Structural organization of [met]enkephalin and endorphin molecules. II. Theoretical conformation analysis of alpha-, gamma- and delta-endorphins]

Conformational energy calculations were carried out for neuropeptides alpha-, gamma- and delta-endorphins, which are 1-16, 1-17 and 1-19 fragments respectively, of beta-endorphin. The proposed computational scheme yielded all possible low-energy conformational sets for these hormones. Specific features of spatial organization of each compound and similarities of their structures are discussed.     

Conformational changes of contractile proteins accompanying modulation of skeletal muscle contraction. Polarized microfluorometry investigations

Results of studies on the modulation of skeletal muscle contraction by phosphorylation of myosin regulatory light chains and by exchange of magnesium for calcium in myosin heads were reviewed. The polarized fluorescence method was used in these studies, and conformational changes of contractile proteins accompanying modulation of skeletal muscle contraction were investigated. It was found that both the exchange of bound magnesium for calcium on myosin heads and the phosphorylation of myosin regulatory light chains control the ability of myosin heads to induce, upon binding to actin, conformational changes of thin filament leading to decrease or increase of its flexibility. The changes in actin filament flexibility may be caused by alteration of both the inter- and the intramonomer structural organization.     

Conformational properties of the CalliFMRF-amide series neuropeptides

Conformational properties of five neuropeptides belonging to the calliFMRF-amide series with the Xaa-Pro-Yaa-Gln-Asp-Phe-Met-Arg-Phe-NH2 homologous sequences were studied by the method of theoretical conformational analysis. Three members of these group (1) (Xaa = Thr, Yaa = Gln), (2) (Xaa = Thr, Yaa = Ser), and (3) (Xaa = Yaa = Ser) can stimulate the saliva secretion from the separated salivary gland of the Calliphora vomitoria fly, whereas two other calliFMRF-amides (4) (Xaa = Lys, Yaa = Asn) and (5) (Xaa = Ala, Yaa = Gly) are inactive in this biological test. Low-energy spatial structures of the studied compounds were determined by a conformational analysis. A comparison of the stable structures of the biologically active and inactive neuropeptides revealed a similarity in their conformational properties and allowed determination of the role of separate residues in the peptide folding. The calculations demonstrated that the C-terminal hexapeptide fragment identical in all the five peptides tends to form alpha-helical structure, whereas the variable N-terminal tripeptide regions of CalliFMRF-amides (1)-(5) form more conformationally flexible structures.     

Conformational properties of neuromedin NmU-8 and its modified analogs

The comparative study of the spatial organization and conformational properties of NmU-8 neuropeptide and its modified analogs with available experimental data has been carried out. The effect of amino acids point mutation on conformational states of native neuropeptide has been discussed. The low-energy conformations responsible for neuropeptide contractile activity was revealed.     

Conservation of Flexible Residue Clusters among Structural and Functional Enzyme Homologues

Conformational flexibility between structural ensembles is an essential component of enzyme function. Although the broad dynamical landscape of proteins is known to promote a number of functional events on multiple time scales, it is yet unknown whether structural and functional enzyme homologues rely on the same concerted residue motions to perform their catalytic function. It is hypothesized that networks of contiguous and flexible residue motions occurring on the biologically relevant millisecond time scale evolved to promote and/or preserve optimal enzyme catalysis. In this study, we use a combination of NMR relaxation dispersion, model-free analysis, and ligand titration experiments to successfully capture and compare the role of conformational flexibility between two structural homologues of the pancreatic ribonuclease family: RNase A and eosinophil cationic protein (or RNase 3). In addition to conserving the same catalytic residues and structural fold, both homologues show similar yet functionally distinct clusters of millisecond dynamics, suggesting that conformational flexibility can be conserved among analogous protein folds displaying low sequence identity. Our work shows that the reduced conformational flexibility of eosinophil cationic protein can be dynamically and functionally reproduced in the RNase A scaffold upon creation of a chimeric hybrid between the two proteins. These results support the hypothesis that conformational flexibility is partly required for catalytic function in homologous enzyme folds, further highlighting the importance of dynamic residue sectors in the structural organization of proteins.     

