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Dengue

Volume 1138 of the series Methods in Molecular Biology pp 241-252

Date:

Use of Small-Angle X-ray Scattering to Investigate the Structure and Function of Dengue Virus NS3 and NS5

  • Kyung H. ChoiAffiliated withDepartment of Biochemistry and Molecular Biology, University of Texas Medical Branch Email author 
  • , Marc MoraisAffiliated withDepartment of Biochemistry and Molecular Biology, University of Texas Medical Branch

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Abstract

Small-angle X-ray scattering (SAXS) is a powerful reemerging biophysical technique that can be used to directly analyze many properties related to the size and shape of a macromolecule in solution. For example, the radius of gyration and maximum diameter of a macromolecule can be readily extracted from SAXS data, as can information regarding how well folded a protein is. Similarly, the molecular weight of macromolecular complexes can be directly determined from the complex’s scattering profile, providing insight into the oligomeric state and stoichiometry of the assembly. Furthermore, recently developed procedures for ab initio shape determination can provide low-resolution (~20 Å) molecular envelopes of proteins/complexes in their native state. In conjunction with high-resolution structural data, more sophisticated analysis of SAXS data can help address questions regarding conformational change, molecular flexibility, and populations of states within molecular ensembles. Because SAXS samples are easy to prepare and SAXS data is relatively easy to collect, the technique holds great promise for investigating the structure of macromolecules and their assemblies as well as monitoring and modeling their conformational changes. Here we describe typical steps in SAXS sample preparation and data collection and analysis and provide examples of SAXS analysis to investigate the structure and function of dengue virus NS3 and NS5.

Key words

Small-angle X-ray scattering Ab initio shape determination Radius of gyration Pair-wise distribution function