The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first-principles calculations

Protein kinases are important enzymes controlling the majority of cellular signaling events via a transfer of the gamma-phosphate of ATP to a target protein. Even after many years of study, the mechanism of this reaction is still poorly understood. Among many factors that may be responsible for the 1011-fold rate enhancement due to this enzyme, the role of the conserved aspartate (Asp166) has been given special consideration. While the essential presence of Asp166 has been established by mutational studies, its function is still debated. The general base catalyst role assigned to Asp166 on the basis of its position in the active site has been brought into question by the pH dependence of the reaction rate, isotope measurements, and pre-steady-state kinetics. Recent semiempirical calculations have added to the controversy surrounding the role of Asp166 in the catalytic mechanism. No major role for Asp166 has been found in these calculations, which have predicted the reaction process consisting of an early transfer of a substrate proton onto the phosphate group. These conclusions were inconsistent with experimental observations. To address these differences between experimental results and theory with a more reliable computational approach and to provide a theoretical platform for understanding catalysis in this important enzyme family, we have carried out first-principles structural and dynamical calculations of the reaction process in cAPK kinase. To preserve the essential features of the reaction, representations of all of the key conserved residues (82 atoms) were included in the calculation. The structural calculations were performed using the local basis density functional (DFT) approach with both hybrid B3LYP and PBE96 generalized gradient approximations. This kind of calculation has been shown to yield highly accurate structural information for a large number of systems. The optimized reactant state structure is in good agreement with X-ray data. In contrast to semiempirical methods, the lowest energy product state places the substrate proton on Asp166. First-principles molecular dynamics simulations provide additional support for the stability of this product state. The latter also demonstrate that the proton transfer to Asp166 occurs at a point in the reaction where bond cleavage at the PO bridging position is already advanced. This mechanism is further supported by the calculated structure of the transition state in which the substrate hydroxyl group is largely intact. A metaphoshate-like structure is present in the transition state, which is consistent with the X-ray structures of transition state mimics. On the basis of the calculated structure of the transition state, it is estimated to be 85% dissociative. Our analysis also indicates an increase in the hydrogen bond strength between Asp166 and substrate hydroxyl and a small decrease in the bond strength of the latter in the transition state. In summary, our calculations demonstrate the importance of Asp166 in the enzymatic mechanism as a proton acceptor. However, the proton abstraction from the substrate occurs late in the reaction process. Thus, in the catalytic mechanism of cAPK protein kinase, Asp166 plays a role of a "proton trap" that locks the transferred phosphoryl group to the substrate. These results resolve prior inconsistencies between theory and experiment and bring new understanding of the role of Asp166 in the protein kinase catalytic mechanism.     

Synthesis of Diels–Alder adducts of the quinolizidine alkaloids N-methylcytisine, (−)-leontidine,and (−)-thermopsine with N-phenylmaleimide

The Diels–Alder adducts of the quinolizidine alkaloids N-methylcytisine, (?)-leontidine, and (?)-thermopsine with N-phenylmaleimide have been synthesized. The structures and absolute configurations of the new asymmetric centers of the products were determined by NMR spectroscopy experiments, QC-calculations, and X-ray data.     

Chitosan nanostructures deposited from solutions in carbonic acid on a model substrate as resolved by AFM

Chitosan macromolecules can be dissolved in water saturated with CO₂ under high pressure, i.e. in carbonic acid. This unique biocompatible solvent with acidity regulated by the variation of applied CO₂ pressure is rather promising for biomedical applications. In this work the main features of deposition of chitosan structures on the model substrate from solutions in this media were examined. After deposition on the mica surface, the obtained structures have been successfully visualised by atomic force microscopy (AFM). It has been found out that they adsorb as rather peculiar elongated objects with an average length of about 70?nm. Such conformations are believed to appear due to amphiphilic nature of chitosan semiflexible chains in agreement with recent theoretical findings. The well-defined geometry of the elongated monodispersed structures allows them to demonstrate some elements of liquid crystalline-like ordering.     

Multiarm Star-Shaped Polydimethylsiloxanes with a Dendritic Branching Center

New multiarm stars have been synthesized based on polylithium derivatives of high-generation carbosilane dendrimers. In the synthesis of multiarm stars based on the eighth-generation dendrimer, steric hindrances were observed even during the synthesis of a polylithium initiator. Subsequently, this led to chain transfer reactions between growing arms, as well as other side effects. As a result, dense nanogel formations with a higher tendency of ordering than in classical objects of this type were isolated from the reaction mixture. The study of the rheology of multiarm stars based on sixth-generation dendrimers made it possible to determine the activation energies of viscous flow in these objects, which makes it possible to consider them as objects with a macromolecular nature and a reptation flow mechanism.     

Umbilic point screening in random optical fields

Umbilic points--singular points of curvature characterized by a fractional topological charge q=+/-1/2--are the most numerous of all special points in the landscape of random optical fields (speckle patterns), outnumbering maxima, minima, saddle points, and optical vortices. To the best of our knowledge, we present the first experimental evidence that positive and negative umbilic points screen one another. Theory predicts that in the absence of screening the charge variance in a bounded region is proportional to the area of the region, whereas in the presence of screening the variance is drastically reduced and is proportional to the perimeter. Our data confirm this latter prediction and provide the first estimates of the screening lengths for umbilic points of the intensity and of the amplitude (field modulus).     

The Electronic Ground State of [Fe(CO)3(NO)]−: A Spectroscopic and Theoretical Study

During the past 10 years iron‐catalyzed reactions have become established in the field of organic synthesis. For example, the complex anion [Fe(CO)₃(NO)]^?, which was originally described by Hogsed and Hieber, shows catalytic activity in various organic reactions. This anion is commonly regarded as being isoelectronic with [Fe(CO)₄]^2?, which, however, shows poor catalytic activity. The spectroscopic and quantum chemical investigations presented herein reveal that the complex ferrate [Fe(CO)₃(NO)]^? cannot be regarded as a Fe^?II species, but rather is predominantly a Fe⁰ species, in which the metal is covalently bonded to NO^? by two π‐bonds. A metal–N σ‐bond is not observed.     

On non-linear dynamics and control designs applied to the ideal and non-ideal variants of the Fitzhugh–Nagumo (FN) mathematical model

The Fitzhugh–Nagumo (FH) mathematical model is considered a simplification of the Hodgkin–Huxley (HH) model. This paper analyzes the non-linear dynamics of the Fitzhugh–Nagumo (FN) mathematical model, and still presents some modifications in the governing equations of the system in order to transform it into a non-ideal one (taking into account that an energy source has limited power supply). We also developed an optimal linear control design and used Sinhas’s theory for the membrane’s action potential in order to stabilize the variation of this potential.     

Vortex fluctuations in underdoped Bi(2)Sr(2)CaCu(2)O(8+delta) crystals

Vortex thermal fluctuations in heavily underdoped Bi(2)Sr(2)CaCu(2)O(8+delta) (T(c)=69.4 K) are studied using Josephson plasma resonance. From the zero-field data, we obtain the c-axis penetration depth lambda(L,c)(0)=230+/-10 micrometer and the anisotropy ratio gamma(T). The low plasma frequency allows us to study phase correlations over the whole vortex solid state and to extract a wandering length r(w) of vortex pancakes. The temperature dependence of r(w) as well as its increase with dc magnetic field is explained by the renormalization of the vortex line tension by the fluctuations, suggesting that this softening is responsible for the dissociation of the vortices at the first order transition.     

Complements for enumeration Π 1 0 -degrees

We consider the question of the existence of complements for the enumeration degrees of cocomputably enumerable sets in the local structure of e-degrees.