Reverse-phase separation and electrochemical detection of neuropeptides

The reverse-phase separation of neuropeptides using isocratic conditions is described. Each component of the mobile phase was examined for its ability to influence the separation of complex mixtures of neuropeptides. Manipulation of buffer strength, pH, organic modifier and column type provided sufficient flexibility to resolve closely related neuropeptides. Amperometric detection of oxidizable amino acids in the peptide sequence of a number of endogenous neuropeptides proved suitable for the identification of peptide standards and quantification of neural lobe arginine vasopressin and striatal methionine enkephalin.     

Atomistic and coarse-grained analysis of double spectrin repeat units: the molecular origins of flexibility

Spectrin is an ubiquitous protein in metazoan cells, and its flexibility is one of the keys to maintaining cellular structure and organization. Both alpha-spectrin and beta-spectrin polypeptides consist primarily of triple coiled-coil modular repeat units, and two important factors that determine spectrin flexibility are the bending flexibility between two consecutive repeat units and the conformational flexibility of individual repeat units. Atomistic molecular dynamics (MD) simulations are used here to study double spectrin repeat units (DSRUs) from the human erythrocyte beta-spectrin (HEbeta89) and the chicken brain alpha-spectrin (CBalpha1617). From the results of MD simulations, a highly conserved Trp residue in the A-helix of most repeat units that has been suggested to be important in conferring stability to the coiled-coil structures is found not to have a significant effect on the conformational flexibility of individual repeat units. Characterization of the bending flexibility for two consecutive repeats of spectrin via atomistic simulations and coarse-grained (CG) modeling indicate that the bending flexibility is governed by the interactions between the AB-loop of the first repeat unit, the BC-loop of the second repeat unit and the linker region. Specifically, interactions between residues in these regions can lead to a strong directionality in the bending behavior of two repeat units. The biological implications of these finding are discussed.     

Conformational stability of serine proteinase inhibitor from the sea anemone Heteractis crispa

The influence of different environmental values of the pH and temperature on the spatial organization of serine proteinase inhibitor from the sea anemone Heteractis crispa (=Radianthus macrodactylus) on the level of tertiary and secondary structure was studied by CD spectroscopy. The molecule InhVJ was shown to possess a high conformational thermo- and pH-stability. We determined the point of conformational thermotransition of polypeptide (70 degrees C) after which the molecule gets denaturational stable state with conservation of 80% proteinase inhibitory activity. The significant partial reversible changes of molecule spatial organization were established to occur at the level of tertiary structure in the process of acid-base titration in the range of pH 11.0-13.0. This can be explained by of ionization of tyrosine residues. The molecule InhVJ is conformationally stable at the low pH values (2.0). The quenching of tyrosine residues by acrylamide showed that two of these residues are accessible to the quencher in full, while the third part is available.     

Bordatella pertussis adenylate cyclase: a toxin with multiple talents

Bordetella pertussis secretes a calmodulin-activated adenylate cyclase toxin (CyaA) that is able to deliver its amino-terminal catalytic domain into the cytosol of eukaryotic cells. The novelty of the structural organization and conformational flexibility of the CyaA catalytic domain has opened up the way for exploiting this protein as a tool for several biological applications, including epitope delivery, protein targeting and characterization of protein-protein interactions.     

