Methods and Tools for the Prediction of Hydrodynamic Coefficients and Other Solution Properties of Flexible Macromolecules in Solution. A Tutorial Minireview

• Published in: Macromolecular bioscience 2010-07, Vol.10 (7), p.721-730
• Main Authors: de la Torre, José García, Ortega, Álvaro, Amorós, Diego, Schmidt, Ricardo Rodríguez, Cifre, José G. Hernández
• Format: Article
• Language: English
• Subjects: Brownian dynamics simulation; Coefficients; computer modeling; Computer programs; Computer Simulation; DNA; Dynamics; Hydrodynamics; Macromolecular Substances - analysis; Macromolecules; Mathematical models; Monte Carlo methods; Monte Carlo simulation; Pliability; Sedimentation; Solutions - chemistry; ultracentrifugation; Ultracentrifugation - instrumentation; Ultracentrifugation - methods
• ISSN: 1616-5187; 1616-5195
• DOI: 10.1002/mabi.200900464

The calculation of solution properties of flexible macromolecules and other nanoparticles requires, in addition to the hydrodynamic formalisms needed for the sedimentation coefficient and other transport properties, the consideration of the conformational statistics and internal dynamics. The latter aspects can be handled with simulation methods like Monte Carlo and Brownian dynamics. An example of a Monte Carlo simulation for a model specific of DNA is illustrated with results for the several solution properties over an extremely wide range of molecular weight. The convenience of having computational tools of a quite general applicability has prompted us to implement the simulation and hydrodynamic treatments in software packages, MONTEHYDRO for Monte Carlo, and SIMUFLEX for Brownian dynamics which—with a scope similar to the HYDRO suite for rigid particles—can handle a variety of situations. As an application of the new methodology to a yet unclear problem in analytical ultracentrifugation, in a simple application of the SIMUFLEX software, we present a simulation of the so‐called anomalous sedimentation of very long DNA molecules, obtaining results for the experimentally observable rotor‐speed‐dependence of the sedimentation coefficient. We have developed procedures to carry out Monte Carlo and Brownian dynamics simulations of flexible molecules, which have been implemented in public domain programs. As an application to the computation of solution properties of macromolecules, we show the rotor‐speed‐dependence of the sedimentation coefficient of large DNA molecules.