.R. Molecular dimensions and their distributions in early folding intermediates. Curr Opin Struct Biol 16 (2006) 86-93. This is a comprehensive review of the use of solution X-ray scattering, in particular time-resolved experiments, and other complementary physical methods in the studies on early protein folding intermediates.
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(2006)
Curr Opin Struct Biol
, vol.16
, pp. 86-93
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Bilsel, O.1
Matthews, C.R.2
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18
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28844509318
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Concordant exploration of the kinetics of RNA folding from global and local perspectives
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2+-mediated folding of a Tetrahymena ribozyme in the time scale of a millisecond to hundreds of seconds. Two-stage compaction was observed. Time-resolved hydroxyl radical foot-printing analysis was used to examine the role of long-range tertiary contacts among different structural domains.
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2+-mediated folding of a Tetrahymena ribozyme in the time scale of a millisecond to hundreds of seconds. Two-stage compaction was observed. Time-resolved hydroxyl radical foot-printing analysis was used to examine the role of long-range tertiary contacts among different structural domains.
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(2006)
J Mol Biol
, vol.355
, pp. 282-293
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Kwok, L.W.1
Shcherbakova, I.2
Lamb, J.S.3
Park, H.Y.4
Andresen, K.5
Smith, H.6
Brenowitz, M.7
Pollack, L.8
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19
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33947315248
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Microsecond hydrophobic collapse in the folding of Escherichia coli dihydrofolate reductase, an alpha/beta-type protein
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Arai M., Kondrashkina E., Kayatekin C., Matthews C.R., Iwakura M., and Bilsel O. Microsecond hydrophobic collapse in the folding of Escherichia coli dihydrofolate reductase, an alpha/beta-type protein. J Mol Biol 368 (2007) 219-229
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(2007)
J Mol Biol
, vol.368
, pp. 219-229
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Arai, M.1
Kondrashkina, E.2
Kayatekin, C.3
Matthews, C.R.4
Iwakura, M.5
Bilsel, O.6
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20
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35148879631
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Detection of functional ligand-binding events using synchrotron X-ray scattering
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Rodi D.J., Mandava S., Gore D.B., Makowski L., and Fischetti R.F. Detection of functional ligand-binding events using synchrotron X-ray scattering. J Biomol Screen 12 (2007) 994-998
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(2007)
J Biomol Screen
, vol.12
, pp. 994-998
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Rodi, D.J.1
Mandava, S.2
Gore, D.B.3
Makowski, L.4
Fischetti, R.F.5
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21
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36549080494
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Molecular crowding inhibits intramolecular breathing motions in proteins
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This article examines the spatial scale of protein conformational fluctuations using solution X-ray scattering data recorded up to the Bragg spacing of 2.5 Å. Their computational modeling shows that rigid-body motions of secondary structures are consistent with the degree of fluctuations. The authors provide evidence for suppressed conformational fluctuations at high protein concentration, depending on tertiary or quaternary structures of the protein.
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Makowski L., Rodi D.J., Mandava S., Minh D.D., Gore D.B., and Fischetti R.F. Molecular crowding inhibits intramolecular breathing motions in proteins. J Mol Biol 375 (2008) 529-546. This article examines the spatial scale of protein conformational fluctuations using solution X-ray scattering data recorded up to the Bragg spacing of 2.5 Å. Their computational modeling shows that rigid-body motions of secondary structures are consistent with the degree of fluctuations. The authors provide evidence for suppressed conformational fluctuations at high protein concentration, depending on tertiary or quaternary structures of the protein.
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(2008)
J Mol Biol
, vol.375
, pp. 529-546
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Makowski, L.1
Rodi, D.J.2
Mandava, S.3
Minh, D.D.4
Gore, D.B.5
Fischetti, R.F.6
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22
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11844289660
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Resolving conflicting crystallographic and NMR models for solution-state DNA with solution X-ray diffraction
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Zuo X., and Tiede D.M. Resolving conflicting crystallographic and NMR models for solution-state DNA with solution X-ray diffraction. J Am Chem Soc 127 (2005) 16-17
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(2005)
J Am Chem Soc
, vol.127
, pp. 16-17
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Zuo, X.1
Tiede, D.M.2
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23
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33644861376
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X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation
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DNA oligomer structures generated by molecular dynamics simulations were examined on the basis of experimental solution X-ray scattering profiles. Scattering maxima in the Bragg spacing range between 3 and 15 Å are shown highly sensitive to base pair stacking as well as sugar-phosphate backbone structures. Discrepancies between experimental and theoretical scattering profiles suggest that the molecular dynamics force field is biased by short-range interactions while X-ray scattering reflects global structure as well.
