Difference between revisions of "BioSAXS"
KevinYager (talk | contribs) (→References) |
KevinYager (talk | contribs) (→References) |
||
| (5 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
'''BioSAXS''' refers to the use of small-angle [[x-ray]] [[scattering]] ([[SAXS]]) to probe biologically-relevant systems, such as proteins (or protein aggregates) in solution. | '''BioSAXS''' refers to the use of small-angle [[x-ray]] [[scattering]] ([[SAXS]]) to probe biologically-relevant systems, such as proteins (or protein aggregates) in solution. | ||
| + | |||
| + | Unlike [[crystallography]] or [[diffraction]] experiments, BioSAXS experiments typically do not generate distinct [[Bragg peaks]] or rings. Instead, a smooth decay of scattering intensity is observed at small scattering angles (which may look like [[diffuse scattering]]). However, with appropriate modeling, the specific form of this intensity decay can be fit in order to extract parameters of physical interest, including: | ||
| + | * Radius of gyration, or molecular weight, of macromolecules (including proteins) | ||
| + | * Particle shape (at low resolution) | ||
| + | * Inter-particle distances | ||
| + | * Aggregation or [[Kratky plot|conformational]] state of macromolecules (degree of folding, denaturation, disorder) | ||
==References== | ==References== | ||
| + | * Svergun, D. I. and M. H. J. Koch [http://iopscience.iop.org/0034-4885/66/10/R05/ Small-angle scattering studies of biological macromolecules in solution] ''Reports on Progress in Physics'' '''2003''', 66(10), 1735-1782. [http://dx.doi.org/10.1088/0034-4885/66/10/R05 doi: 10.1088/0034-4885/66/10/R05] | ||
| + | * Putnam, C. D., M. Hammel, et al. [http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=1581636&fileId=S0033583507004635 X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution] ''Quarterly Reviews of Biophysics'' '''2007''', 40(3), 191-285. [http://dx.doi.org/10.1017/S0033583507004635 doi: 10.1017/S0033583507004635] | ||
| + | * Mertens, H. D. T. and D. I. Svergun [http://www.sciencedirect.com/science/article/pii/S1047847710001905 Structural characterization of proteins and complexes using small-angle X-ray solution scattering] ''Journal of Structural Biology'' '''2010''', 172(1), 128-141. [http://dx.doi.org/10.1016/j.jsb.2010.06.012 doi: 10.1016/j.jsb.2010.06.012] | ||
| + | * Jacques, D. A. and J. Trewhella [http://onlinelibrary.wiley.com/doi/10.1002/pro.351/abstract;jsessionid=A09814CA57DE7CB1577442B2923C1C9E.f01t04 Small-angle scattering for structural biology — Expanding the frontier while avoiding the pitfalls] ''Protein Science'' '''2010''', 19(4), 642-657. [http://dx.doi.org/10.1002/pro.351 doi: 10.1002/pro.351] | ||
| + | * Nielsen, S. S., Moller, M. & Gillilan, R. E. [http://journals.iucr.org/j/issues/2012/02/00/issconts.html High-throughput biological small-angle X-ray scattering with a robotically loaded capillary cell] ''J. Appl. Cryst.'' '''2012''', 45, 213-223. [http://dx.doi.org/10.1107/S0021889812000957 doi: 10.1107/S0021889812000957] | ||
| + | * D. A. Jacques, J. M. Guss, D. I. Svergun and J. Trewhella [http://scripts.iucr.org/cgi-bin/paper?S0907444912012073 Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution] ''Acta Cryst.'' '''2012''' D68, 620-626 [http://dx.doi.org/10.1107/S0907444912012073 doi: 10.1107/S0907444912012073] | ||
| + | * Clement E. Blanchet and Dmitri I. Svergun [http://www.annualreviews.org/doi/abs/10.1146/annurev-physchem-040412-110132 Small-Angle X-Ray Scattering on Biological Macromolecules and Nanocomposites in Solution] ''Annual Review of Physical Chemistry'' '''2013''', 64, 37-54. [http://dx.doi.org/10.1146/annurev-physchem-040412-110132 doi: 10.1146/annurev-physchem-040412-110132] | ||
