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Helix Structure (helix + structure)
Selected AbstractsAgeing of soft thermoplastic starch with high glycerol contentJOURNAL OF APPLIED POLYMER SCIENCE, Issue 1 2007Rui Shi Abstract In this study, a soft and thermoplastic starch with an improved ageing-resistant property was prepared by melt blending method for a biodegradable biomaterial. The glycerol content varies from 30 to 60 wt %. The aging temperature and humidity of the glycerol-plasticized thermoplastic starch (GTPS) was 37°C and 50 ± 5 RH %, respectively. The retrogradation was characterized by X-ray diffraction (XRD), dynamic mechanical thermal analysis (DMTA), Fourier transform infrared (FTIR), and the stress-strain mechanical properties. The XRD results suggest that high content of glycerol promotes the formation of single helix structure of V-type, but inhibits double helix structure of B-type. Changing of the tan ,, storage modules (E,), and the glass transition temperatures as a function of glycerol content and ageing time was detected by DMTA. FTIR result shows that the shifting speed of the peak of hydroxyl group stretching fell as the glycerol content increased. The glycerol content has no obvious effect on the mechanical properties when it is high enough. Results from all characterizations demonstrate that the ageing speed is closely relative to the plasticizers content. The higher content of glycerol possesses an obviously inhibitory effect on the ageing. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 103: 574,586, 2007 [source] The conformation of fusogenic B18 peptide in surfactant solutions,JOURNAL OF PEPTIDE SCIENCE, Issue 4 2008Sandra Rocha Abstract The interaction of B18 peptide with surfactants has been studied by circular dichroism spectroscopy and fluorescence measurements. B18 is the fusogenic motif of the fertilization sea urchin protein. The peptide forms an ,-helix structure when interacting with positively or negatively charged surfactants below and above the critical micellar concentration (CMC). The ,-helix formation is due to binding of surfactant monomers rather than the formation of surfactant micelles on the peptide. Fluorescence measurements show that the CMC of the negatively charged surfactant increases in the presence of B18, supporting the fact that there is a strong interaction between the peptide and monomers. Nonionic surfactant monomers have no effect on the peptide structure, whereas the micelles induce an ,-helical conformation. In this case the helix stabilization results from the formation of surfactant micelles on the peptide. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] Vibrational Spectroscopic Studies on the Disulfide Formation and Secondary Conformational Changes of Captopril,HSA Mixture after UV-B IrradiationPHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 6 2005Mei-Jane Li ABSTRACT The effects of pH and ultraviolet-B (UV-B) irradiation on the secondary structure of human serum albumin (HSA) in the absence or presence of captopril were investigated by an attenuated total reflection (ATR)/Fourier transform infrared (FTIR) spectroscopy. The UV-B exposure affecting the stability of captopril before and after captopril,HSA interaction was also examined by using confocal Raman microspectroscopy. The results indicate that the transparent pale-yellow solution for captopril,HSA mixture in all pH buffer solutions, except pH 5.0,7.0, changed into a viscous form then a gel form with UV-B exposure time. The secondary structural transformation of HSA in the captopril,HSA mixture with or without UV-B irradiation was found to shift the maxima amide I peak in IR spectra from 1652 cm,1 assigned to ,-helix structure to 1622 cm,1 because of a ,-sheet structure, which was more evident in pH 3.0, 8.0 or 9.0 buffer solutions. The Raman shift from 1653 cm,1 (,-helix) to 1670 cm,1 (,-sheet) also confirmed this result. Captopril dissolved in distilled water with or without UV-B irradiation was determined to form a captopril disulfide observed from the Raman spectra of 512 cm,1, which was exacerbated by UV-B irradiation. There was little disulfide formation in the captopril,HSA mixture even with long-term UV-B exposure, but captopril might interact with HSA to change the protein secondary structure of HSA whether there was UV-B irradiation or not. The pH of the buffer solution and captopril,HSA interaction may play more important roles in transforming the secondary structure of HSA from ,-helix to ,-sheet in the corresponding captopril,HSA mixture than UV-B exposure. The present study also implies that HSA has the capability to protect the instability of captopril in the course of UV-B irradiation. In addition, a partial unfolding of HSA induced by pH or captopril-HSA interaction under UV-B exposure is proposed. [source] Neuro-fuzzy structural classification of proteins for improved protein secondary structure predictionPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 8 2003Joachim A. Hering Abstract Fourier transform infrared (FTIR) spectroscopy is a very flexible technique for characterization of protein secondary structure. Measurements can be carried out rapidly in a number of different environments based on only small quantities of proteins. For this technique to become more widely used for protein secondary structure characterization, however, further developments in methods to accurately quantify protein secondary structure are necessary. Here we propose a structural classification of proteins (SCOP) class specialized neural networks architecture combining an adaptive neuro-fuzzy inference system (ANFIS) with SCOP class specialized backpropagation neural networks for improved protein secondary structure prediction. Our study shows that proteins can be accurately classified into two main classes "all alpha proteins" and "all beta proteins" merely based on the amide I band maximum position of their FTIR spectra. ANFIS is employed to perform the classification