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Zuo X., Cui G., Merz Jr. K.M., Zhang L., Lewis F.D., and Tiede D.M. X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation. Proc Natl Acad Sci U S A 103 (2006) 3534-3539. DNA oligomer structures generated by molecular dynamics simulations were examined on the basis of experimental solution X-ray scattering profiles. Scattering maxima in the Bragg spacing range between 3 and 15 Å are shown highly sensitive to base pair stacking as well as sugar-phosphate backbone structures. Discrepancies between experimental and theoretical scattering profiles suggest that the molecular dynamics force field is biased by short-range interactions while X-ray scattering reflects global structure as well.
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(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 3534-3539
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Zuo, X.1
Cui, G.2
Merz Jr., K.M.3
Zhang, L.4
Lewis, F.D.5
Tiede, D.M.6
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24
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4143088433
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Ageing and vision: structure, stability and function of lens crystallins
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This is a highly comprehensive review of properties and structures of crystallines. Chapter 4 is dedicated to the crystalline intermolecular interactions that lead to eye transparency, which was first demonstrated by an X-ray scattering study by Delaye and Tardieu in 1983.
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Bloemendal H., de Jong W., Jaenicke R., Lubsen N.H., Slingsby C., and Tardieu A. Ageing and vision: structure, stability and function of lens crystallins. Prog Biophys Mol Biol 86 (2004) 407-485. This is a highly comprehensive review of properties and structures of crystallines. Chapter 4 is dedicated to the crystalline intermolecular interactions that lead to eye transparency, which was first demonstrated by an X-ray scattering study by Delaye and Tardieu in 1983.
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(2004)
Prog Biophys Mol Biol
, vol.86
, pp. 407-485
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Bloemendal, H.1
de Jong, W.2
Jaenicke, R.3
Lubsen, N.H.4
Slingsby, C.5
Tardieu, A.6
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26
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34547292656
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Induced long-range attractive potentials of human serum albumin by ligand binding
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Sato T., Komatsu T., Nakagawa A., and Tsuchida E. Induced long-range attractive potentials of human serum albumin by ligand binding. Phys Rev Lett 98 (2007) 208101
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(2007)
Phys Rev Lett
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, pp. 208101
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Sato, T.1
Komatsu, T.2
Nakagawa, A.3
Tsuchida, E.4
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27
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45449090418
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Complementing structural information of modular proteins with small angle neutron scattering and contrast variation
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Grossmann J.G., Callaghan A.J., Marcaida M.J., Luisi B.F., Alcock F.H., and Tokatlidis K. Complementing structural information of modular proteins with small angle neutron scattering and contrast variation. Eur Biophys J 37 (2008) 603-611
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Eur Biophys J
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, pp. 603-611
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Grossmann, J.G.1
Callaghan, A.J.2
Marcaida, M.J.3
Luisi, B.F.4
Alcock, F.H.5
Tokatlidis, K.6
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28
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33748539706
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Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution
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Petoukhov M.V., and Svergun D.I. Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution. Eur Biophys J 35 (2006) 567-576
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Eur Biophys J
, vol.35
, pp. 567-576
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Petoukhov, M.V.1
Svergun, D.I.2
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29
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38349018735
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Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints
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2 value was included in the NMR refinement process as a pseudo energy term in CNS, following initial RDC and RCSA refinements. The resulting solution NMR structure of the 82 kDa enzyme malate synthase G demonstrated an improved accuracy by a smaller backbone rmsd value between the derived model and crystal structure: 3.3 vs. 4.5 Å without the SAXS refinement.
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2 value was included in the NMR refinement process as a pseudo energy term in CNS, following initial RDC and RCSA refinements. The resulting solution NMR structure of the 82 kDa enzyme malate synthase G demonstrated an improved accuracy by a smaller backbone rmsd value between the derived model and crystal structure: 3.3 vs. 4.5 Å without the SAXS refinement.
