TY - CHAP
T1 - Hydrodynamic Modeling and Its Application in AUC
AU - Rocco, Mattia
AU - Byron, Olwyn
PY - 2015
Y1 - 2015
N2 - 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.
AB - 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.
KW - AtoB
KW - Bead modeling
KW - BEST program
KW - Boundary elements
KW - HYDROPRO
KW - Macromolecular solution conformation
KW - Multiresolution modeling
KW - Shell modeling
KW - US-SOMO
KW - Zeno program
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U2 - 10.1016/bs.mie.2015.04.010
DO - 10.1016/bs.mie.2015.04.010
M3 - Chapter
C2 - 26412648
AN - SCOPUS:84948566540
VL - 562
T3 - Methods in Enzymology
SP - 81
EP - 108
BT - Methods in Enzymology
PB - Academic Press Inc.
ER -