| + | * Sichun Yang [http://onlinelibrary.wiley.com/doi/10.1002/adma.201304475/full Methods for SAXS-Based Structure Determination of Biomolecular Complexes] ''Advanced Materials'' '''2014''', 26 (46), 7902–7910. [http://dx.doi.org/10.1002/adma.201304475 doi: 10.1002/adma.201304475] | ||
* Kevin N. Dyer, Michal Hammel, Robert P. Rambo, Susan E. Tsutakawa, Ivan Rodic, Scott Classen, John A. Tainer, Greg L. Hura [http://link.springer.com/protocol/10.1007%2F978-1-62703-691-7_18 High-Throughput SAXS for the Characterization of Biomolecules in Solution: A Practical Approach] ''Methods in Molecular Biology'' '''2014''', 1091, 245-258 [http://dx.doi.org/10.1007/978-1-62703-691-7_18 10.1007/978-1-62703-691-7_18] | * Kevin N. Dyer, Michal Hammel, Robert P. Rambo, Susan E. Tsutakawa, Ivan Rodic, Scott Classen, John A. Tainer, Greg L. Hura [http://link.springer.com/protocol/10.1007%2F978-1-62703-691-7_18 High-Throughput SAXS for the Characterization of Biomolecules in Solution: A Practical Approach] ''Methods in Molecular Biology'' '''2014''', 1091, 245-258 [http://dx.doi.org/10.1007/978-1-62703-691-7_18 10.1007/978-1-62703-691-7_18] | ||
* Soren Skou, Richard E Gillilan & Nozomi Ando [http://www.nature.com/nprot/journal/v9/n7/full/nprot.2014.116.html Synchrotron-based small-angle X-ray scattering of proteins in solution] ''Nature Protocols'' '''2014''', 9, 1727-1739 [http://dx.doi.org/10.1038/nprot.2014.116 doi: 10.1038/nprot.2014.116] | * Soren Skou, Richard E Gillilan & Nozomi Ando [http://www.nature.com/nprot/journal/v9/n7/full/nprot.2014.116.html Synchrotron-based small-angle X-ray scattering of proteins in solution] ''Nature Protocols'' '''2014''', 9, 1727-1739 [http://dx.doi.org/10.1038/nprot.2014.116 doi: 10.1038/nprot.2014.116] | ||
* Lachlan W. Casey, Alan E. Mark and Bostjan Kobe [http://www.publish.csiro.au/paper/CH14396.htm Small-Angle X-Ray Scattering for the Discerning Macromolecular Crystallographer] ''Australian Journal of Chemistry'' '''2014''', 67 (12) 1786-1792 [http://dx.doi.org/10.1071/CH14396 doi: 10.1071/CH14396] | * Lachlan W. Casey, Alan E. Mark and Bostjan Kobe [http://www.publish.csiro.au/paper/CH14396.htm Small-Angle X-Ray Scattering for the Discerning Macromolecular Crystallographer] ''Australian Journal of Chemistry'' '''2014''', 67 (12) 1786-1792 [http://dx.doi.org/10.1071/CH14396 doi: 10.1071/CH14396] | ||
| − | |||
* Bente Vestergaarda and Zehra Sayersb [http://journals.iucr.org/m/issues/2014/06/00/tj5006/index.html Investigating increasingly complex macromolecular systems with small-angle X-ray scattering] ''IUCrJ'' '''2014''', 1 (6), 523-529 [http://dx.doi.org/10.1107/S2052252514020843 doi: 10.1107/S2052252514020843] | * Bente Vestergaarda and Zehra Sayersb [http://journals.iucr.org/m/issues/2014/06/00/tj5006/index.html Investigating increasingly complex macromolecular systems with small-angle X-ray scattering] ''IUCrJ'' '''2014''', 1 (6), 523-529 [http://dx.doi.org/10.1107/S2052252514020843 doi: 10.1107/S2052252514020843] | ||
| + | |||
| + | ==See Also== | ||
| + | * [[Software#BioSAXS|BioSAXS Software]] | ||
| + | * [http://www.macchess.cornell.edu/MacCHESS/biosaxs_whatis.html CHESS guide to BioSAXS] | ||
| + | * [http://bl1231.als.lbl.gov/saxs_protocols/saxs_data_collection_evaluatio.php SIBYLS beamline (ALS) BioSAXS workflow] | ||
| + | * [http://bioisis.net/tutorial BIOISIS (ALS) tutorial] | ||
| + | * [http://www.oumedicine.com/docs/default-source/peds-hem-onc-workfiles/small-angle-scattering-links.html?sfvrsn=0 BioSAXS Links] | ||
Latest revision as of 15:36, 4 February 2015
BioSAXS refers to the use of small-angle x-ray scattering (SAXS) to probe biologically-relevant systems, such as proteins (or protein aggregates) in solution.
