Molecular dynamics study of 4-OH-phenylacetyl-D-Y(Me)FQNRPR-NH2 selectivity to V1a receptor

G protein-coupled receptors relay diverse extracellular signals into cells via a common mechanism, involving activation of cytosol G proteins. The mechanism underlies the actions of ~50% of all drugs. In this work, we focus on simulating three protein–ligand complexes of the neurohypophyseal hormone analog 4-OH-phenylacetyl-D-Y(Me)FQNRPR-NH₂ (I) with the human V1a, V2 and oxytocin receptors. The peptide I is a potent selective V1a receptor antagonist. To obtain relaxed models of the complexes, the following techniques were used: docking of I into the vasopressin V1a, V2 and oxytocin receptor models, optimization of the geometry of the resulting complexes and molecular dynamics in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine lipid bilayer. The results of the simulations allow us to draw some conclusions about the ligand selectivity to V1aR.     

AMI and PM3 study of a low molecular weight structural mimic of hydrogen exchange within the catalytic center of aspartic proteases

Based on recent X-ray studies, a low molecular weight model of the active center of aspartic proteases is proposed. The model is small enough to enable unattended geometry optimizations (including search for saddle-points) by molecular orbital methods. It consists of two malonic acid molecules and a water molecule; there is a carboxylic dimer at one end and the water molecule is located between the carboxylate and the carboxyl group at the other. The latter structure reproduces the geometry of the catalytic center of the native enzyme penicillopepsin with a root-mean-square deviation of 0.46 Å for five O--O distances. The AMI and PM3 molecular orbital methods were used to study the H-bond exchange within the model. Both methods lead consistently to the following conclusions: Among 2 pairs of symmetry-equivalent stationary states of the catalytic center there are at least 4 symmetry-independent hydrogen-exchange pathways, and many more when including symmetry of the center. Energetics and geometry of all identified pathways are presented. In summary, they result in juggling all three active center protons (COON and HOH) among all five active center oxygens (COO^–, COOH and H₂O) providing the center with a high delocalisation with respect to the actual position of its anionic site and/or its protonation status. The relevance of the delocalisation of the acidic proton to the mechanism of enzymatic action is briefly discussed. Correspondence to: J. Ciarkowski     

CNDO/2 quantum-mechanical calculations of the conformational flexibility of the diketopiperazine skeleton

Eight conformers typical of diketopiperazine (DKP) ring folding were chosen for analysis. Conformational energy calculations were carried out using the semiempirical quantummechanical CNDO/2 method. The results obtained confirm considerable flexibility of the DKP skeleton. As the degree of folding increases, twisted boat conformations with the nonplanar peptide bonds tend to be more stable, while more rigid regular boat conformations with planar peptide bonds appear to be less stable than a flat one. The CNDO/2 method was found to be reliable enough for conformational studies of cyclic peptide skeletons with cis-peptide bonds.     

A hypothesis for GPCR activation

Growing evidence that rhodopsin (RD) and related G protein-coupled receptors form functional dimers/oligomers, followed by direct proof (using atomic force microscopy) that in the retina disc membrane RD associates into a paracrystalline network of rows of dimers, need models of the RD-transducin (Gt) complex that would envision an optimal RD dimer/oligomer able to satisfy all well-documented interactions with Gt. Of the models proposed so far, only a few refer to RD dimers and only one of them proposes a complex of Gt with an RD oligomer (Filipek S, Krzyko KA, Fotiadis D, Liang Y, Saperstein DA, Engel, A, Palczewski K Photochem Photobiol Sci 3: 628–638, 2004). This paper puts forward a hypothesis on another arrangement of RD monomers into the reported network of rows of dimers. Arguments for the compatibility of this set-up with interactions and activation of RD in the complex with Gt, in particular, with the well-documented movement of transmembrane helix 6 and cytosolic loop 3, which is vital for RD activation, are provided and discussed.This revised version was published online in June 2005 with corrections to the acknowledgements.     

The role of the L2 loop in the regulation and maintaining the proteolytic activity of HtrA (DegP) protein from Escherichia coli

The aim of this study was to characterize the role of particular elements of the regulatory loop L2 in the activation process and maintaining the proteolytic activity of HtrA (DegP) from Escherichia coli. We measured the effects of various mutations introduced to the L2 loop’s region (residues 228-238) on the stability of HtrA molecule and its proteolytic activity. We demonstrated that most mutations affected the activity of HtrA. In the case of the following substitutions: L229N, N235I, I238N, the proteolytic activity was undetectable. Thus, the majority of interactions mediated by the studied amino-acid residues seem to play important role in maintaining the active conformation. Formation of contacts between the apical parts (residues 231-234) of the L2 loops within the HtrA trimer, in particular the residues D232, was shown to play a crucial role in the activation process of HtrA. Stabilization of these intermolecular interactions by substitution of D232 with valine caused a stimulation of proteolytic activity whereas deletion of this region abolished the activity. Since the pathogenic E. coli strains require active HtrA for virulence, the apical part of L2 is of particular interest in terms of structure-based drug design for treatment E. coli infections.     

Interaction of class A G protein-coupled receptors with G proteins

A model for interaction of classA G protein-coupled receptor with the G protein G(alpha) subunit is proposed using the rhodopsin-transducin (RD/Gt) prototype. The model combines the resolved interactions/distances, essential in the active RD*/Gt system, with the structure of Gt(alpha) C-terminal peptide bound to RD* while stabilizing it. Assuming the interactions involve conserved parts of the partners, the model specifies the conserved Helix 2 non-polar X- - -X, Helix 3 DRY and Helix 7/8 NP- -Y- - F RD* motifs interacting with the Gt(alpha) C-terminal peptide, in compliance with the structure of the latter. A concomitant role of Gt(alpha) and Gt(gamma) C-termini in stabilizing RD* could possibly be resolved assuming a receptor dimer as requisite for G protein activation.