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(2008)
J Biomol NMR
, vol.40
, pp. 95-106
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Grishaev, A.1
Tugarinov, V.2
Kay, L.E.3
Trewhella, J.4
Bax, A.5
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30
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33746427173
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Macromolecular envelope determination and envelope-based phasing
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Hao Q. Macromolecular envelope determination and envelope-based phasing. Acta Crystallogr D Biol Crystallogr 62 (2006) 909-914
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Acta Crystallogr D Biol Crystallogr
, vol.62
, pp. 909-914
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Hao, Q.1
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36349016373
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The regulatory SCR-1/5 and cell surface-binding SCR-16/20 fragments of factor H reveal partially folded-back solution structures and different self-associative properties
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Okemefuna A.I., Gilbert H.E., Griggs K.M., Ormsby R.J., Gordon D.L., and Perkins S.J. The regulatory SCR-1/5 and cell surface-binding SCR-16/20 fragments of factor H reveal partially folded-back solution structures and different self-associative properties. J Mol Biol 375 (2008) 80-101
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(2008)
J Mol Biol
, vol.375
, pp. 80-101
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Okemefuna, A.I.1
Gilbert, H.E.2
Griggs, K.M.3
Ormsby, R.J.4
Gordon, D.L.5
Perkins, S.J.6
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32
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51249118082
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Integration of small angle X-ray scattering data into structural modeling of proteins and assemblies
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Förster F., Webb B., Krukenberg K.A., Tsuruta H., Agard D.A., and Sali A. Integration of small angle X-ray scattering data into structural modeling of proteins and assemblies. J Mol Biol 382 (2008) 1089-1106
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J Mol Biol
, vol.382
, pp. 1089-1106
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Förster, F.1
Webb, B.2
Krukenberg, K.A.3
Tsuruta, H.4
Agard, D.A.5
Sali, A.6
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33
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23944515334
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Wheat streak mosaic virus-structural parameters for a Potyvirus
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Parker L., Kendall A., Berger P.H., Shiel P.J., and Stubbs G. Wheat streak mosaic virus-structural parameters for a Potyvirus. Virology 340 (2005) 64-69
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(2005)
Virology
, vol.340
, pp. 64-69
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Parker, L.1
Kendall, A.2
Berger, P.H.3
Shiel, P.J.4
Stubbs, G.5
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0344443362
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Crystal structure and hydrogen bonding system in cellulose I(alpha) from synchrotron X-ray and neutron fiber diffraction
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Nishiyama Y., Sugiyama J., Chanzy H., and Langan P. Crystal structure and hydrogen bonding system in cellulose I(alpha) from synchrotron X-ray and neutron fiber diffraction. J Am Chem Soc 125 (2003) 14300-14306
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(2003)
J Am Chem Soc
, vol.125
, pp. 14300-14306
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Nishiyama, Y.1
Sugiyama, J.2
Chanzy, H.3
Langan, P.4
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35
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33749076838
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Recent improvements in small angle X-ray diffraction for the study of muscle physiology
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A review of recent applications of X-ray diffraction for understanding muscle physiology including a thorough explanation of the interferometric technique for measuring axial motions in crossbridges in working muscle.
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Reconditi M. Recent improvements in small angle X-ray diffraction for the study of muscle physiology. Reports on Progress in Physics 69 (2006) 2709-2759. A review of recent applications of X-ray diffraction for understanding muscle physiology including a thorough explanation of the interferometric technique for measuring axial motions in crossbridges in working muscle.
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(2006)
Reports on Progress in Physics
, vol.69
, pp. 2709-2759
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Reconditi, M.1
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36
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36148935250
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Skeletal muscle performance determined by modulation of number of myosin motors rather than motor force or stroke size
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This paper provides a molecular level explanation for one of the most fundamental phenomena in muscle physiology, the force/velocity curve requiring a rethinking of the conventional view that had been in place for over 30 years.
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Piazzesi G., Reconditi M., Linari M., Lucii L., Bianco P., Brunello E., Decostre V., Stewart A., Gore D.B., Irving T.C., et al. Skeletal muscle performance determined by modulation of number of myosin motors rather than motor force or stroke size. Cell 131 (2007) 784-795. This paper provides a molecular level explanation for one of the most fundamental phenomena in muscle physiology, the force/velocity curve requiring a rethinking of the conventional view that had been in place for over 30 years.
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(2007)
Cell
, vol.131
, pp. 784-795
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Piazzesi, G.1
Reconditi, M.2
Linari, M.3
Lucii, L.4
Bianco, P.5
Brunello, E.6
Decostre, V.7
Stewart, A.8
Gore, D.B.9
Irving, T.C.10
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37
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12744261252
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Molecular dynamics of cyclically contracting insect flight muscle in vivo
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Dickinson M., Farman G., Frye M., Bekyarova T., Gore D., Maughan D., and Irving T. Molecular dynamics of cyclically contracting insect flight muscle in vivo. Nature 433 (2005) 330-334
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(2005)
Nature
, vol.433
, pp. 330-334
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Dickinson, M.1
Farman, G.2
Frye, M.3
Bekyarova, T.4
Gore, D.5
Maughan, D.6
Irving, T.7
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38
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3042608195
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In situ measurements of crossbridge dynamics and lattice spacing in rat hearts by X-ray diffraction: sensitivity to regional ischemia
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This is one of a series of papers where the high flux, high beam quality from third generation sources have allowed measurements of muscle function in vivo in beating hearts. Together with Dickinson et al. [37], they show that X-ray diffraction now can be used to obtain useful structural parameters that could not be obtained any other way, under truly physiological conditions.
