Biomedical subjects

R Zangi

Publications and source records attributed to R Zangi.

3 recordsLinked to original sources

PubMed2001

Free energy barrier estimation of unfolding the alpha-helical surfactant-associated polypeptide C.

Molecular dynamics simulations were conducted to estimate the free energy barrier of unfolding surfactant-associated polypeptide C (SP-C) from an alpha-helical conformation. Experimental studies indicate that while the helical fold of SP-C is thermodynamically stable in phospholipid micelles, it is metastable in a mixed organic solvent of CHCl3/CH3OH/0.1 M HCl at 32:64:5 (v/v/v), in which it undergoes an irreversible transformation to an insoluble aggregate that contains beta-sheet. On the basis of experimental observations, the free energy barrier was estimated to be approximately 100 kJ/mole by applying Eyring's transition state theory to the experimental rate of unfolding [Protein Sci 1998;7:2533-2540]. These studies prompted us to carry out simulations to investigate the unwinding process of two helical turns encompassing residues 25-32 in water and in methanol. The results give an upper bound estimation for the free energy barrier of unfolding of SP-C of approximately 20 kJ/mole. The results suggest a need to reconsider the applicability of a single-mode activated process theory to protein unfolding.

Amino Acid Sequence↗

PubMed2000

Nature of the transition from two- to three-dimensional ordering in a confined colloidal suspension

We report the results of extensive molecular dynamics simulations of solid-to-solid transitions in two- to six-layer colloidal suspensions confined between two smooth parallel walls. The studies are designed to elucidate the ordered particle packings that interpolate between the structures of two- and three-dimensional crystals in a confined space. At a fixed density per layer, as the wall separation increases we find a sequence of stable phases, each characterized by uniform amplitude buckling along the normal to the layer planes. The buckling is coupled to an in-plane ordering transition. The buckled phases alternate with phases whose structures contain only parallel planes of particles. The relative densities of the positively and negatively displaced particles in a buckled layer, the in-plane structures, and the behavior with respect to increasing wall separation of the split density distribution that characterizes a buckled layer, clearly identify these layers as intermediates in the reconstructive transformations ntriangle up-->(n+1) square that occur when the character of the constrained space evolves from being two dimensional to being three dimensional (triangle up denotes layers with hexagonal packing symmetry, while square denotes layers with square packing symmetry). The two transitions, ntriangle up-->n-buckled-->(n+1) square, are found to be first order.

Journal Article↗

PubMed2000

Hexagonal to square lattice conversion in bilayer systems

We report the results of extensive molecular dynamics simulations of the reconstructive hexagonal to square lattice conversion in bilayer colloid systems. Two types of interparticle potential were used to represent the colloid-colloid interactions in the suspension. One potential, due to Marcus and Rice, is designed to describe the interaction of sterically stabilized colloid particles. This potential has a term that represents the attraction between colloid particles when there is incipient overlap between the stabilizing brushes on their surfaces, a (soft repulsion) term that represents the entropy cost associated with interpenetration of the stabilizing brushes, and a term that represents core-core repulsion. The other potential we used is an almost hard core repulsion with continuous derivatives. Our results clearly show that the character of the reconstructive hexagonal to square lattice conversion in bilayer colloid systems is potential dependent. For a system with colloid-colloid interactions of the Marcus-Rice type, the packing of particles in the square array exhibits a large interlayer lattice spacing, with the particles located at the minima of the attractive well. In this case the hexagonal to square lattice transition is first order. For a system with hard core colloid-colloid interactions there are two degenerate stable intermediate phases, linear and zigzag rhombic, that are separated from the square lattice by strong first order transitions, and from the hexagonal lattice by either weak first or second order transitions.

Journal Article↗