126 research outputs found
Inclusion of ionic interactions in force field calculations of charged biomolecules – DNA structural transitions.
The potential of mean force (PMF) approach for treating polyion–diffuse ionic cloud interactions [D. M. Soumpasis (1984) Proceedings of the National Academy of Sciences USA81, 5116–5120] has been combined with the AMBER force field describing intramolecular interactions. The resultant generalized AMBER-PMF force field enables one to treat the conformational stabilities and structural transitions of charged biomolecules in aqueous electrolytes more realistically. For example, we have used it to calculate the relative stabilities of the B and Z conformations of d(C-G)6, and the B and heteronomous (H) conformations of dA12 · dT12, as a function of salt concentration. In the case of d(C-G)6, the predicted B–ZI transition occurs at 2.4M and is essentially driven by the phosphate-diffuse ionic cloud interactions alone as suggested by the results of earlier PMF calculations. The ZII conformer is less stable than the B form under all conditions. It is found that the helical parameters of the refined B and Z structures change with salt concentration. For example, the helical rise of B-DNA increases about 10% and the twist angle decreases by the same amount above 1M NaCl. In the range of 0.01–0.3M NaCl, the H form of dA12 · dT12 is found to be more stable than the B form and its stability increases with increasing salt concentration. The computed greater relative stability of the H conformation is likely due to noninclusion of the free energy contribution from the spine of hydration, a feature presumed to stabilize the B form of this sequence
A FRAP model to investigate reaction-diffusion of proteins within a bounded domain: a theoretical approach
Temporally and spatially resolved measurements of protein transport inside
cells provide important clues to the functional architecture and dynamics of
biological systems. Fluorescence Recovery After Photobleaching (FRAP) technique
has been used over the past three decades to measure the mobility of
macromolecules and protein transport and interaction with immobile structures
inside the cell nucleus. A theoretical model is presented that aims to describe
protein transport inside the nucleus, a process which is influenced by the
presence of a boundary (i.e. membrane). A set of reaction-diffusion equations
is employed to model both the diffusion of proteins and their interaction with
immobile binding sites. The proposed model has been designed to be applied to
biological samples with a Confocal Laser Scanning Microscope (CLSM) equipped
with the feature to bleach regions characterised by a scanning beam that has a
radially Gaussian distributed profile. The proposed model leads to FRAP curves
that depend on the on- and off-rates. Semi-analytical expressions are used to
define the boundaries of on- (off-) rate parameter space in simplified cases
when molecules move within a bounded domain. The theoretical model can be used
in conjunction to experimental data acquired by CLSM to investigate the
biophysical properties of proteins in living cells.Comment: 25 pages. Abstracts Proceedings, The American Society for Cell
Biology, 46th Annual Meeting, December 9-13, 2006, San Dieg
Effective interaction between helical bio-molecules
The effective interaction between two parallel strands of helical
bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using
computer simulations of the "primitive" model of electrolytes. In particular we
study a simple model for B-DNA incorporating explicitly its charge pattern as a
double-helix structure. The effective force and the effective torque exerted
onto the molecules depend on the central distance and on the relative
orientation. The contributions of nonlinear screening by monovalent counterions
to these forces and torques are analyzed and calculated for different salt
concentrations. As a result, we find that the sign of the force depends
sensitively on the relative orientation. For intermolecular distances smaller
than it can be both attractive and repulsive. Furthermore we report a
nonmonotonic behaviour of the effective force for increasing salt
concentration. Both features cannot be described within linear screening
theories. For large distances, on the other hand, the results agree with linear
screening theories provided the charge of the bio-molecules is suitably
renormalized.Comment: 18 pages, 18 figures included in text, 100 bibliog
Protein Diffusion in Mammalian Cell Cytoplasm
We introduce a new method for mesoscopic modeling of protein diffusion in an entire cell. This method is based on the construction of a three-dimensional digital model cell from confocal microscopy data. The model cell is segmented into the cytoplasm, nucleus, plasma membrane, and nuclear envelope, in which environment protein motion is modeled by fully numerical mesoscopic methods. Finer cellular structures that cannot be resolved with the imaging technique, which significantly affect protein motion, are accounted for in this method by assigning an effective, position-dependent porosity to the cell. This porosity can also be determined by confocal microscopy using the equilibrium distribution of a non-binding fluorescent protein. Distinction can now be made within this method between diffusion in the liquid phase of the cell (cytosol/nucleosol) and the cytoplasm/nucleoplasm. Here we applied the method to analyze fluorescence recovery after photobleach (FRAP) experiments in which the diffusion coefficient of a freely-diffusing model protein was determined for two different cell lines, and to explain the clear difference typically observed between conventional FRAP results and those of fluorescence correlation spectroscopy (FCS). A large difference was found in the FRAP experiments between diffusion in the cytoplasm/nucleoplasm and in the cytosol/nucleosol, for all of which the diffusion coefficients were determined. The cytosol results were found to be in very good agreement with those by FCS
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