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Pearson J.T., Shirai M., Ito H., Tokunaga N., Tsuchimochi H., Nishiura N., Schwenke D.O., Ishibashi-Ueda H., Akiyama R., Mori H., et al. In situ measurements of crossbridge dynamics and lattice spacing in rat hearts by X-ray diffraction: sensitivity to regional ischemia. Circulation 109 (2004) 2976-2979. This is one of a series of papers where the high flux, high beam quality from third generation sources have allowed measurements of muscle function in vivo in beating hearts. Together with Dickinson et al. [37], they show that X-ray diffraction now can be used to obtain useful structural parameters that could not be obtained any other way, under truly physiological conditions.
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(2004)
Circulation
, vol.109
, pp. 2976-2979
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Pearson, J.T.1
Shirai, M.2
Ito, H.3
Tokunaga, N.4
Tsuchimochi, H.5
Nishiura, N.6
Schwenke, D.O.7
Ishibashi-Ueda, H.8
Akiyama, R.9
Mori, H.10
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39
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33646439760
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Evolution of long-range myofibrillar crystallinity in insect flight muscle as examined by X-ray cryomicrodiffraction
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A technically impressive paper that required ground-breaking work in techniques of cryo-preservation, sample manipulation and micro-beam diffraction to obtain 'end-on' diffraction patterns from a range of insect muscles.
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Iwamoto H., Inoue K., and Yagi N. Evolution of long-range myofibrillar crystallinity in insect flight muscle as examined by X-ray cryomicrodiffraction. Proc Biol Sci 273 (2006) 677-685. A technically impressive paper that required ground-breaking work in techniques of cryo-preservation, sample manipulation and micro-beam diffraction to obtain 'end-on' diffraction patterns from a range of insect muscles.
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(2006)
Proc Biol Sci
, vol.273
, pp. 677-685
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Iwamoto, H.1
Inoue, K.2
Yagi, N.3
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40
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33745181159
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Microfibrillar structure of type I collagen in situ
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The authors used multiple isomorphous replacements to solve crystallographically the supermolecular packing structure of collagen type I in its natural fibrous form at a level where the molecular conformation of each collagen segment is defined in the very large unit cell. This structure paves the way to a molecular understanding of the action of collagen binding proteins such as decorin and the Matrix Metallo-Proteinase (MMP) collagenase.
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Orgel J.P., Irving T.C., Miller A., and Wess T.J. Microfibrillar structure of type I collagen in situ. Proc Natl Acad Sci U S A 103 (2006) 9001-9005. The authors used multiple isomorphous replacements to solve crystallographically the supermolecular packing structure of collagen type I in its natural fibrous form at a level where the molecular conformation of each collagen segment is defined in the very large unit cell. This structure paves the way to a molecular understanding of the action of collagen binding proteins such as decorin and the Matrix Metallo-Proteinase (MMP) collagenase.
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(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 9001-9005
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Orgel, J.P.1
Irving, T.C.2
Miller, A.3
Wess, T.J.4
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41
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33845199750
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Cooperative deformation of mineral and collagen in bone at the nanoscale
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This paper is an excellent example of how X-ray diffraction on third generation sources can be used to provide a structural explanation for the physical properties of a complex biological material, in this case, bone. We can expect that the study of naturally occurring and synthetic biomaterials will become even more important in future.
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Gupta H.S., Seto J., Wagermaier W., Zaslansky P., Boesecke P., and Fratzl P. Cooperative deformation of mineral and collagen in bone at the nanoscale. Proc Natl Acad Sci U S A 103 (2006) 17741-17746. This paper is an excellent example of how X-ray diffraction on third generation sources can be used to provide a structural explanation for the physical properties of a complex biological material, in this case, bone. We can expect that the study of naturally occurring and synthetic biomaterials will become even more important in future.
