Biomedical subjects

M X Fernandes

Publications and source records attributed to M X Fernandes.

7 recordsLinked to original sources

PubMed2003

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

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.

Centrifugation, Density Gradient↗

PubMed2002

Joint determination by Brownian dynamics and fluorescence quenching of the in-depth location profile of biomolecules in membranes.

The in-depth molar distribution function of fluorophores is revealed by a new methodology for fluorescence quenching data analysis in membranes. Brownian dynamics simulation was used to study the in-depth location profile of quenchers. A Lorentzian profile was reached. Since the Stern-Volmer equation is valid at every depth in the membrane for low quencher concentrations, the molar distribution of the fluorophore (also regarded as a Lorentzian) can be achieved. The average location and the broadness of the fluorophore distribution can be calculated. The importance of the knowledge of the location width is demonstrated and discussed, since this parameter reveals important conclusions on structural features of the interaction of membranes with probes and biomolecules (e.g., conformational freedom in proteins), as well as photophysical properties (e.g., differential fluorophore quantum yields). Subsequent use of this methodology by the reader does not, necessarily, involve the performance of simulations and is not limited to the use of Lorentzian function distributions.

Cell Membrane↗

PubMed2002

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

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.

Base Sequence↗

PubMed2001

An analytical solution to the problem of the orientation of rigid particles by planar obstacles. Application to membrane systems and to the calculation of dipolar couplings in protein NMR spectroscopy.

Nonspherical particles or molecules experience an ordering effect in the presence of obstacles due to the restrictions they place on the orientation of those molecules that are in their proximity. Obstacles may be the limits of a membrane in which the molecule is embedded, oriented mesoscopic systems such as bicelles, or membrane fragments used to induce weak protein alignment in a magnetic field. The overall shape of most proteins can be described to a good approximation by an ellipsoidal particle. Here we describe and solve analytically the problem of the orientation of ellipsoidal particles by planar obstacles. Simple expressions are derived for the orientational distribution function and the order parameter. These expressions allow the analytical calculation of the residual dipolar couplings for a protein of known three-dimensional structure oriented by steric effects. The results are in good agreement with experiment and with the results of previously described simulations. However, they are obtained analytically in a fraction of the time and therefore open the possibility to include the optimization of the overall shape in the determination of three-dimensional structures using residual dipolar coupling constraints. The equations derived are general and can also be applied to problems of a completely different nature. In particular, previous equations describing the orientation of particles embedded in membranes are verified and generalized here.

Membrane Proteins↗

PubMed2000

Conformation and dynamic properties of a saturated hydrocarbon chain confined in a model membrane: a Brownian dynamics simulation.

A Brownian dynamics simulation of a saturated hydrocarbon chain with simple mean-field potentials, namely anchorage, orientation and enclosing, reproducing a biological membrane environment is presented. The simulation was performed for a time equivalent to 1.4 micros thanks to the simplicity of our model. The results are compared with those obtained for a hydrocarbon chain simulated in the absence of the membrane potentials but with confinement. With the appropriate choice of parameters, equilibrium properties, such as deuterium order parameter, chain length, tilt angle and geometry, and dynamic properties, such as dihedral angle transition rate, rotational and translational diffusion, recovered from our simulations, correctly reproduced, are consistent with hydrocarbon-derived molecule experimental results and simulation results obtained from other more complex studies.

Hydrocarbons↗

PubMed1999

Simulation of the distribution and diffusion of a rigid amphipathic particle embedded in a model membrane.

We simulate, by Brownian dynamics, the distribution, orientation and diffusion of a rigid molecule, represented as a dumbbell, with amphipathic nature, embedded in a model membrane. The significant features of a biological membrane are reproduced by means of a Maier-Saupe orienting potential, an enclosing potential and a lipophobic potential. We also evaluate the equilibrium quantities, such as order parameter, and dynamic features, such as rotational or translational diffusivity, of the embedded molecule in terms of the system parameters and compare the obtained results with those obtained from model independent theory.

Diffusion↗

PubMed1998

Continuous particle size distribution analysis with dynamic light scattering. MAXAMPER: a regularization method using the maximum amplitude for the average error and the Lagrange's multipliers method.

This work deals with a new method to evaluate the scattered light intensity distributions with particle size by means of photon correlation spectroscopy. Basically, the data analysis consists in: 1) To find the least squares solution (L2 norm), and 2) To find the solution that is not significantly different from the least squares solution (within a certain significance level) that simultaneously minimizes the sum of the modulus of the residuals (L1 norm). A simple procedure is achieved by using the Lagrange's multipliers method. The two aspects that debilitate CONTIN (a rather empirical regularization based on the continuity of the distributions and the non-suitable use of the Fisher's F test) are prevented in this work, granting more meaningful results. The method was applied to simulated curves, in several typical situations (mono-modal and bi-modal, narrow and broad distributions). The quality of the results is better for narrower mono-modal distributions and bi-modal distributions having well separated peaks, as expected. Latex beads (nanospheres) having 114 nm in diameter were used to test the method in experimental conditions. MAXAMPER better reproduces monodispersed distribution profiles than CONTIN and the first moments of the distributions are in agreement with the expected value in most of the analysis.

Algorithms↗