Mechanism of proteolysis in matrix metalloproteinase‐2 revealed by QM/MM modeling

The mechanism of enzymatic peptide hydrolysis in matrix metalloproteinase‐2 (MMP‐2) was studied at atomic resolution through quantum mechanics/molecular mechanics (QM/MM) simulations. An all‐atom three‐dimensional molecular model was constructed on the basis of a crystal structure from the Protein Data Bank (ID: 1QIB), and the oligopeptide Ace‐Gln‐Gly～Ile‐Ala‐Gly‐Nme was considered as the substrate. Two QM/MM software packages and several computational protocols were employed to calculate QM/MM energy profiles for a four‐step mechanism involving an initial nucleophilic attack followed by hydrogen bond rearrangement, proton transfer, and C? N bond cleavage. These QM/MM calculations consistently yield rather low overall barriers for the chemical steps, in the range of 5–10 kcal/mol, for diverse QM treatments (PBE0, B3LYP, and BB1K density functionals as well as local coupled cluster treatments) and two MM force fields (CHARMM and AMBER). It, thus, seems likely that product release is the rate‐limiting step in MMP‐2 catalysis. This is supported by an exploration of various release channels through QM/MM reaction path calculations and steered molecular dynamics simulations. © 2015 Wiley Periodicals, Inc.     

The effect of a low-molecular-mass salt on stoichiometric polyelectrolyte complexes composed of oppositely charged macromolecules with different solvent affinities

The effect of a low-molecular-mass salt on the thermodynamic stability of stoichiometric interpolymer complexes composed of oppositely charged macromolecules with different solvent affinities has been theoretically studied. It has been shown that the dissociation of such complexes with an increase in the concentration of the salt proceeds via several stages. At a low concentration of the salt, complexes retain their structure and dimensions. When a certain critical concentration of the salt n _s^cr is achieved, the dimensions of the complex increase abruptly. At this concentration, macromolecules involved in the complex begin to separate, and at concentration n _s^*, they fully move apart but remain soluble owing to the polyelectrolyte effect. Upon a further increase in the concentration of the salt, the polyelectrolyte effect is shielded and the dimensions of macromolecules decrease. The critical concentration of the low-molecular-mass salt, n _s^cr, increases with an increase in the degree of ionization of macromolecules and a decrease in the affinity of the hydrophilic component for water and diminishes with the degree of polymerization of macromolecules and the degree of hydrophobicity of a polycation. Because of the easy formation of soluble complexes from oppositely charged macromolecules differing in solvent affinities and their high stability in solutions of a low-molecularmass salt, such complexes are promising for wide use in medicine and pharmaceutical practice.     

Minor polyphenols from <Emphasis Type="Italic">Maackia amurensis</Emphasis> wood

The rare α,4,2′,4′-tetrahydroxydihydrochalcone, flavanones liquiritigenin and naringenin, isoflavones calycosin and 5-methoxydaidzein, and reduced stilbene dihydroresveratrol were isolated for the first time from Maackia amurensis wood. The structures of the pure compounds were established using 2D NMR COSY, NOE, HMBC, and HSQC experiments. Translated from Khimiya Prirodnykh Soedinenii, No. 6, pp. 575–577, November–December, 2008.     

Secondary structure of globules of copolymers consisting of amphiphilic and hydrophilic units: Effect of potential range

The relation of the coil-globule transition in macromolecules consisting of amphiphilic and hydrophilic monomer units to the radius of action of the interaction potential is investigated by the method of computer-assisted experiments. The internal structure of globules formed by such macromolecules is significantly dependent on the radius of action of the potential. In the case of the long-range potential, the globule is characterized by the blob structure, while in the case of the short-range potential, a quasi-helical structure forms. In this structure, the skeleton of a macromolecule forms a helical turn, and the direction of twisting may vary from one turn to another. The coil-globule transition in such macromolecules proceeds through formation of the necklace conformation from quasi-helical micelle beads. For sufficiently long macromolecules, the dimensions of such globules are linearly dependent on the degree of polymerization.     

Catalytic reactions in emulsions in the presence of a polymeric catalyst

The theory of reactions between a surface-active substrate and a polymeric catalyst in emulsions has been developed. The conditions under which the rate of reaction in such systems substantially surpasses the rate of reaction in homogeneous systems have been determined and the regimes that make it possible to reduce the total time of the process have been established.     

Distribution of Zinc Oxide Nanocrystals in a Polymer Film

The structure of polymer films modified with zinc oxide nanocrystals was studied by the optical absorption and small-angle X-ray scattering methods. Small-angle X-ray scattering allows determination of the nanoparticle size distribution function, which is the decisive factor in predicting the optical properties of heterophase materials, including filled polymer films. The optical absorption spectrum of an acrylate polymer film doped with 1.6 wt % zinc oxide nanocrystals approaches the ideal absorber spectrum, which allows this material to be recommended for use as a protective color filter.     

Adsorption of amphiphilic comb-shaped macromolecules on a patterned surface

The molecular-dynamics method is used to study the adsorption of A-graft-B macromolecules on patterned planar surfaces consisting of regions a and b that specifically interact with chain units. Surfaces with patterns in the form of circles of different radii and a spiral stripe are discussed. Effective recognition occurs during the adsorption of an A-graft-B macromolecule on these patterned surfaces. Recognition means that, for a proper combination of the architecture of a macromolecule and the energy parameters of its interaction with the plane regions, the macromolecule can be located along the boundary of a circle with a given radius or can stay in a given location of the spiral stripe.