title: Hydrodynamic Modeling and Its Application in AUC.
abstract: The hydrodynamic parameters measured in an AUC experiment, s(20,w) and D(t)(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.
authors.affiliation: Biopolimeri e Proteomica, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy. Electronic address: mattia.rocco@hsanmartino.it.
authors.forename: Mattia
authors.initials: M
authors.lastname: Rocco
authors.affiliation: School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, United Kingdom. Electronic address: olwyn.byron@glasgow.ac.uk.
authors.forename: Olwyn
authors.initials: O
authors.lastname: Byron
mesh_terms: D000465:Algorithms; D057446:Hydrodynamics; D046911:Macromolecular Substances / Q000737:chemistry / Q000302:isolation & purification*; D008956:Models, Chemical; D008958:Models, Molecular; D008970:Molecular Weight; D012984:Software; D012996:Solutions; D014461:Ultracentrifugation / Q000379:methods
chemical_list: D046911:Macromolecular Substances; D012996:Solutions
keywords: AtoB; BEST program; Bead modeling; Boundary elements; HYDROPRO; Macromolecular solution conformation; Multiresolution modeling; Shell modeling; US-SOMO; Zeno program