Physical-chemical properties of actin in different structural states. New ideas about its folding-unfolding pathways

Results of actin folding-unfolding pathways examination and characterization of intermediate and misfolded states are summarized. Properties of microenvironments and peculiarities of location of tryptophan residues in protein are analysed in detail. This allowed to conclude that the main contribution to the bulk fluorescence of native protein is made by internal tryptophan residues Trp 340 and Trp 356, localized in hydrophobic regions, while tryptophan residues Trp 79 and Trp 86 are quenched. It has been shown that inactivated actin, previously regarded as an intermediate state between native and completely unfolded state of protein is in reality a misfolded aggregated state. The properties of actin in this state were characterized in detail. In particular, it is shown that inactivated actin is a monodisperse associate consisting of 15 monomer unit. Two earlier unknown intermediate states, which precede completely unfolding of protein macromolecule and formation of inactivated actin, were visualized. A new scheme of folding-unfolding processes was proposed. It is shown that the reason of anomalous effects, which are recorded for actin in solutions with small concentrations of GdnHCl, is a specific interaction of actin with a denaturant.     

Features of the structural organization of inactivated actin--an intermediate form of the protein during the folding-unfolding process

The structure of inactivated actin was studied by the methods of intrinsic fluorescence upon stationary and pulse excitation, selective fluorescence quenching with acrylamide, and testing the protein surface with a hydrophobic probe, 8-anilino-1-naphthalenesulfonic acid (ANS). The results are discussed along with earlier data on actin sedimentation, near- and far-UV CD spectra, and fluorescence anisotropy. The thermodynamic stability of inactivated actin, the presence of a secondary structure characteristic of the native protein, and the reversibility of the inactivated actin-completely unfolded actin transition allow inactivated actin to be considered an intermediate form in the process of protein folding into the native globular structure. In vitro actin inactivation is accompanied by specific association of actin macromolecules resulting in the formation of homogeneous stable complexes. The tendency toward aggregation (or specific association, in the case of actin), which is determined by the presence of extended hydrophobic clusters on the molecule surface, appears to be one of the intrinsic properties of any protein in the intermediate state. The mobility of the amino acid side chains in the inactivated actin differs considerably from that in the completely unfolded actin. The relaxation properties of the microenvironment of tryptophan residues determine relatively long-wave fluorescence spectra of the inactivated actin. However, the mobility observed is insufficient to compensate the asymmetry of the microenvironment of aromatic residues, which is confirmed by a characteristic and intense CD spectrum in the near-UV region. The mobility of the indole rings of tryptophans located in the internal regions of the inactivated actin that are solvent-inaccessible although polar is even considerably lower than that in the native actin.     

Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory

The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at multiple levels, from atomistic to coarse-grained representations. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.     

Purification and kinetic characterisation of human erythrocyte actin

Human erythrocyte actin can be extracted from membrane ghosts by low ionic strength treatment in the presence of protective amounts of calcium and ATP. Purification then involves a single chromatographic step. The erythrocyte actin can be labelled with N-(1-prenyl)iodoacetamide. The fluorescence enhancement which accompanies polymerisation can be used to determine the critical concentration for assembly and to follow the polymerisation reaction time-course. The polymerisation kinetics of erythrocyte actin are compared with those of rabbit skeletal muscle actin. The two are shown to be markedly different.     

Tryptophan phosphorescence of nascent and inactivated actin at the room temperature]

Millisecond internal dynamics of native and inactivated actin from rabbit skeletal muscle was examined using room temperature phosphorescence. Inactivated actin was prepared by incubation of G-actin at 70 degrees C, by treatment with 4 M urea or 1.5 M guanidinium hydrochloride, renaturation from fully unfolded state or by Ca2+ ion removal. It was shown that inactivation of actin, irrespective of the denaturation procedure applied, leads to a sharp decrease of millisecond fluctuations of the protein structure. Restriction of the slow intramolecular mobility in inactivated actin can result from changes of the protein conformation and/or specific association of macromolecules.     

The polymerization of actin. III. Aggregates of nonfilamentous actin and its associated proteins: a storage form of actin

When echinoderm sperm are treated with the detergent Triton X-100 at pH 6.4 in 10 mM phosphate buffer, the membranes are solubilized, but the actin which is located in the periacrosomal region remains as a phase-dense cup. These cups can be isolated free from the flagella and chromatin and can be solubilized by increasing the pH to 8.0 and by changing the ionic strength and type of buffer used. Since the actin does not exist in the "F" state in unreacted sperm, and since the actin remains as a unit that does not diffuse away, it must be present in the mature sperm in a bound or storage state. The actin is, in fact, associated with a pair of proteins whose mol wt are 250,000 and 230,000. When the isolated cups are digested with trypsin, these high molecular weight proteins are digested, thereby liberating the actin. The actin will polymerize if heavy meromyosin or subfragment 1 is added to a preparation of isolated cups. Evidence is presented that this pair of high molecular weight proteins is similar in molecular weight and properties to erythrocyte spectrin. Attempts at transforming the storage form of actin in the cup into filaments were only moderately successful. The best conditions for filament formation involve incubating the cup in ATP and divalent salts. Careful examination of these cups reveals that the actin polymerized preferentially on either end of oriented filaments that already exist in the cup, indicating that self-nucleation is inefficacious. I conclude that the actin can exist in the storage form by its association with spectrin-like molecules and that the actin in this state polymerizes preferentially onto existing filaments.     