The conformational stability and flexibility of insulin with an additional intramolecular cross-link

The conformational stability and flexibility of insulin containing a cross-link between the alpha-amino group of the A-chain to the epsilon-amino group of Lys29 of the B-chain was examined. The cross-link varied in length from 2 to 12 carbon atoms. The conformational stability was determined by guanidine hydrochloride-induced equilibrium denaturation and flexibility was assessed by H2O/D2O amide exchange. The cross-link has substantial effects on both conformational stability and flexibility which depend on its length. In general, the addition of a cross-link enhances conformational stability and decreases flexibility. The optimal length for enhanced stability and decreased flexibility was the 6-carbon link. For the 6-carbon link the Gibbs free energy of unfolding was 8.0 kcal/mol compared to 4.5 kcal/mol for insulin, and the amide exchange rate decreased by at least 3-fold. A very short cross-link (i.e. the 2-carbon link) caused conformational strain that was detectable by a lack of stabilization in the Gibbs free energy of unfolding and enhancement in the amide exchange rate compared to insulin. The effect of the cross-link length on insulin hydrodynamic properties is discussed relative to previously obtained receptor binding results.     

Spatial organization and conformational mobility of DNA complexed with nucleoproteins]

The importance of spatial organization of DNA for the regulation of genome activity is discussed. The main problem reviewed in this paper includes cooperative interactions of proteins with DNA, formation of DNA loops in the regulatory domains of the genome and conformational mobility of DNA in chromatin.     

Biophysical and biochemical mechanisms by which dietary N-3 polyunsaturated fatty acids from fish oil disrupt membrane lipid rafts

N-3 polyunsaturated fatty acids (PUFAs) from fish oil exert their functional effects by targeting multiple mechanisms. One mechanism to emerge in the past decade is the ability of n-3 PUFA acyl chains to perturb the molecular organization of plasma membrane sphingolipid/cholesterol-enriched lipid raft domains. These domains are nanometer-scale assemblies that coalesce to compartmentalize select proteins for optimal function. Here we review recent evidence on how n-3 PUFAs modify lipid rafts from biophysical and biochemical experiments from several different model systems. A central theme emerges from these studies. N-3 PUFA acyl chains display tremendous conformational flexibility and a low affinity for cholesterol and saturated acyl chains. This unique flexibility of n-3 PUFA acyl chains impacts the organization of inner and outer leaflet lipid rafts by disrupting acyl chain packing and molecular order within rafts. Ultimately, the disruption in raft organization has consequences for protein clustering and thereby signaling. Overall, elucidating the complex mechanisms by which n-3 PUFA acyl chains reorganize membrane architecture will enhance the translation of these fatty acids into the clinic for treating several diseases.     

Space use in the root vole: basic patterns and variability

Home range characteristics and spatial organization of the root vole Microtus oeconomus were assessed by radio-tracking The aim of this paper is to test the assumption that each microtine species employs a certain modal spatial system around which there is considerable flexibility In the studied population the basic modes of spatial organization were female territoriality and male use of overlapping home ranges Female territories were significantly smaller and less diversified in size than male ranges The size of male home ranges was positively correlated with body mass Each female territory was overlapped by several male ranges, larger male ranges usually overlapped more female territories The above spatial organization suggests that the prevailing mating system in the root vole is promiscuity, and larger males have an access to more receptive females than have small-sized males
Departures from these basic modes were found among young mature females from summer cohort, forming clusters even at low density, and occasionally among females in locally crowded habitat patches, where they held overlapping home ranges A single male usually monopolized such a cluster, excluding other males from the area used by the females     

Molecular organization and structural stability of beta s-crystallin from calf lens

beta s-Crystallin has been purified to homogeneity. Its structural features and conformational behavior have been studied in solution. Protein secondary structure was estimated by curve fitting of far-UV circular dichroism spectra, which gave 16% alpha-helix, 45% beta-sheet, 12% bends, and 27% remainders. This result indicates that the structural organization of beta s-crystallin is reasonably similar to that of other beta and gamma family members. A comparison assessed between beta s- and gamma 2-crystallin by the use of predictive methods (flexibility and volume plots) reveals that the two proteins differ in respect to their local flexibility and packing, although they show similar overall organization. The interdomain and the C-terminal regions were found to be more flexible in beta s-crystallin. This finding can be explained by the presence of smaller amino acid residues within these structural districts. The location of one out of four tryptophans, i.e., Trp-162, in a flexible and exposed region of the protein was found to be the origin of the fluorescence heterogeneity. In fact, the fluorescence emission maximum of the native protein, centered at 328 nm, is due to two emitting centers, whose emission maxima are located at 323 and 330 nm, respectively, as evidenced by acrylamide quenching of fluorescence. The effect of perturbing agents, such as pH and guanidine hydrochloride, on the conformational behavior of beta s has also been evaluated by numerous spectroscopic techniques. The range of pH stability was between 6.5 and 8.(ABSTRACT TRUNCATED AT 250 WORDS)     

