Background activity of neurons of the supraoptic hypothalamic nucleus in rats under conditions of vibrational stimulation and electromagnetic extrahigh-frequency irradiation

We analyzed background impulse activity of neurons of the supraoptic nucleus of the rat hypothalamus in the course of 15-day-long isolated action of generalized vibrational stimulation and combination of such stimulation with irradiation of the animal’s head with low-intensity extrahigh-frequency (EHF, millimeter-range) electromagmetic waves. The distributions of the neurons by the level of regularity and dynamics of spike trains, separate frequency ranges of impulsation, and pattern of interspike interval (ISI) histograms were estimated. We also calculated the mean frequency of discharges and coefficient of variation of ISIs. A trend toward decreases in the deviations of some parameters of neuronal spike activity generated by supraoptic neurons, which were evident within early time intervals of isolated action of vibration (5 to 10 days), was observed under the influence of EHF electromagnetic irradiation; thus, the latter factor probably exerts a sedative effect. Neirofiziologiya/Neurophysiology, Vol. 39, No. 6, pp. 433–442, November–December, 2007.     

Influence of aggressive computer games on the brain cortex activity level in adolescents

Dynamic changes in the activities of different areas of the brain cortex were studied in order to determine cortical structures responsible for playing aggressive computer games, with the degree of initial aggression of the adolescent subjects taken into account. Changes in anxiety and aggression produced by aggressive computer games were found to depend on the initial level of aggression of the subjects. In adolescents with a high baseline level of aggression, the amplitude of the N200 component increased in the frontal and decreased in the temporal areas of the cortex, whereas, in adolescents with a low baseline aggression level, N200 decreased in the frontal and increased in the temporal cortical areas.     

Computing van der Waals energies in the context of the rotamer approximation

The rotamer approximation states that protein side-chain conformations can be described well using a finite set of rotational isomers. This approximation is often applied in the context of computational protein design and structure prediction to reduce the complexity of structural sampling. It is an effective way of reducing the structure space to the most relevant conformations. However, the appropriateness of rotamers for sampling structure space does not imply that a rotamer-based energy landscape preserves any of the properties of the true continuous energy landscape. Specifically, because the energy of a van der Waals interaction can be very sensitive to small changes in atomic separation, meaningful van der Waals energies are particularly difficult to calculate from rotamer-based structures. This presents a problem for computational protein design, where the total energy of a given structure is often represented as a sum of precalculated rigid rotamer self and pair contributions. A common way of addressing this issue is to modify the van der Waals function to reduce its sensitivity to atomic position, but excessive modification may result in a strongly nonphysical potential. Although many different van der Waals modifications have been used in protein design, little is known about which performs best, and why. In this paper, we study 10 ways of computing van der Waals energies under the rotamer approximation, representing four general classes, and compare their performance using a variety of metrics relevant to protein design and native-sequence repacking calculations. Scaling van der Waals radii by anywhere from 85 to 95% gives the best performance. Linearizing and capping the repulsive portion of the potential can give additional improvement, which comes primarily from getting rid of unrealistically large clash energies. On the other hand, continuously minimizing individual rotamer pairs prior to evaluating their interaction works acceptably in native-sequence repacking, but fails in protein design. Additionally, we show that the problem of predicting relevant van der Waals energies from rotamer-based structures is strongly nonpairwise decomposable and hence further modifications of the potential are unlikely to give significant improvement.     

Ultra-fast evaluation of protein energies directly from sequence

The structure, function, stability, and many other properties of a protein in a fixed environment are fully specified by its sequence, but in a manner that is difficult to discern. We present a general approach for rapidly mapping sequences directly to their energies on a pre-specified rigid backbone, an important sub-problem in computational protein design and in some methods for protein structure prediction. The cluster expansion (CE) method that we employ can, in principle, be extended to model any computable or measurable protein property directly as a function of sequence. Here we show how CE can be applied to the problem of computational protein design, and use it to derive excellent approximations of physical potentials. The approach provides several attractive advantages. First, following a one-time derivation of a CE expansion, the amount of time necessary to evaluate the energy of a sequence adopting a specified backbone conformation is reduced by a factor of 10(7) compared to standard full-atom methods for the same task. Second, the agreement between two full-atom methods that we tested and their CE sequence-based expressions is very high (root mean square deviation 1.1-4.7 kcal/mol, R2 = 0.7-1.0). Third, the functional form of the CE energy expression is such that individual terms of the expansion have clear physical interpretations. We derived expressions for the energies of three classic protein design targets-a coiled coil, a zinc finger, and a WW domain-as functions of sequence, and examined the most significant terms. Single-residue and residue-pair interactions are sufficient to accurately capture the energetics of the dimeric coiled coil, whereas higher-order contributions are important for the two more globular folds. For the task of designing novel zinc-finger sequences, a CE-derived energy function provides significantly better solutions than a standard design protocol, in comparable computation time. Given these advantages, CE is likely to find many uses in computational structural modeling.     

