Hydrodynamic Modeling and Its Application in AUC

Mattia Rocco, Olwyn Byron

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

The hydrodynamic parameters measured in an AUC experiment, s20w and Dt(20,w)0, can be used to gain information on the solution structure of (bio)macromolecules and their assemblies. This entails comparing the measured parameters with those that can be computed from usually "dry" structures by "hydrodynamic modeling." In this chapter, we will first briefly put hydrodynamic modeling in perspective and present the basic physics behind it as implemented in the most commonly used methods. The important "hydration" issue is also touched upon, and the distinction between rigid bodies versus those for which flexibility must be considered in the modeling process is then made. The available hydrodynamic modeling/computation programs, HYDROPRO, BEST, SoMo, AtoB, and Zeno, the latter four all implemented within the US-SOMO suite, are described and their performance evaluated. Finally, some literature examples are presented to illustrate the potential applications of hydrodynamics in the expanding field of multiresolution modeling.

Original languageEnglish
Title of host publicationMethods in Enzymology
PublisherAcademic Press Inc.
Pages81-108
Number of pages28
Volume562
DOIs
Publication statusPublished - 2015

Publication series

NameMethods in Enzymology
Volume562
ISSN (Print)00766879
ISSN (Electronic)15577988

Keywords

  • AtoB
  • Bead modeling
  • BEST program
  • Boundary elements
  • HYDROPRO
  • Macromolecular solution conformation
  • Multiresolution modeling
  • Shell modeling
  • US-SOMO
  • Zeno program

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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  • Cite this

    Rocco, M., & Byron, O. (2015). Hydrodynamic Modeling and Its Application in AUC. In Methods in Enzymology (Vol. 562, pp. 81-108). (Methods in Enzymology; Vol. 562). Academic Press Inc.. https://doi.org/10.1016/bs.mie.2015.04.010