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Developing advanced X-ray scattering methods combined with crystallography and computation.

Publication Type : Journal Article

Publisher : Methods (San Diego, Calif.)

Source : Methods (San Diego, Calif.), Volume 59, Number 3, p.363-371 (2013)

Url : is external)

Keywords : chemistry, crystallography, Databases, methodology, protein, protein database, protein folding, Proteins, review, Scattering, Small Angle, small angle scattering, X ray diffraction, X-Ray Diffraction

Campus : Amritapuri

School : School of Biotechnology

Center : Biotechnology

Department : biotechnology

Verified : Yes

Year : 2013

Abstract : The extensive use of small angle X-ray scattering (SAXS) over the last few years is rapidly providing new insights into protein interactions, complex formation and conformational states in solution. This SAXS methodology allows for detailed biophysical quantification of samples of interest. Initial analyses provide a judgment of sample quality, revealing the potential presence of aggregation, the overall extent of folding or disorder, the radius of gyration, maximum particle dimensions and oligomerization state. Structural characterizations include ab initio approaches from SAXS data alone, and when combined with previously determined crystal/NMR, atomistic modeling can further enhance structural solutions and assess validity. This combination can provide definitions of architectures, spatial organizations of protein domains within a complex, including those not determined by crystallography or NMR, as well as defining key conformational states of a protein interaction. SAXS is not generally constrained by macromolecule size, and the rapid collection of data in a 96-well plate format provides methods to screen sample conditions. This includes screening for co-factors, substrates, differing protein or nucleotide partners or small molecule inhibitors, to more fully characterize the variations within assembly states and key conformational changes. Such analyses may be useful for screening constructs and conditions to determine those most likely to promote crystal growth of a complex under study. Moreover, these high throughput structural determinations can be leveraged to define how polymorphisms affect assembly formations and activities. This is in addition to potentially providing architectural characterizations of complexes and interactions for systems biology-based research, and distinctions in assemblies and interactions in comparative genomics. Thus, SAXS combined with crystallography/NMR and computation provides a unique set of tools that should be considered as being part of one's repertoire of biophysical analyses, when conducting characterizations of protein and other macromolecular interactions. Copyright © 2013 Elsevier Inc. All rights reserved.

Cite this Research Publication : J. J. Perry and Tainer, J. A., “Developing advanced X-ray scattering methods combined with crystallography and computation.”, Methods (San Diego, Calif.), vol. 59, pp. 363-371, 2013.

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