Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution.

In this paper, we evaluated the ability of four coarse-grained methods to predict protein flexible regions with potential biological importance, UNRES-flex, UNRES-DSSP-flex (based on the united residue model of polypeptide chains without and with secondary structure restraints, respectively), CABS-flex (based on the C-α, C-ß, and side chain model), and nonlinear rigid block normal mode analysis (NOLB) with a set of 100 protein structures determined by NMR spectroscopy or X-ray crystallography, with all secondary structure types. End regions with high fluctuations were excluded from analysis. The Pearson and Spearman correlation coefficients were used to quantify the conformity between the calculated and experimental fluctuation profiles, the latter determined from NMR ensembles and X-ray B-factors, respectively. For X-ray structures (corresponding to proteins in a crowded environment), NOLB resulted in the best agreement between the predicted and experimental fluctuation profiles, while for NMR structures (corresponding to proteins in solution), the ranking of performance is CABS-flex > UNRES-DSSP-flex > UNRES-flex > NOLB; however, CABS-flex sometimes exaggerated the extent of small fluctuations, as opposed to UNRES-DSSP-flex.

Controlling the europium oxidation state in diopside through flux concentration.

This paper explores the connection between the H3BO3 flux concentration and the co-existence of Eu2+ and Eu3+ dopants within CaMgSi2O6 crystals (diopside). The samples were synthesised using a solid-state synthesis method under varying atmospheric conditions, including oxidative (air), neutral (N2), and reductive (H2/N2 mixture) environments. Additionally, some materials underwent chemical modification by partially substituting Si4+ with Al3+ ions acting as charge compensation defects stabilizing Eu3+ luminescence. Depending on the specific synthesis conditions, the materials predominantly displayed either the orange-red luminescence of Eu3+ (under oxidising conditions) or the blue luminescence of Eu2+; however, the comprehensive results confirmed the co-existence of Eu3+/Eu2+ luminescence in both cases. This work shows that varying flux concentrations added during synthesis significantly affect the relative strength of Eu2+ and Eu3+ emissions in a manner dependent on the synthesis atmosphere. The emission of Eu2+ increases with a higher flux concentration in materials synthesised under oxidative and neutral atmospheres independent of the chemical modification. In contrast, for materials obtained under a reductive atmosphere, the changes in the Eu3+ emission intensity depended on the presence or absence of Al3+ ions namely the increase of flux increased the Eu3+ intensity in the case of unmodified materials and decreased in the Al-modified ones. All observed effects were qualitatively explained considering the double role of the flux in the studied system, which besides facilitating the diffusion of chemical species during synthesis acts as a charge compensating agent by creating B'Si centres stabilizing Eu3+ emission.

Molecular docking-based test for affinities of two ligands toward vasopressin and oxytocin receptors.

Molecular docking simulations are now fast developing area of research. In this work we describe an effective procedure of preparation of the receptor-ligand complexes. The amino-acid residues involved in ligand binding were identified and described.

Molecular modeling of interactions of the non-peptide antagonist YM087 with the human vasopressin V1a, V2 receptors and with oxytocin receptors.

The nonapeptide hormones arginine vasopressin (CYFQNCPRG-NH2, AVP) and oxytocin (CYIQNCPLG-NH2, OT), control many essential functions in mammals. Their main activities include the urine concentration (via stimulation of AVP V2 receptors, V2R, in the kidneys), blood pressure regulation (via stimulation of vascular V1a AVP receptors, V1aR), ACTH control (via stimulation of V1b receptors, V1bR, in the pituitary) and labor and lactation control (via stimulation of OT receptors, OTR, in the uterus and nipples, respectively). All four receptor subtypes belong to the GTP-binding (G) protein-coupled receptor (GPCR) family. This work consists of docking of YM087, a potent non-peptide V1aR and V2R - but not OTR - antagonist, into the receptor models based on relatively new theoretical templates of rhodopsin (RD) and opiate receptors, proposed by Mosberg et al. (Univ. of Michigan, Ann Arbor, USA). It is simultaneously demonstrated that this RD template satisfactorily compares with the first historical GPCR structure of bovine rhodopsin (Palczewski et al., 2000) and that homology-modeling of V2R, V1aR and OTR using opiate receptors as templates is rational, based on relatively high (20-60%) sequence homology among the set of 4 neurophyseal and 4 opiate receptors. YM087 was computer-docked to V1aR, V2R and OTR using the AutoDock (Olson et al., Scripps Research Institute, La Jolla, USA) and subsequently relaxed using restrained simulated annealing and molecular dynamics, as implemented in AMBER program (Kollman et al., University of California, San Francisco, USA). From about 80 diverse configurations, sampled for each of the three ligand/receptor systems, 3 best energy-relaxed complexes were selected for mutual comparisons. Similar docking modes were found for the YM087/V1aR and YM087/V2R complexes, diverse from those of the YM087/OTR complexes, in agreement with the molecular affinity data.

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.