Calculation of hydrodynamic properties of globular proteins from their atomic-level structure.

Translational diffusion is the most fundamental form of transport in chemical and biochemical systems. Pulsed-field gradient nuclear magnetic resonance provides a convenient and noninvasive means for measuring translational motion. In this method the attenuation of the echo signal from a Hahn spin-echo pulse sequence containing a magnetic field gradient pulse in each τ period is used to measure the displacement of the observed spins. In the present article, the physical basis of this method is considered in detail. Starting from the Bloch equations containing diffusion terms, the (analytical) equation linking the echo attenuation to the diffusion of the spin for the case of unrestricted isotropic diffusion is derived. When the motion of the spin occurs within a confined geometry or is anisotropic, such as in in vivo systems, the echo attenuation also yields information on the surrounding structure, but as the analytical approach becomes mathematically intractable, approximate or numerical means must be used to extract the motional information. In this work, two common approximations are considered and their limitations are examined. Measurements in anisotropic systems are also considered in some detail. ©1997 John Wiley & Sons, Inc. Concepts Magn Reson 9: 299–336, 1997

Pulsed-field gradient nuclear magnetic resonance as a tool for studying translational diffusion, part 1: basic theory

http://leonardo.inf.um.es/macromol/publications/211BIJ11Main.pdf

Prediction of Hydrodynamic and Other Solution Properties of Rigid Proteins from Atomic- and Residue-Level Models

Dynamic light scattering (DLS) techniques for studying sizes and shapes of nanoparticles in liquids are reviewed. In photon correlation spectroscopy (PCS), the time fluctuations in the intensity of light scattered by the particle dispersion are monitored. For dilute dispersions of spherical nanoparticles, the decay rate of the time autocorrelation function of these intensity fluctuations is used to directly measure the particle translational diffusion coefficient, which is in turn related to the particle hydrodynamic radius. For a spherical particle, the hydrodynamic radius is essentially the same as the geometric particle radius (including any possible solvation layers). PCS is one of the most commonly used methods for measuring radii of submicron size particles in liquid dispersions. Depolarized Fabry-Perot interferometry (FPI) is a less common dynamic light scattering technique that is applicable to optically anisotropic nanoparticles. In FPI the frequency broadening of laser light scattered by the particles is analyzed. This broadening is proportional to the particle rotational diffusion coefficient, which is in turn related to the particle dimensions. The translational diffusion coefficient measured by PCS and the rotational diffusion coefficient measured by depolarized FPI may be combined to obtain the dimensions of non-spherical particles. DLS studies of liquid dispersions of nanometer-sized oligonucleotides in a water-based buffer are used as examples.

Dynamic Light Scattering Measurement of Nanometer Particles in Liquids

HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.

HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules

Hydrodynamic properties of a double-helical model for DNA.

Simulation of the conformation and dynamics of a double-helical model for DNA

The effect of a tensile stress or an electric field on the conformation of a flexible polymer chain has been studied by combining theory with numerical simulation. In the presence of such external agents, the macromolecule experiences the action of two opposite forces at the chain ends. Two models are considered: the Gaussian bead-and-spring chain, and the freely jointed chain with segments of fixed length. From simulated Brownian trajectories we calculate steady-state properties of the polymer under the continuing action of the external forces. Thus, we compute the chain deformation and expansion, measured by the square radius of gyration, and analyze the influence of the external force on low-angle scattering of radiation. The effect of the link orientation in the optical anisotropy or birefringence is also analyzed. From existing theories, we predict very simple relationships between expansion, low-angle scattering, and birefringence, valid for Gaussian chains of any length, and for long freely jointed chains. The simulation results confirm those relationships. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys, 35: 689–697, 1997

S. Navarro

Papers

HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules

Hydrodynamic properties of a double-helical model for DNA.

Simulation of the conformation and dynamics of a double-helical model for DNA

Deformation, scattering, and birefringence of flexible polymer chains under external forces or electric fields