Mechanism of bovine liver glutamate dehydrogenase self-assembly. III. Characterization of the association-dissociation stoichiometry with quasi-elastic light scattering

Self-assembling enzymes and the origins of the cytoskeleton

The bacterial cytoskeleton is composed of a complex and diverse group of proteins that self-assemble into linear filaments. These filaments support and organize cellular architecture and provide a dynamic network controlling transport and localization within the cell. Here, we review recent discoveries related to a newly appreciated class of self-assembling proteins that expand our view of the bacterial cytoskeleton and provide potential explanations for its evolutionary origins. Specifically, several types of metabolic enzymes can form structures similar to established cytoskeletal filaments and, in some cases, these structures have been repurposed for structural uses independent of their normal roles. The behaviors of these enzymes suggest that some modern cytoskeletal proteins may have evolved from dual-role proteins with catalytic and structural functions.

Fitting neurological protein aggregation kinetic data via a 2-step, minimal/"Ockham's razor" model: the Finke-Watzky mechanism of nucleation followed by autocatalytic surface growth

The aggregation of proteins has been hypothesized to be an underlying cause of many neurological disorders including Alzheimer's, Parkinson's, and Huntington's diseases; protein aggregation is also important to normal life function in cases such as G to F-actin, glutamate dehydrogenase, and tubulin and flagella formation. For this reason, the underlying mechanism of protein aggregation, and accompanying kinetic models for protein nucleation and growth (growth also being called elongation, polymerization, or fibrillation in the literature), have been investigated for more than 50 years. As a way to concisely present the key prior literature in the protein aggregation area, Table 1 in the main text summarizes 23 papers by 10 groups of authors that provide 5 basic classes of mechanisms for protein aggregation over the period from 1959 to 2007. However, and despite this major prior effort, still lacking are both (i) anything approaching a consensus mechanism (or mechanisms), and (ii) a generally useful, and thus widely used, simplest/"Ockham's razor" kinetic model and associated equations that can be routinely employed to analyze a broader range of protein aggregation kinetic data. Herein we demonstrate that the 1997 Finke-Watzky (F-W) 2-step mechanism of slow continuous nucleation, A --> B (rate constant k1), followed by typically fast, autocatalytic surface growth, A + B --> 2B (rate constant k2), is able to quantitatively account for the kinetic curves from all 14 representative data sets of neurological protein aggregation found by a literature search (the prion literature was largely excluded for the purposes of this study in order provide some limit to the resultant literature that was covered). The F-W model is able to deconvolute the desired nucleation, k1, and growth, k2, rate constants from those 14 data sets obtained by four different physical methods, for three different proteins, and in nine different labs. The fits are generally good, and in many cases excellent, with R2 values >or=0.98 in all cases. As such, this contribution is the current record of the widest set of protein aggregation data best fit by what is also the simplest model offered to date. Also provided is the mathematical connection between the 1997 F-W 2-step mechanism and the 2000 3-step mechanism proposed by Saitô and co-workers. In particular, the kinetic equation for Saitô's 3-step mechanism is shown to be mathematically identical to the earlier, 1997 2-step F-W mechanism under the 3 simplifying assumptions Saitô and co-workers used to derive their kinetic equation. A list of the 3 main caveats/limitations of the F-W kinetic model is provided, followed by the main conclusions from this study as well as some needed future experiments.

The role of oligomerization in regulation of maize phosphoenolpyruvate carboxylase activity. Influence of Mg-PEP and malate on the oligomeric equilibrium of PEP carboxylase

A purification procedure which yields a near homogenous preparation of phosphoenolpyruvate (PEP) carboxylase from the leaves of Zea mays is reported. The enzyme had a final specific activity of 33.3 micromoles per minute per milligram protein. Size exclusion high performance liquid chromatography and dynamic laser-light scattering spectroscopy showed that PEP carboxylase exists in an equilibrium of aggregates. Enzyme predominantly in the dimeric configuration is less active (when assayed at sub-optimal Mg-PEP concentrations, less than 0.4 millimolar) than when in its tetrameric arrangement. The difference in activity diminishes and disappears as the concentration of the substrate Mg-PEP increases. The substrate drives the equilibrium toward the tetramer, while malate, an inhibitor of PEP carboxylase, shifts the equilibrium toward the dimer. It thus appears that the quaternary structure (oligomeric state) of maize PEP carboxylase can be regulated by the naturally occurring effector molecules Mg-PEP and malate which in turn can control the enzyme's activity.

Light scattering study on polydisperse TMV solutions

The calculations of the angular dependence of the scattered intensity and of the linewidth have been compared with the measured quantities for model distributions of rodlike scatterers. TMV rods were broken up by means of ultrasonic waves, and the length distributions (0-800 nm) for different samples were determined from electron micrographs. Good agreement between the calculated and experimental light scattering data was found for q.L ranging between 1.5 and 20.

Dynamic light scattering of biopolymers and biocolloids

Widespread applications of dynamic light scattering techniques to the study of macromolecular Brownian motion have yielded not only a valuable store of factual information concerning solution conformations and conformational changes, but have also provided an important window through which to view the dynamics of internal modes of motion. These techniques have coincided with a resurgence of interest in the solution physical chemistry of macromolecules, including hydrodynamic properties, and the profound effect of intermolecular interactions on both the disposition and dynamics of macromolecules in solution.