Structure-function organization of neurokinin A and neurokinin B molecules. III. A conformational study of glycine-monosubstituted analogues of neurokinins A and B

The conformational features of some glycine-monosubstituted analogues of neurokinins A and B were investigated by the method of theoretical conformational analysis. The calculated geometry and energy parameters permitted one to determine the structural role of each of these substituted amino acids in the mechanism of folding of the low-energy conformational states of neuropeptides. On the basis of the calculated data and the results of biological tests of these analogues, the structure-function relationships of neurokinins A and B were discussed.     

Conformational Properties of the CalliFMRF-Amide Series Neuropeptides

Conformational properties of five neuropeptides belonging to the calliFMRF-amide series with the Xaa-Pro-Yaa-Gln-Asp-Phe-Met-Arg-Phe-NH₂ homologous sequences were studied by the method of theoretical conformational analysis. Three members of these group [(1) (Xaa = Thr, Yaa = Gln), (2) (Xaa = Thr, Yaa = Ser), and (3) (Xaa = Yaa = Ser)] can stimulate the saliva secretion from the separated salivary gland of the Calliphora vomitoria fly, whereas two other calliFMRF-amides [(4) (Xaa = Lys, Yaa = Asn) and (5) (Xaa = Ala, Yaa = Gly)] are inactive in this biological test. Low-energy spatial structures of the studied compounds were determined by a conformational analysis. A comparison of the stable structures of the biologically active and inactive neuropeptides revealed a similarity in their conformational properties and allowed determination of the role of separate residues in the peptide folding. The calculations demonstrated that the C-terminal hexapeptide fragment identical in all the five peptides tends to form -helical structure, whereas the variable N-terminal tripeptide regions of calliFMRF-amides (1)–(5) form more conformationally flexible structures.     

Resistance to heating and trypsin of glutamate dehydrogenase from liver mitochondria of frogs differing in thermotaxis]

The resistances to heat and trypsin hydrolysis served as indirect indices of conformational flexibility of glutamate dehydrogenase molecules. No difference in heat resistance was found between crystalline eletrophoretically homogeneous preparations of glutamate dehydrogenase from liver mitochondria of two species of frogs, the more southern Rana ridibunda and the more northern R. temporaria. However, glutamate dehydrogenase from R. ridibunda is digested by trypsin at a lower rate than that from R. temporaria, which may be explained by its lower conformational flexibility. Therefore positive correlation between conformational flexibility of glutamate dehydrogenase and mean ambient temperature of the species studied is revealed only with respect to resistance to proteolysis.     

The spatial configuration of ordered polynucleotide chains. II. The poly(rA) helix.

Approximate details of the spatial configuration of the ordered single-stranded poly(rA) molecule in dilute solution have been obtained in a combined theoretical analysis of base stacking and chain flexibility. Only those regularly repeating structures which fulfill the criterion of conformational flexibility (based upon all available experimental and theoretical evidence of preferred bond rotations) and which also exhibit the right-handed base stacking pattern observed in nmr investigations of poly(rA) are deemed suitable single-stranded helices. In addition, the helical geometry of the stacked structures is required to be consistent with the experimentally observed dimensions of both completely ordered and partially ordered poly(rA) chains. Only a single category of poly(rA) helices (very similar in all conformational details to the individual chains of the poly(rA) double-stranded X-ray structure) is thus obtained. Other conformationally feasible polynucleotide helices characterized simply by a parallel and overlapping base stacking arrangement are also discussed.