Effects of medium polarization and pre-existing field on activation energy of enzymatic charge-transfer reactions

The highly organized spatial structure of proteins' polar groups results in the existence of a permanent intraprotein electric field and in protein's weak dielectric response, i.e. its low dielectric constant. The first factor affects equilibrium free energy gap of a charge-transfer reaction, the second (medium polarization effect) influences both equilibrium and non-equilibrium (reorganization) energies, decreasing the latter substantially. In the framework of the rigorous 'fixed-charge-density' formalism, the medium polarization component of the reaction activation energy has been calculated, both for the activation energy of the elementary act proper, and the effective activation energy accounting for the charges' transfer from water into a low-dielectric structureless medium. In all typical cases of reactions, the energy spent for charge transfer from water into structureless 'protein' is larger than the gain in activation energy due to the protein's low reorganization energy. Therefore, the low dielectric constant of proteins is not sufficient to ensure their high catalytic activity, and an additional effect of the pre-existing intraprotein electric field, compensating for an excessive charging energy, is necessary. Only a combined action of low reorganization energy and pre-existing electric field provides proteins with their high catalytic activity. The dependence of activation energy on the globule geometry has been analyzed. It is shown that, for each reaction, an optimum set of geometric parameters exists. For five hydrolytic enzymes, the optimum globule radii have been calculated using the experimental geometry of their active sites. The calculated radii agree satisfactorily with the real sizes of these macromolecules, both by absolute and by relative values.     

Prediction of the three-dimensional structure of aflatoxin of Aspergillus flavus by homology modelling

Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus spp. The toxic effects of aflatoxins have adverse consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a protein containing a zinc-finger DNA-binding motif. AFLR-Protein three-dimensional model was generated using Robetta server. The modeled AFLR-Protein was further optimization and validation using Rampage. In the simulations, we monitored the backbone atoms and the C-α-helix of the modeled protein. The low RMSD and the simulation time indicate that, as expected, the 3D structural model of AFLR-protein represents a stable folding conformation. This study paves the way for generating computer molecular models for proteins whose crystal structures are not available and which would aid in detailed molecular mechanism of inhibition of aflatoxin.     

Mapping the amino acid properties of constituent nucleoporins onto the yeast nuclear pore complex

Visualization of molecular structures aids in the understanding of structural and functional roles of biological macromolecules. Macromolecular transport between the cell nucleus and cytoplasm is facilitated by the nuclear pore complex (NPC). The ring structure of the NPC is large and contains several distinct proteins (nucleoporins) which function as a selective gate for the passage of certain molecules into and out of the nucleus. In this note we demonstrate the utility of a python code that allows direct mapping of the physiochemical properties of the constituent nucleoporins on the scaffold of the yeast NPC׳s cytoplasmic view. We expect this tool to be useful for researchers to visualize the NPC based on their physiochemical properties and how it alters when specific mutations are introduced in one or more of the nucleoporins. The code developed using Python is available freely from the authors.     

The treatment of isolated genera

Problems presented by genera, or small groups of genera, which have been given family rank are reviewed, and the genera are divided into a number of categories according to the closeness of their affinity to other genera or families. Satellite genera that stand in close relation to families should be united with them. Binary families, that have been divided into two (or more) related families, should be re–united. Families connected by linking genera, should, logically, be united but practical considerations usually prevent this. Clusters of diverse but more or less distantly related genera present unusual problems, being treated either as several, often monogeneric families or as a loosely structured family. Truly isolated genera must be given family and often ordinal rank.     

Adsorption of dimethylsulfoxide on proteins

A method for measuring the adsorption of dimethyl sulfoxide on native and denatured trypsin and albumin was developed. On native proteins, no positive adsorption was registered, and a slight negative adsorption within the limits of experimental error was observed. It was shown that the properties of denatured proteins depend on the mode and conditions of denaturation. On one of denatured trypsin specimens, positive adsorption of dimethyl sulfoxide was registered, on other specimens no adsorption was observed. The reason for this behavior lies in the hydrophobic nature of adsorption of dimethyl sulfoxide at the interface, while the surface of native protein globules and, probably, most denatured protein specimens is hydrophilic.     

The intraglobular electrostatic field of an enzyme. II. Effect of environment polarization

The influence of polarization of surrounding medium on the intraglobular electric field of the alpha-chymotrypsin molecule is considered. The polarization is taken into account by the image charges method, the proper approximations for calculation of the fields due to intraglobular and surface charges are suggested. The polarization of surroundings does not change the qualitative picture of the electric field in the active center of the alpha-chymotrypsin molecule set up by protein dipoles, but reduces almost to zero the intraglobular field set up by surface ions.     

The intraglobular electrostatic field of an enzyme. 1. The primary field created by the polypeptide core, functional groups and ions of the alpha-chymotrypsin molecule

The electric field set up by the dipoles of peptide groups ad other dipoles at the atoms of substrate and catalytic groups of alpha-chymotrypsin is considered. It is shown that substantial electric potentials reaching some tenths of volts exist in the active center of the enzyme, the fact which must influence significantly the reactivity of corresponding groups. In contrast to low molecular weight liquids, the contribution to the total potential of dipoles located at different distances from the point under consideration often changes nonmonotonically with the distance, sometimes the predominant influence being exerted not by the nearest polar groups but by the more distant ones. The existence of electric fields having a complex spatial configuration determined by the protein structure can be defined as the effect of the polar medium preorganization. Emphasis is placed on the necessity of taking into account the polarization of the external medium by charges of protein atoms and ions (the difference of primary and secondary electric fields).     

Intraglobular electrostatic field of an enzyme. Calculation of the dissociation constant of a protein ionogenic group. Dissociation of Asp-102 chymotrypsin

Factors determining the change of dissociation constants of ionogenic groups upon their transfer from water into a protein globule are considered. The change of the short-range interaction is simulated with the aid of two model solvents: dimethylformamide (DMF) and formamide (FA). The change of Bornian solvation energy is calculated taking into account the interaction of ions situated inside a protein globule with the surrounding electrolyte solution. The change of ion energy due to the intraglobular electric field preexisting in the enzyme molecule is calculated. Each of the factors listed above gives a large contribution into the ion energy in the case of Asp-102 these contributions compensate each other to a great extent.