Unlike crystallography or diffraction experiments, BioSAXS experiments typically do not generate distinct Bragg peaks or rings. Instead, a smooth decay of scattering intensity is observed at small scattering angles (which may look like diffuse scattering). However, with appropriate modeling, the specific form of this intensity decay can be fit in order to extract parameters of physical interest, including:
- Radius of gyration, or molecular weight, of macromolecules (including proteins)
- Particle shape (at low resolution)
- Inter-particle distances
- Aggregation or conformational state of macromolecules (degree of folding, denaturation, disorder)
References
- Svergun, D. I. and M. H. J. Koch Small-angle scattering studies of biological macromolecules in solution Reports on Progress in Physics 2003, 66(10), 1735-1782. doi: 10.1088/0034-4885/66/10/R05
- Putnam, C. D., M. Hammel, et al. X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution Quarterly Reviews of Biophysics 2007, 40(3), 191-285. doi: 10.1017/S0033583507004635
- Mertens, H. D. T. and D. I. Svergun Structural characterization of proteins and complexes using small-angle X-ray solution scattering Journal of Structural Biology 2010, 172(1), 128-141. doi: 10.1016/j.jsb.2010.06.012
- Jacques, D. A. and J. Trewhella Small-angle scattering for structural biology — Expanding the frontier while avoiding the pitfalls Protein Science 2010, 19(4), 642-657. doi: 10.1002/pro.351
- Nielsen, S. S., Moller, M. & Gillilan, R. E. High-throughput biological small-angle X-ray scattering with a robotically loaded capillary cell J. Appl. Cryst. 2012, 45, 213-223. doi: 10.1107/S0021889812000957
- D. A. Jacques, J. M. Guss, D. I. Svergun and J. Trewhella Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution Acta Cryst. 2012 D68, 620-626 doi: 10.1107/S0907444912012073
- Clement E. Blanchet and Dmitri I. Svergun Small-Angle X-Ray Scattering on Biological Macromolecules and Nanocomposites in Solution Annual Review of Physical Chemistry 2013, 64, 37-54. doi: 10.1146/annurev-physchem-040412-110132
- Sichun Yang Methods for SAXS-Based Structure Determination of Biomolecular Complexes Advanced Materials 2014, 26 (46), 7902–7910. doi: 10.1002/adma.201304475
- Kevin N. Dyer, Michal Hammel, Robert P. Rambo, Susan E. Tsutakawa, Ivan Rodic, Scott Classen, John A. Tainer, Greg L. Hura High-Throughput SAXS for the Characterization of Biomolecules in Solution: A Practical Approach Methods in Molecular Biology 2014, 1091, 245-258 10.1007/978-1-62703-691-7_18
- Soren Skou, Richard E Gillilan & Nozomi Ando Synchrotron-based small-angle X-ray scattering of proteins in solution Nature Protocols 2014, 9, 1727-1739 doi: 10.1038/nprot.2014.116
- Lachlan W. Casey, Alan E. Mark and Bostjan Kobe Small-Angle X-Ray Scattering for the Discerning Macromolecular Crystallographer Australian Journal of Chemistry 2014, 67 (12) 1786-1792 doi: 10.1071/CH14396
- Bente Vestergaarda and Zehra Sayersb Investigating increasingly complex macromolecular systems with small-angle X-ray scattering IUCrJ 2014, 1 (6), 523-529 doi: 10.1107/S2052252514020843
