Dynamic and electrophoretic light scattering measurements on microtubules at low concentrations.

The accurate characterization of microtubules is essential for understanding their roles in various biological activities in eukaryotic cellular processes. In vitro, experimental data on these systems often need more details and information on sample preparation protocols and experimental techniques. This deficiency leads to unreproducible or contradictory outcomes.

In vitro Preparation of Homogenous Actin Filaments for Dynamic and Electrophoretic Light Scattering Measurements.

Actin filaments are essential for various biological activities in eukaryotic cellular processes. Available in vitro experimental data on these systems often lack details and information on sample preparation protocols and experimental techniques, leading to unreproducible results. Additionally, different experimental techniques and polymerization buffers provide different, sometimes contradictory results on the properties of these systems, making it substantially difficult to gather meaningful data and conclusive information from them.

Characterization of the interaction of metal-protoporphyrins photosensitizers with β- lactoglobulin.

We investigated the interaction of a series of metal-protoporphyrins (PPIXs) with bovine β- lactoglobulin (BLG) using a combination of optical spectroscopy and computational simulations. Unlike other studies, the simulations were not merely used to rationalize the experimental data but were employed to refine the experimental data itself. The study was carried out at two pH values, 5 and 9, where BLG is known to have different conformation dictated by the so-called Tanford transition which occurs near pH 7.

Hydrodynamic and Polyelectrolyte Properties of Actin Filaments: Theory and Experiments.

Actin filament's polyelectrolyte and hydrodynamic properties, their interactions with the biological environment, and external force fields play an essential role in their biological activities in eukaryotic cellular processes. In this article, we introduce a unique approach that combines dynamics and electrophoresis light-scattering experiments, an extended semiflexible worm-like chain model, and an asymmetric polymer length distribution theory to characterize the polyelectrolyte and hydrodynamic properties of actin filaments in aqueous electrolyte solutions. A fitting approach was used to optimize the theories and filament models for hydrodynamic conditions.

A 200 nanoseconds all-atom simulation of the pH-dependent EF loop transition in bovine β-lactoglobulin. The role of the orientation of the E89 side chain.

molecular dynamics (MD) using crystallographic and NMR data was used to simulate the effects of the protonation state of E89 on the pH-dependent conformational rearrangement of the EF loop, also known as the Tanford transition, in a series of apo-β-lactoglobulin (BLG) structures. Compared to existing studies these simulations were carried out over a much longer time scale (200 ns where the stability of the transition can be evaluated) and used an explicit water model. We considered eight different entries from the Brookhaven Protein Data Bank (PDB) separated into two groups.