Protein ubiquitination controls the cellular fate of numerous eukaryotic proteins. Despite its importance, many fundamental questions remain regarding its mechanism. One such question is how ubiquitination alters the biophysical properties of the modified protein and whether these alterations are significant in the cellular context. In this study, we investigate the effects of ubiquitination on...

We investigate the effect of temperature and pressure on polypeptide conformational stability using a two-dimensional square lattice model in which water is represented explicitly. The model captures many aspects of water thermodynamics, including the existence of density anomalies, and we consider here the simplest representation of a protein: a hydrophobic homopolymer. We show that an explici...

Thermal unfolding of P. cepacia lipase was observed by adiabatic differential scanning microcalorimetry in the absence and presence of calcium ions at pH 8, and thermodynamic parameters of unfolding were evaluated to analyze the unfolding mechanism of the enzyme. The temperature of unfolding was higher at higher concentrations of Ca2+. From the Ca2+ concentration-dependence of the unfolding tem...

Statistical analyses of forced unfolding data for protein tandems, i.e., unfolding forces (force-ramp) and unfolding times (force-clamp), used in single-molecule dynamic force spectroscopy rely on the assumption that the unfolding transitions of individual protein domains are independent (uncorrelated) and characterized, respectively, by identically distributed unfolding forces and unfolding ti...

We show that the hypercube has a face-unfolding that tiles space, and that unfolding has an edge-unfolding that tiles the plane. So the hypercube is a “dimension-descending tiler.” We also show that the hypercube cross unfolding made famous by Dali tiles space, but we leave open the question of whether or not it has an edge-unfolding that tiles the plane.

The deflection of a cantilever is measured using a laser beam and position-sensing detector to obtain force and displacement for both imaging and force spectroscopy. In force spectroscopy, the cantilever is attached to one end of the protein or DNA sample while the other end is immobilized on the surface. The force and position of the tip are measured as the surface is moved away from the tip, ...

An effective free energy potential, developed originally for binding free energy calculation, is compared to calorimetric data on protein unfolding, described by a linear combination of changes in polar and nonpolar surface areas. The potential consists of a molecular mechanics energy term calculated for a reference medium (vapor or nonpolar liquid), and empirical terms representing solvation a...