task to demonstrate the potential of this architecture with moderately complex problems. Based on studies using a reference set of 17 proteins and an evaluation set of 4 proteins, improved predictions were achieved compared to a conventional neural network approach, where structure specialized neural networks are trained based on protein spectra of both "all alpha" and "all beta" proteins. The standard errors of prediction (SEPs) in % structure were improved by 4.05% for helix structure, by 5.91% for sheet structure, by 2.68% for turn structure, and by 2.15% for bend structure. For other structure, an increase of SEP by 2.43% was observed. Those results were confirmed by a "leave-one-out" run with the combined set of 21 FTIR spectra of proteins. [source] Structural analysis of an MK2,inhibitor complex: insight into the regulation of the secondary structure of the Gly-rich loop by TEI-I01800ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2010Aiko Fujino Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2 or MK2) is a Ser/Thr kinase from the p38 mitogen-activated protein kinase signalling pathway and plays an important role in inflammatory diseases. The crystal structure of the complex of human MK2 (residues 41,364) with the potent MK2 inhibitor TEI-I01800 (pKi = 6.9) was determined at 2.9,Å resolution. The MK2 structure in the MK2,TEI-I01800 complex is composed of two domains, as observed for other Ser/Thr kinases; however, the Gly-rich loop in the N-terminal domain forms an ,-helix structure and not a ,-sheet. TEI-I01800 binds to the ATP-binding site as well as near the substrate-binding site of MK2. Both TEI-I01800 molecules have a nonplanar conformation that differs from those of other MK2 inhibitors deposited in the Protein Data Bank. The MK2,TEI-I01800 complex structure is the first active MK2 with an ,-helical Gly-rich loop and TEI-I01800 regulates the secondary structure of the Gly-rich loop. [source] A strained DNA binding helix is conserved for site recognition, folding nucleation, and conformational modulation,BIOPOLYMERS, Issue 6 2009Diana E. Wetzler Abstract Nucleic acid recognition is often mediated by ,-helices or disordered regions that fold into ,-helix on binding. A peptide bearing the DNA recognition helix of HPV16 E2 displays type II polyproline (PII) structure as judged by pH, temperature, and solvent effects on the CD spectra. NMR experiments indicate that the canonical ,-helix is stabilized at the N-terminus, while the PII forms at the C-terminus half of the peptide. Re-examination of the dihedral angles of the DNA binding helix in the crystal structure and analysis of the NMR chemical shift indexes confirm that the N-terminus half is a canonical ,-helix, while the C-terminal half adopts a 310 helix structure. These regions precisely match two locally driven folding nucleii, which partake in the native hydrophobic core and modulate a conformational switch in the DNA binding helix. The peptide shows only weak and unspecific residual DNA binding, 104 -fold lower affinity, and 500-fold lower discrimination capacity compared with the domain. Thus, the precise side chain conformation required for modulated and tight physiological binding by HPV E2 is largely determined by the noncanonical strained ,-helix conformation, "presented" by this unique architecture. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 432,443, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Structure of the ,-Homo-DNA:RNA Duplex and the Function of Twist and Slide To Catalogue Nucleic Acid DuplexesCHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2007Koen Nauwelaerts Dr. Abstract High-resolution NMR studies of an ,-homo-DNA:RNA duplex reveal the formation of a right-handed parallel-oriented helix. It differs significantly from a standard A- or B-type helix by a small twist value (26.2°), which leads to a helical pitch of 13.7 base pairs per helical turn, a negative inclination (,1.78 Å) and a large x displacement (5.90 Å). The rise (3.4 Å) is similar to that found in B-DNA. The solution of this new helix structure has stimulated us to develop a mathematical and geometrical model based on slide and twist parameters to describe nucleic acid duplexes. All existing duplexes can be positioned within this landscape, which can be used to understand the helicalization process. [source] Self-assembling properties of ionic-complementary peptides,JOURNAL OF PEPTIDE SCIENCE, Issue 3 2009Gabriella D'Auria Abstract Self-complementary synthetic peptides, composed by 8 and 16 residues, were analyzed by CD, NMR and small angle neutron scattering (SANS) techniques in order to investigate the relevance of charge and hydrophobic interactions in determining their self-assembling properties. All the sequences are potentially able to form fibrils and membranes as they share, with the prototype EAK16, a strictly alternating arrangement of polar and nonpolar residues. We find that 16-mer peptides show higher self-assembling propensities than the 8-mer analogs and that the aggregation processes are favored by salts and neutral pH. Peptide hydrophobic character appears as the most relevant factor in determining self-assembling. Solution conformational analysis, diffusion and SANS measurements all together show that the sequences with a higher self-assemble propensity are distributed, in mild conditions, between light and heavy forms. For some of the systems, the light form is mostly constituted by monomers in a random conformation, while the heavy one is constituted by ,-aggregates. In our study we also verified that sequences designed to adopt extended conformation, when dissolved in alcohol-water mixtures, can easily fold in helix structures. In that media, the prototype of the series appears distributed between helical monomers and ,-aggregates. It is worth noticing that the structural conversion from helical monomer to ,-aggregates, mimics ,-amyloid peptide aggregation mechanisms. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] | ||||||||||