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Structure Elements (structure + element)
Kinds of Structure Elements Selected AbstractsHierarchical structure of niobate nanosheets in aqueous solutionJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2007Satoshi Koizumi The hierarchical structure of an aqueous dispersion of niobate nanosheets was explored by using a combined method of ultra-small-angle and small-angle scattering of neutrons and X-rays. The concentration of the sheets studied was in the range where the dispersion exhibits a liquid-crystal phase as evidenced by observation between crossed polarizers in a previous report. The scattering data covered a wide q scale of more than four orders of magnitude [3 × 10,4,q, 10,nm,1, where q = (4,/,)sin(,/2), , and , being the wavelength of the incident beam and the scattering angle, respectively], corresponding to the length scale l = 2,/q from ~1,nm to ~20,µm. The scattering analyses provided information on the hierarchical structural elements including: (i) single nanosheets as a structure element (hierarchy I), (ii) parallel stacks of the sheets (hierarchy II), and (iii) spatial arrangements of the stacks (hierarchy III), in order of increasing length scale. Hierarchy II is closely related to the liquid-crystal nature of the dispersion in which the spacing and the persistence length, normal and parallel to the stack surface, respectively, were disclosed. Hierarchy III gives rise to the low- q upturn in the scattering profile, which may be characterized by mass-fractal-like power-law scattering behavior. This finding is a surprise from the viewpoint of the liquid-crystal nature of the dispersion, a possible model of which is proposed in the text. [source] HCV RNA-dependent RNA polymerase replicates in vitro the 3, terminal region of the minus-strand viral RNA more efficiently than the 3, terminal region of the plus RNAFEBS JOURNAL, Issue 22 2001Sandrine Reigadas The NS5B protein, or RNA-dependent RNA polymerase of the hepatitis virus type C, catalyzes the replication of the viral genomic RNA. Little is known about the recognition domains of the viral genome by the NS5B. To better understand the initiation of RNA synthesis on HCV genomic RNA, we used in vitro transcribed RNAs as templates for in vitro RNA synthesis catalyzed by the HCV NS5B. These RNA templates contained different regions of the 3, end of either the plus or the minus RNA strands. Large differences were obtained depending on the template. A few products shorter than the template were synthesized by using the 3, UTR of the (+) strand RNA. In contrast the 341 nucleotides at the 3, end of the HCV minus-strand RNA were efficiently copied by the purified HCV NS5B in vitro. At least three elements were found to be involved in the high efficiency of the RNA synthesis directed by the HCV NS5B with templates derived from the 3, end of the minus-strand RNA: (a) the presence of a C residue as the 3, terminal nucleotide; (b) one or two G residues at positions +2 and +3; (c) other sequences and/or structures inside the following 42-nucleotide stretch. These results indicate that the 3, end of the minus-strand RNA of HCV possesses some sequences and structure elements well recognized by the purified NS5B. [source] Towards protein folding with evolutionary techniquesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2005Florian Koskowski Abstract We present design details and first tests of a new evolutionary algorithm approach to ab initio protein folding. It does not focus on dihedral angles exclusively, but mainly operates on introduction, extension, break-up, and destruction of secondary structure elements, given as correlated dihedral angle values. In first test applications to polyalanines (up to 60 residues) and random primary sequences (up to 40 residues), we demonstrate that this use of prior knowledge is well balanced: On the one hand, it ensures quick introduction of secondary structure elements if they are favorable for a given primary sequence, but still allows for efficient location of pure random coil solutions without enforcing any secondary structure elements, if folds of this type are preferred by the given primary sequence. Furthermore, the algorithm is clearly able to pack several secondary structure elements into favorable tertiary structure arrangements, although no part of the algorithm is explicitly designed to do this. In first test examples on real-life peptides between 21 and 44 residues from the Protein Data Bank, the quality of the results depends on the force field used (as expected); nevertheless, we can show that the algorithm is able to find structures in good agreement with the targets easily and consistently, if the force field allows for that. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1169,1179, 2005 [source] New energy terms for reduced protein models implemented in an off-lattice force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2001Tommi Hassinen Abstract Parameterization and test calculations of a reduced protein model with new energy terms are presented. The new energy terms retain the steric properties and the most significant degrees of freedom of protein side chains in an efficient way using only one to three virtual atoms per amino acid residue. The energy terms are implemented in a force field containing predefined secondary structure elements as constraints, electrostatic interaction terms, and a solvent-accessible surface area term to include the effect of solvation. In the force field the main-chain peptide units are modeled as electric dipoles, which have constant directions in ,-helices and ,-sheets and variable conformation-dependent directions in loops. Protein secondary structures can be readily modeled using these dipole terms. Parameters of the force field were derived using a large