Docking ligands to vasopressin and oxytocin receptors via genetic algorithm.

The aim of the study was to computer-dock selected ligands to neurophyseal receptors in order to identify amino acid residues responsible for ligand-receptor interactions. To this aim, reliable oxytocin receptor (OTR) and arginine-vasopressin receptor (V1aR/V2R) models were built. The OTR-selective agonist [Thr4,Gly7]OT, the OTR-selective cyclohexapeptide antagonist L-366,948 and OT itself were docked via genetic algorithm to OTR, V1aR, and V2R and relaxed using a constrained simulated annealing protocol. For the analysis of receptor/ligand interactions a subset of initial conformations was chosen using energetic and steric criteria. All three ligands seem to prefer similar modes of binding to the receptors, manifested by repetitive residues of the receptors which directly interact with the ligands. Taking into account that many aspects of mechanisms of G protein-coupled receptor (GPCR) action are still unsolved, the results obtained with the docking simulations may propose future experimental research, especially in site-directed mutagenesis analysis and searching for key amino acid residues responsible for drug activities.

The investigation of the effects of counterions in protein dynamics simulations.

Molecular simulations able to exactly represent solvated charged proteins are helpful in understanding protein dynamics, structure and function. In the present study we have used two different starting structures of papain (a typical, stable, globular protein of intermediate net charge) and different modeling procedures to evaluate some effects of counterions in simulations. A number of configurations have been generated and relaxed for each system by various combinations of constrained simulated annealing and molecular dynamics procedures, using the AMBER force field. The analysis of trajectories shows that the simulations of solvated proteins are moderately sensitive to the presence of counterions. However, this sensitivity is highly dependent on the starting model and different procedures of equilibration used. The neutralized systems tend to evince smaller root mean square deviations regardless of the system investigated and the simulation procedure used. The results of parameterized fitting of the simulated structures to the crystallographic data, giving quantitative measure of the total charge influence on the stability of various elements of the secondary structure, revealed a clear scatter of different reactions of various systems' secondary structures to counterions addition: some systems apparently were stabilized when neutralized, while the others were not. Thus, one cannot unequivocally state, despite consideration of specific simulation conditions, whether protein secondary structures are more stable when they have neutralized charges. This suggests that caution should be taken when claiming the stabilizing effect of counterions in simulations other than those involving small, unstable polypeptides or highly charged proteins.

Structural studies of cysteine proteases and their inhibitors.

Cysteine proteases (CPs) are responsible for many biochemical processes occurring in living organisms and they have been implicated in the development and progression of several diseases that involve abnormal protein turnover. The activity of CPs is regulated among others by their specific inhibitors: cystatins. The main aim of this review is to discuss the structure-activity relationships of cysteine proteases and cystatins, as well as of some synthetic inhibitors of cysteine proteases structurally based on the binding fragments of cystatins.

Signal transmission via G protein-coupled receptors in the light of rhodopsin structure determination.

G protein-coupled receptors (GPCRs) transducing diverse external signals to cells via activation of heterotrimeric GTP-binding (G) proteins, estimated to mediate actions of 60% of drugs, had been resistant to structure determination until summer 2000. The first atomic-resolution experimental structure of a GPCR, that of dark (inactive) rhodopsin, thus provides a trustworthy 3D prototype for antagonist-bound forms of this huge family of proteins. In this work, our former theoretical GPCR models are evaluated against the new experimental template. Subsequently, a working hypothesis regarding the signal transduction mechanism by GPCRs is presented.

Theoretical studies of binding modes of two covalent inhibitors of cysteine proteases.

Physiological and pathological roles of cysteine proteases make them important targets for inhibitor development. Although highly potent inhibitors of this group of enzymes are known, their major drawback is a lack of sufficient specificity. Two cysteine protease covalent inhibitors, viz. (i) Z-RL-deoxo-V-peptide-epoxysuccinyl hybrid, and (ii) Z-RLVG-methyl-, have been developed and modeled in the catalytic pocket of papain, an archetypal thiol protease. A number of configurations have been generated and relaxed for each system using the AMBER force field. The catalytic pockets S3 and S4 appear rather elusive in view of the observed inhibitors' flexibility. This suggest rather limited chances for the development of selective structure-based inhibitors of thiol proteases, designed to exploit differences in the structure of catalytic pockets of various members of this family.