Allosteric conformational spread: exact results using a simple transfer matrix method

An Element of Determinism in a Stochastic Flagellar Motor Switch

Marine bacterium Vibrio alginolyticus uses a single polar flagellum to navigate in an aqueous environment. Similar to Escherichia coli cells, the polar flagellar motor has two states; when the motor is counter-clockwise, the cell swims forward and when the motor is clockwise, the cell swims backward. V. alginolyticus also incorporates a direction randomization step at the start of the forward swimming interval by flicking its flagellum. To gain an understanding on how the polar flagellar motor switch is regulated, distributions of the forward Δ_f and backward Δ_b intervals are investigated herein. We found that the steady-state probability density functions, P(Δ_f) and P(Δ_b), of freely swimming bacteria are strongly peaked at a finite time, suggesting that the motor switch is not Poissonian. The short-time inhibition is sufficiently strong and long lasting, i.e., several hundred milliseconds for both intervals, which is readily observed and characterized. Treating motor reversal dynamics as a first-passage problem, which results from conformation fluctuations of the motor switch, we calculated P(Δ_f) and P(Δ_b) and found good agreement with the measurements.

Tertiary and quaternary effects in the allosteric regulation of animal hemoglobins

In the last decade, protein allostery has experienced a major resurgence, boosted by the extension of the concept to systems of increasing complexity and by its exploitation for the development of drugs. Expansion of the field into new directions has not diminished the key role of hemoglobin as a test molecule for theory and experimental validation of allosteric models. Indeed, the diffusion of hemoglobins in all kingdoms of life and the variety of functions and of quaternary assemblies based on a common tertiary fold indicate that this superfamily of proteins is ideally suited for investigating the physical and molecular basis of allostery and firmly maintains its role as a main player in the field. This review is an attempt to briefly recollect common and different strategies adopted by metazoan hemoglobins, from monomeric molecules to giant complexes, exploiting homotropic and heterotropic allostery to increase their functional dynamic range. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.

Biophysics of actin filament severing by cofilin

The continuous assembly and disassembly of actin filament networks is vital for cellular processes including division, growth, and motility. Network remodeling is facilitated by cofilins, a family of essential regulatory proteins that fragment actin filaments. Cofilin induces net structural changes in filaments that render them more compliant in bending and twisting. A model in which local stress accumulation at mechanical discontinuities, such as boundaries of bare and cofilin-decorated filament segments, accounts for the cofilin concentration dependence of severing, including maximal activity at sub-stoichiometric binding densities. Real-time imaging of cofilin-mediated filament severing supports the boundary-fracture model. The severing model predicts that fragmentation is promoted by factors modulating filament mechanics (e.g. tethering, cross-linking, or deformation), possibly explaining enhanced in vivo severing activities.