M. C. Lopez Martinez

Bio: M. C. Lopez Martinez is an academic researcher from University of Murcia. The author has contributed to research in topics: Brownian dynamics & Light scattering. The author has an hindex of 10, co-authored 18 publications receiving 599 citations.

Calculation of hydrodynamic properties of small nucleic acids from their atomic structure.

Abstract: Hydrodynamic properties (translational diffusion, sedimentation coefficients and correlation times) of short B-DNA oligonucleotides are calculated from the atomic-level structure using a bead modeling procedure in which each non-hydrogen atom is represented by a bead. Using available experimental data of hydrodynamic properties for several oligonucleotides, the best fit for the hydrodynamic radius of the atoms is found to be approximately 2.8 A. Using this value, the predictions for the properties corresponding to translational motion and end-over-end rotation are accurate to within a few percent error. Analysis of NMR correlation times requires accounting for the internal flexibility of the double helix, and allows an estimation of approximately 0.85 for the Lipari-Szabo generalized order parameter. Also, the degree of hydration can be determined from hydrodynamics, with a result of approximately 0.3 g (water)/g (DNA). These numerical results are quite similar to those found for globular proteins. If the hydrodynamic model for the short DNA is simply a cylindrical rod, the predictions for overall translation and rotation are slightly worse, but the NMR correlation times and the degree of hydration, which depend more on the cross-sectional structure, are more severely affected.

Calculation of the solution properties of flexible macromolecules: methods and applications

Abstract: While the prediction of hydrodynamic properties of rigid particles is nowadays feasible using simple and efficient computer programs, the calculation of such properties and, in general, the dynamic behavior of flexible macromolecules has not reached a similar situation. Although the theories are available, usually the computational work is done using solutions specific for each problem. We intend to develop computer programs that would greatly facilitate the task of predicting solution behavior of flexible macromolecules. In this paper, we first present an overview of the two approaches that are most practical: the Monte Carlo rigid-body treatment, and the Brownian dynamics simulation technique. The Monte Carlo procedure is based on the calculation of properties for instantaneous conformations of the macromolecule that are regarded as if they were instantaneously rigid. We describe how a Monte Carlo program can be interfaced to the programs in the HYDRO suite for rigid particles, and provide an example of such calculation, for a hypothetical particle: a protein with two domains connected by a flexible linker. We also describe briefly the essentials of Brownian dynamics, and propose a general mechanical model that includes several kinds of intramolecular interactions, such as bending, internal rotation, excluded volume effects, etc. We provide an example of the application of this methodology to the dynamics of a semiflexible, wormlike DNA.

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

Abstract: 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

Dynamic Light Scattering Measurement of Nanometer Particles in Liquids

Abstract: 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.

Cross-Correlated Relaxation Enhanced 1H−13C NMR Spectroscopy of Methyl Groups in Very High Molecular Weight Proteins and Protein Complexes

Abstract: A comparison of HSQC and HMQC pulse schemes for recording 1H−13C correlation maps of protonated methyl groups in highly deuterated proteins is presented. It is shown that HMQC correlation maps can be as much as a factor of 3 more sensitive than their HSQC counterparts and that the sensitivity gains result from a TROSY effect that involves cancellation of intra-methyl dipolar relaxation interactions. 1H−13C correlation spectra are recorded on U-[15N,2H], Ileδ1-[13C,1H] samples of (i) malate synthase G, a 723 residue protein, at 37 and 5 °C, and of (ii) the protease ClpP, comprising 14 identical subunits, each with 193 residues (305 kDa), at 5 °C. The high quality of HMQC spectra obtained in short measuring times strongly suggests that methyl groups will be useful probes of structure and dynamics in supramolecular complexes.