Hydrodynamic modeling: the solution conformation of macromolecules and their complexes

Area of Science:

• Biophysics
• Computational Biology
• Physical Chemistry

Background:

• Hydrodynamic bead modeling (HBM) is crucial for understanding macromolecular solution conformations.
• Accurate modeling requires careful consideration of molecular composition and available experimental data.

Purpose of the Study:

• To provide an example-based account of the main stages in HBM for rigid macromolecules.
• To describe model construction using various data resolutions.
• To summarize available software for hydrodynamic calculations and hydration treatment.

Main Methods:

• Model construction based on atomic coordinates or low-resolution data (e.g., electron microscopy).
• Model visualization techniques.
• Accounting for hydrodynamic hydration.
• Performing hydrodynamic calculations using various software.

Main Results:

• Detailed description of HBM stages: model construction, visualization, hydration, and calculations.
• Summary of programs for calculating basic solution parameters (e.g., sedimentation coefficients, Stokes radius) and advanced data (NMR, fluorescence anisotropy).
• Practical guidance on handling hydrodynamic hydration in modeling.

Conclusions:

• HBM is a versatile tool for characterizing macromolecular solution conformations.
• The choice of model and software depends on the macromolecule and experimental data.
• All reviewed programs for HBM are freely available, promoting accessibility in research.