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X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution

Published online by Cambridge University Press:  14 December 2007

Christopher D. Putnam ,
Michal Hammel ,
Greg L. Hura  and
John A. Tainer
Christopher D. Putnam
Affiliation:
Ludwig Institute for Cancer Research, La Jolla, USA
Michal Hammel
Affiliation:
Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
Greg L. Hura*
Affiliation:
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
John A. Tainer*
Affiliation:
Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA Department of Molecular Biology MB4 and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
*
*G. L. Hura: Tel.: 1 510 486 5378; Fax: 1 510 486 5298; Email: GLHura@lbl.gov
*Correspondence may be addressed to either author:J. A. Tainer: Tel.: 1 858 784 8119; Fax: 1 858 784 2277; Email: jat@scripps.edu
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Abstract

Crystallography supplies unparalleled detail on structural information critical for mechanistic analyses; however, it is restricted to describing low energy conformations of macromolecules within crystal lattices. Small angle X-ray scattering (SAXS) offers complementary information about macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 Å to 10 Å resolution, but without the size limitations inherent in NMR and electron microscopy studies. Together these techniques can allow multi-scale modeling to create complete and accurate images of macromolecules for modeling allosteric mechanisms, supramolecular complexes, and dynamic molecular machines acting in diverse processes ranging from eukaryotic DNA replication, recombination and repair to microbial membrane secretion and assembly systems. This review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high-resolution structures. Detailed aspects of SAXS experimental results are considered with a focus on data interpretation tools suitable to model protein and nucleic acid macromolecular structures, including membrane protein, RNA, DNA, and protein–nucleic acid complexes. The methods discussed provide the basis to examine molecular interactions in solution and to study macromolecular flexibility and conformational changes that have become increasingly relevant for accurate understanding, simulation, and prediction of mechanisms in structural cell biology and nanotechnology.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 40 , Issue 3 , August 2007 , pp. 191 - 285
Copyright
Copyright © Cambridge University Press 2007

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