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(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 17741-17746
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Gupta, H.S.1
Seto, J.2
Wagermaier, W.3
Zaslansky, P.4
Boesecke, P.5
Fratzl, P.6
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42
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0347659487
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X-ray diffraction of the molecular substructure of human articular cartilage
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Mollenhauer J., Aurich M., Muehleman C., Khelashvilli G., and Irving T.C. X-ray diffraction of the molecular substructure of human articular cartilage. Connect Tissue Res 44 (2003) 201-207
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(2003)
Connect Tissue Res
, vol.44
, pp. 201-207
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Mollenhauer, J.1
Aurich, M.2
Muehleman, C.3
Khelashvilli, G.4
Irving, T.C.5
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43
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37349124728
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Collagen organization in the chicken cornea and structural alterations in the retinopathy, globe enlarged (rge) phenotype--an X-ray diffraction study
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Boote C., Hayes S., Jones S., Quantock A.J., Hocking P.M., Inglehearn C.F., Ali M., and Meek K.M. Collagen organization in the chicken cornea and structural alterations in the retinopathy, globe enlarged (rge) phenotype--an X-ray diffraction study. J Struct Biol 161 (2008) 1-8
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(2008)
J Struct Biol
, vol.161
, pp. 1-8
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Boote, C.1
Hayes, S.2
Jones, S.3
Quantock, A.J.4
Hocking, P.M.5
Inglehearn, C.F.6
Ali, M.7
Meek, K.M.8
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45
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25444496697
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Helix-turn-helix peptides that form alpha-helical fibrils: turn sequences drive fibril structure
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This paper shows that a very short amino acid sequence in a strategic part of the peptide could induce the fibrilogenesis of α-helical-based fibers including a previously not observed 'cross-α' fibril structure, that is, fibrilogenesis is not exclusively due to cross-β structures as is widely assumed.
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Lazar K.L., Miller-Auer H., Getz G.S., Orgel J.P., and Meredith S.C. Helix-turn-helix peptides that form alpha-helical fibrils: turn sequences drive fibril structure. Biochemistry 44 (2005) 12681-12689. This paper shows that a very short amino acid sequence in a strategic part of the peptide could induce the fibrilogenesis of α-helical-based fibers including a previously not observed 'cross-α' fibril structure, that is, fibrilogenesis is not exclusively due to cross-β structures as is widely assumed.
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(2005)
Biochemistry
, vol.44
, pp. 12681-12689
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Lazar, K.L.1
Miller-Auer, H.2
Getz, G.S.3
Orgel, J.P.4
Meredith, S.C.5
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46
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33845648545
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X-Ray fiber and powder diffraction of PrP prion peptides
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This comprehensive review provides a good overview of prion biology and how diffraction techniques have contributed to our knowledge of prion structure.
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Inouye H., and Kirschner D.A. X-Ray fiber and powder diffraction of PrP prion peptides. Adv Protein Chem 73 (2006) 181-215. This comprehensive review provides a good overview of prion biology and how diffraction techniques have contributed to our knowledge of prion structure.
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(2006)
Adv Protein Chem
, vol.73
, pp. 181-215
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Inouye, H.1
Kirschner, D.A.2
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47
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33747755522
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A microbeam X-ray diffraction study of insulin spherulites
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This paper provides an excellent demonstration of the utility of microbeam diffraction to obtain structural information from complex biological structures.
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Yagi N., Ohta N., Iida T., and Inoue K. A microbeam X-ray diffraction study of insulin spherulites. J Mol Biol 362 (2006) 327-333. This paper provides an excellent demonstration of the utility of microbeam diffraction to obtain structural information from complex biological structures.
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(2006)
J Mol Biol
, vol.362
, pp. 327-333
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Yagi, N.1
Ohta, N.2
Iida, T.3
Inoue, K.4
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48
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37449014872
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Dose, exposure time and resolution in serial X-ray crystallography
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This paper makes the technical case for using a stream of oriented macromolecules in a high intensity, coherent X-ray beam from either specialized beamlines on third generation sources or upcoming fourth generation sources.
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Starodub D., Rez P., Hembree G., Howells M., Shapiro D., Chapman H.N., Fromme P., Schmidt K., Weierstall U., Doak R.B., et al. Dose, exposure time and resolution in serial X-ray crystallography. J Synchrotron Radiat 15 (2008) 62-73. This paper makes the technical case for using a stream of oriented macromolecules in a high intensity, coherent X-ray beam from either specialized beamlines on third generation sources or upcoming fourth generation sources.
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(2008)
J Synchrotron Radiat
, vol.15
, pp. 62-73
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Starodub, D.1
Rez, P.2
Hembree, G.3
Howells, M.4
Shapiro, D.5
Chapman, H.N.6
Fromme, P.7
Schmidt, K.8
Weierstall, U.9
Doak, R.B.10
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