set of experimental protein structures and refined by minimizing RMS errors between the experimental structures and structures generated using molecular dynamics simulations. The final average RMS error was 3.7 Å for the main-chain virtual atoms (C, atoms) and 4.2 Å for all virtual atoms for a test set of 10 proteins with 58,294 amino acid residues. The force field was further tested with a substantially larger test set of 608 proteins yielding somewhat lower accuracy. The fold recognition capabilities of the force field were also evaluated using a set of 27,814 misfolded decoy structures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1229,1242, 2001 [source] Limited tendency of ,-helical residues to form disulfide bridges: a structural explanationJOURNAL OF PEPTIDE SCIENCE, Issue 12 2006Alfonso De Simone Abstract Disulfide bridges have an enormous impact on the structure of a large number of proteins and polypeptides. Understanding the structural basis that regulates their formation may be important for the design of novel peptide-based molecules with a specific fold and stability. Here we report a statistical analysis of the relationships between secondary structure and disulfide bond formation, carried out using a large database of protein structures. Our analyses confirm the observation sporadically reported in previous investigations that cysteine residues located in ,-helices display a limited tendency to form disulfide bridges. The very low occurrence of the disulfide bond in all ,-chains compared to all ,-chains indicates that this property is also evident when proteins with different topologies are investigated. Taking advantage of the large database that endorsed the analysis on relatively rare motifs, we demonstrate that cysteine residues embedded in 310 helices present a good tendency to form disulfide bonds. This result is somewhat surprising since 310 helices are commonly assimilated into ,-helices. A plausible structural explanation for the observed data has been derived combining analyses of disulfide bond sequence separation and of the length of the different secondary structure elements. Copyright © 2006 European Peptide Society and John Wiley & Sons, Ltd. [source] Self-Assembled PEO-Peptide Nanotapes as Ink for Plotting Nonwoven Silica Nanocomposites and Mesoporous Silica Fiber NetworksMACROMOLECULAR RAPID COMMUNICATIONS, Issue 4 2008Stefanie Kessel Abstract Macroscopic networks of oriented polymer-silica composite fibers can be accessed via a convenient 2D-plotting process. By using self-assembled PEO-peptide nanotapes as an ink to draw the composite fibers, the macroscopic form of the fiber networks, the line width, and both network orientation as well as network anisotropy can be defined. The plotting process relies on a biomimetic silicification route, which combines self-assembly and peptide-directed silicification in a cooperative manner. The local injection of PEO-peptide nanotapes into a thin layer of a dilute solution of pre-hydrolyzed TMOS leads to the rapid formation of the composite fibers, which exhibit several levels of hierarchical order. It was shown, that the rate of plotting is a parameter, enabling one to control the line width and the orientation of the nano- and sub-micrometer structure elements in the network. Moreover, the plotted composite fibers can be used as precursors for networks of oriented, mesoporous silica-fibers. After calcination procedures, nonwoven silica fabrics can be obtained with high surface areas and cylindrical pores aligned in plot direction. [source] Numerical Analysis of a Cyclical Loaded Construction under Corrosion DegradationPROCEEDINGS IN APPLIED MATHEMATICS & MECHANICS, Issue 1 2005W. Dudda A contribution for analytical and numerical tools that permits of a deterministic evaluation of structure behavior in external conditions, under multiparameter and/or cyclic mechanical, thermal and chemical loads, is the aim of this paper. Particular structure elements undergo the plastic and corrosion degradation and they dissipate energy, which consists of irreversible contributions, like a work on the inelastic strains. The construction and its unit lifetime are estimated according to a dissipated energy criterion. The paper emphasizes the modeling and numerical implementation of degradation effects, such as cyclic plasticity, generated by mechanical and thermal loads, stress corrosion, electrochemical corrosion and low-cyclic corrosion. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structurePROTEIN SCIENCE, Issue 1 2006Russell Schwartz Abstract Patterns of alternation of hydrophobic and polar residues are a profound aspect of amino acid sequences, but a feature not easily interpreted for soluble proteins. Here we report statistics of hydrophobicity patterns in proteins of known structure in a current protein database as compared with results from earlier, more limited structure sets. Previous studies indicated that long hydrophobic runs, common in membrane proteins, are underrepresented in soluble proteins. Long runs of hydrophobic residues remain significantly underrepresented in soluble proteins, with none longer than 16 residues observed. These long runs most commonly occur as buried , helices, with extended hydrophobic strands less common. Avoiding aggregation of partially folded intermediates during intracellular folding remains a viable explanation for the rarity of long hydrophobic runs in soluble proteins. Comparison between database editions reveals robustness of statistics on aqueous proteins despite an approximately twofold increase in nonredundant sequences. The expanded database does now allow us to explain several deviations of hydrophobicity statistics from models of random sequence in terms of requirements of specific secondary structure elements. Comparison to prior membrane-bound