Pseudo-esterase activity of human albumin: slow turnover on tyrosine 411 and stable acetylation of 82 residues including 59 lysines

Human albumin is thought to hydrolyze esters because multiple equivalents of product are formed for each equivalent of albumin. Esterase activity with p-nitrophenyl acetate has been attributed to turnover at tyrosine 411. However, p-nitrophenyl acetate creates multiple, stable, acetylated adducts, a property contrary to turnover. Our goal was to identify residues that become acetylated by p-nitrophenyl acetate and determine the relationship between stable adduct formation and turnover. Fatty acid-free human albumin was treated with 0.5 mm p-nitrophenyl acetate for 5 min to 2 weeks, or with 10 mm p-nitrophenyl acetate for 48 h to 2 weeks. Aliquots were digested with pepsin, trypsin, or GluC and analyzed by mass spectrometry to identify labeled residues. Only Tyr-411 was acetylated within the first 5 min of reaction with 0.5 mm p-nitrophenyl acetate. After 0.5-6 h there was partial acetylation of 16-17 residues including Asp-1, Lys-4, Lys-12, Tyr-411, Lys-413, and Lys-414. Treatment with 10 mm p-nitrophenyl acetate resulted in acetylation of 59 lysines, 10 serines, 8 threonines, 4 tyrosines, and Asp-1. When Tyr-411 was blocked with diisopropylfluorophosphate or chlorpyrifos oxon, albumin had normal esterase activity with beta-naphthyl acetate as visualized on a nondenaturing gel. However, after 82 residues had been acetylated, esterase activity was almost completely inhibited. The half-life for deacetylation of Tyr-411 at pH 8.0, 22 degrees C was 61 +/- 4 h. Acetylated lysines formed adducts that were even more stable. In conclusion, the pseudo-esterase activity of albumin is the result of irreversible acetylation of 82 residues and is not the result of turnover.     

Mechanism of hydrolysis of dicholine esters with long polymethylene chain by human butyrylcholinesterase

Human butyrylcholinesterase hydrolyzes long chain dicholine esters more rapidly than short chain dicholine esters. The active site of butyrylcholinesterase is deeply buried within the enzyme molecule and there is limited space for binding of large compounds. Our goal was to understand how butyrylcholinesterase accommodates long chain dicholine esters to make them better substrates than short chain dicholine esters. For this purpose we studied the rate of hydrolysis of adipyldicholine (n=4) and sebacyldicholine (n=8) with mass spectrometry, a method that allowed monitoring the dicholine substrates, the monocholine intermediates, the dicarboxylic acid and choline products. It was shown that hydrolysis of adipyldicholine involves two consecutive steps, dicholine ester hydrolysis followed by relatively slow monocholine ester hydrolysis. However, sebacyldicholine was hydrolyzed at both choline ester sites, though hydrolysis of dicholine was faster than hydrolysis of monocholine. Sebacyldicholine was completely converted to sebacic acid and choline within 90 min, whereas only 15% of the adipyldicholine was converted to adipic acid in this time. Molecular modeling indicated that these dicholine esters can bind to butyrylcholinesterase in two energetically equivalent alternative conformations that may theoretically lead to hydrolysis. The long chain dicholine ester makes closer contact than the short chain ester between one of its carbonyl carbons and the catalytic Ser198, thus explaining why long-chain dicholine esters are hydrolyzed more rapidly by butyrylcholinesterase.     

Changes in the Relative Number of Bipolar-Like Cells in the Retina of Pleurodeles waltl as a Function of Age and as a Result of Light Exposure

The study of the population of bipolar-like cells (displaced bipolars) was continued in order to establish their role in development and regeneration of the retina in lower vertebrates. The size of the population of these cells was estimated on serial semithin sections in the retina of normal eyes in adult and young newt Pleurodeles waltl, as well as in adult newts subjected to long-term bright illumination. The population of displaced bipolars was significantly increased with reference to all cells of the outer nuclear layer. In young and illuminated animals, their numbers were approximately 1.3 and 1.4 times that in the adult animals not exposed to constant light. The results obtained favor the earlier suggestion of the involvement of the displaced bipolars in growth and restoration of the outer nuclear layer in the retina of newts during development and after trauma.     

A spin-label for RNA study

The compound 2,2,6,6-tetramethyl-4-[β-N-ethyleneiminopropionyl] oxypiperidine-I-oxyl is used as a spin-label for RNA. The reaction, effected under rather mild conditions, results in 50–70 nucleotides per spin-label. The temperature dependence of the ESR spectra of spin-labeled RNA is used to estimate temperatures corresponding to the beginning of melting, T_crit (“critical” points of the structure) and to calculate the effective activation energies of the rotational mobility of spin-labels, Δ E_eff.; the dependence of T_crit. on the ionic strength of the solution is also determined.