Everything in its right place

Clever design strategies enable researchers to harness nonspecific interactions to achieve highly specific arrangements of nucleic acid nanostructures.     

The intermediate nerve and its place in the system of cranial nerves

The intermediate nerve (IN) in embryogenesis of man, cat and white rat is formed similarly. From the common with the VIII cranial nerve anlage the geniculum node, the vestibular and cochlear ganglia are emerged. A separated root of the IN connects the geniculum node with the nuclei, situating in the CNS. From the geniculum node main branches of the IN get off: the greater petrosal nerve and the cord of the tympanum, its fibers in the temporal bone canal run in the facial nerve trunk. In the periphery the IN branches unite with other cranial nerves, make connections with branches of vegetative (parasympathetic) ganglia and plexuses. They spread along a large territory, forming a system of parasympathetic innervation in the area of the head and ensuring with specific nervous apparatuses the gustatory organ. It is expedient to select the IN into an independent cranial nerve and confirm it the number of the regular pair.     

Effect of self-association on the structural organization of partially folded proteins: inactivated actin

The propensity to associate or aggregate is one of the characteristic properties of many nonnative proteins. The aggregation of proteins is responsible for a number of human diseases and is a significant problem in biotechnology. Despite this, little is currently known about the effect of self-association on the structural properties and conformational stability of partially folded protein molecules. G-actin is shown to form equilibrium unfolding intermediate in the vicinity of 1.5 M guanidinium chloride (GdmCl). Refolding from the GdmCl unfolded state is terminated at the stage of formation of the same intermediate state. An analogous form, known as inactivated actin, can be obtained by heat treatment, or at moderate urea concentration, or by the release of Ca(2+). In all cases actin forms specific associates comprising partially folded protein molecules. The structural properties and conformational stability of inactivated actin were studied over a wide range of protein concentrations, and it was established that the process of self-association is rather specific. We have also shown that inactivated actin, being denatured, is characterized by a relatively rigid microenvironment of aromatic residues and exhibits a considerable limitation in the internal mobility of tryptophans. This means that specific self-association can play an important structure-forming role for the partially folded protein molecules.     

The variable twist of actin and its modulation by actin-binding proteins

Previous studies demonstrated that actin filaments have variable twist in which the intersubunit angles vary by approximately +/- 10 degrees within a filament. In this work we show that this variability was unchanged when different methods were used to prepare filaments for electron microscopy. We also show that actin-binding proteins can modulate the variability in twist. Three preparations of actin filaments were photographed in the electron microscope: negatively stained filaments, replicas of rapidly frozen, etched filaments, and frozen hydrated filaments. In addition, micrographs of actin + tropomyosin + troponin (thin filaments), of actin + myosin S1 (decorated filaments), and of filaments frayed from the acrosomal process of Limulus sperm (Limulus filaments) were obtained. We used two independent methods to measure variable twist based on Fourier transforms of single filaments. The first involved measuring layer line intensity versus filament length and the second involved measuring layer line position. We measured a variability in the intersubunit angle of actin filaments of approximately 12 degrees independent of the method of preparation or of measurement. Thin filaments have 15 degrees of variability, but the increase over pure actin is not statistically significant. Decorated filaments and Limulus filaments, however, have significantly less variability (approximately 2 and 1 degree, respectively), indicating a torsional stiffening relative to actin. The results from actin alone using different preparative methods are evidence that variable twist is a property of actin in solution. The results from actin filaments in the presence of actin-binding proteins suggest that the angular variability can be modulated, depending on the biological function.     

A comparison between radiochromic EBT2 film model and its predecessor EBT film model

The manufacturer has introduced the new EBT2 film model so as to improve its predecessor, the EBT radiochromic film model. According to the manufacturer, some of its main advantages include a higher tolerance to light exposure and it can correct non-uniformity of the active layer thickness using a marker dye. However, the equivalence in uniformity between both models was questioned by some authors, and the asymmetrical configuration of layers of the EBT2 film model produces a new dependence on the film side being scanned (front and back orientation). In this study, the EBT2 radiochromic film model was compared with the EBT model and the new marker dye feature was assessed. We also compared this correction method with a pre-irradiated pixel value correction method. An Epson Expression 10000XL scanner in transmission mode was used to scan the films and the red channel response was analyzed. We confirmed the lower-measured signal dependence on the visible light exposure of the EBT2 film model. Differences in pixel values remained below 0.5% for a minimum of 15 days. In regard to the uniformity, similar results for EBT2 and EBT film models were obtained; in both cases inhomogeneity was found to be less than 1%, in relative pixel value from the mean. However, we found that the signal-to-noise ratio was reduced for low doses by 37% for old EBT2 batch and by 21% for new EBT2 batch compared to signal-to-noise ratio for EBT. The EBT2 film model's pixel value difference for the front and back orientation reached up to 1.0% in the red channel. Our results did not show a clear advantage between to use a pre-irradiated pixel value correction and to use the manufacturer's correction.