protein sequences, however, shows significant qualitative changes, with the average hydrophobicity and frequency of long runs of hydrophobic residues noticeably increasing between the database editions. These results suggest that the aqueous proteins of solved structure may represent an essentially complete sample of the universe of aqueous sequences, while the membrane proteins of known structure are not yet representative of the universe of membrane-associated proteins, even by relatively simple measures of hydrophobic patterns. [source] Intermediates and the folding of proteins L and GPROTEIN SCIENCE, Issue 4 2004Scott Brown Abstract We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G, which are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted ,-1 and ,-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding, and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third ,-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally, the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first-order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment. [source] The structure and dynamics in solution of Cu(I) pseudoazurin from Paracoccus pantotrophusPROTEIN SCIENCE, Issue 5 2000Gary S. Thompson Abstract The solution structure and backbone dynamics of Cu(I) pseudoazurin, a 123 amino acid electron transfer protein from Paracoccus pantotrophus, have been determined using NMR methods. The structure was calculated to high precision, with a backbone RMS deviation for secondary structure elements of 0.35 ± 0.06 A, using 1,498 distance and 55 torsion angle constraints. The protein has a double-wound Greek-key fold with two ,-helices toward its C-terminus, similar to that of its oxidized counterpart determined by X-ray crystallography. Comparison of the Cu(I) solution structure with the X-ray structure of the Cu(II) protein shows only small differences in the positions of some of the secondary structure elements. Order parameters S2, measured for amide nitrogens, indicate that the backbone of the protein is rigid on the picosecond to nanosecond timescale. [source] Fourier transform infrared spectroscopy suggests unfolding of loop structures precedes complete unfolding of pig citrate synthaseBIOPOLYMERS, Issue 4 2003Feride Severcan Abstract Pig citrate synthase (PCS) can be used as a model enzyme to gain some insight into the structural basis of protein thermostability. The thermal unfolding characteristics of the specific secondary structure elements within PCS were monitored in detail by following changes in its amide I band components. The result of our study indicates that PCS undergoes irreversible thermal denaturation. Detailed analysis reveals that the different secondary structures display a multistep transition with a major and a minor transition at different temperatures and a very small initial transition at the same temperature (30°C). A plot of temperature-induced changes in 1H,2H exchange, the decrease in the absorbance of the ,-helical structures, and the increase in the absorbance of aggregated structures all have in common a multistep transition, the minor one centered at 45°C and the major one around 59°C. In contrast, a band that is tentatively assigned to loop structures displays these same minor and major transitions but at lower temperatures (39 and 52°C, respectively). The transition, which occurs at 39,45°C, is not associated with the appearance of aggregated structures. This transition may reflect a change in the tertiary structure of the protein. However, the final transition, which occurs at a higher temperature (52,59°C), reflects unfolding and aggregation of the polypeptide chains. The Fourier transform infrared (FTIR) analysis suggests that PCS has a thermolabile region that unfolds first, some 7°C below the main unfolding of the protein. We propose that this reflects the unfolding of the highly flexible loop segments, which in turn triggers the unfolding of the predominantly helical core structure of PCS. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 440,447, 2003 [source] Distinct effects of atypical 1,4-dihydropyridines on 1-methyl-4-phenylpyridinium-induced toxicityCELL BIOCHEMISTRY AND FUNCTION, Issue 1 2007Linda Klimaviciusa Abstract Our previous data obtained from in vivo experiments demonstrated high neuroprotective effects of three novel atypical neuronal non-calcium antagonistic 1,4-dihydropyridine (DHP) derivatives cerebrocrast, glutapyrone and tauropyrone. The present studies were carried out in vitro to clarify, at least in part, their mechanism of action in primary culture of cerebellar granule cells by use of 1-methyl-4-phenylpyridinium (MPP+) as a neurotoxic agent which causes dramatic oxidative stress. Cerebrocrast (highly lipophilic, with a classical two-ring structure) dose-dependently (0.01,10.0,µM, EC50,=,13,nM) reduced MPP+ -induced cell death. At the same time, the calcium antagonist nimodipine (reference drug) protected cell death at much higher concentrations (EC50,=,12.4,µM). Cerebrocrast decreased also the generation of reactive oxygen species and loss of mitochondrial membrane potential. In contrast, low lipophilic amino acid-containing DHPs glutapyrone and tauropyrone (glutamate- and taurine-containing, correspondingly) were without significant effects indicating their distinct mode of action in comparison to cerebrocrast. We have demonstrated for the first time an ability of atypical non-calcium antagonistic DHP cerebrocrast (which has classical DHP structure elements and high lipophilicity) to protect MPP+ -induced deterioration of mitochondrial bioenergetics. One may suggest mitochondria as an essential intracellular target for the neuroprotective action of cerebrocrast and indicate its usefulness in the treatment of Parkinson's disease. Copyright © 2006 John Wiley & Sons, Ltd. [source] | ||||||||||