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Helix Conformation (helix + conformation)
Selected AbstractsExtraction of native collagen from limed bovine split wastes through improved pretreatment methodsJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 7 2008Dong Li Abstract BACKGROUND: The large amount of limed bovine split wastes discharged by the leather industry has raised concerns regarding their environmental effect. The objective of this work was to perform pilot plant trials to extract high-value native collagen from these wastes through improved pretreatment methods. RESULTS: EDTA- and HCl-pretreatment gave similar removal percentages of inorganic substances. Owing to the open structure of fibers, the collagen yield of HCl-pretreated splits (HPS) (41.31%) was higher than that of EDTA-pretreated splits (EPS) (10.42%). Furthermore, HCl-pretreated split collagen (HPC) had a more acidic isoelectric point, lower content of primary amino groups, larger Z-average particle size and higher relative viscosity than EDTA-pretreated split collagen (EPC). Electrophoretic analysis and circular dichroism spectra revealed the maintenance of polypeptide and triple helix conformation, respectively. In addition, the transition temperatures of EPC (34.7 °C) and HPC (34.6 °C) detected by differential scanning calorimetry (DSC) were close to that of commercial collagen from calfskin (CCC) (35.7 °C). CONCLUSION: A process of native collagen extraction from limed bovine split wastes was proposed. While both EPC and HPC represented similar physicochemical properties to those of CCC, the collagen yield of HPS was much higher than that of EPS. Copyright © 2008 Society of Chemical Industry [source] Influence of response factors on determining equilibrium association constants of non-covalent complexes by electrospray ionization mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2003Valérie Gabelica Abstract A method for determining the equilibrium association constant of a complexation reaction A + B , AB by electrospray ionization mass spectrometry is described. The method consists in measuring the relative intensities of the peaks corresponding to A and to AB in equimolar A,B solutions at different concentrations C0. The results are fitted by a non-linear least-squares procedure, with the two variable parameters being the equilibrium association constant Ka and a factor R, defined by I(AB)/I(A) = R × [AB]/[A]. The factor R is the ratio between the response factors of AB and A, and corrects for the relative electrospray responses of the complex and the free substrate A, mass discrimination of instrumental origin and/or moderate in-source dissociation. The method is illustrated with the following two systems: complexes between a double-stranded 12-base pair oligonucleotide and minor groove binders, and cyclodextrin complexes with ,,,-dicarboxylic acids. For the oligonucleotide complexes, it is found that the response of the complex is not dramatically different to the response of the free oligonucleotide duplex, as the double helix conformation is disturbed by the drug only to a minor extent. In the case of cyclodextrin complexes, these complexes were found to have a much higher response than free cyclodextrin. This may be due to the fact that cyclodextrin is neutral in solution, whereas the complex is charged, but it can also stem from the fact that a significant proportion of the complex is in a non-inclusion geometry. The present method requires the exact determination of the concentrations of the reactants and is applicable to 1 : 1 complexes. Copyright © 2003 John Wiley & Sons, Ltd. [source] 4-Fluoroproline derivative peptides: effect on PPII conformation and SH3 affinityJOURNAL OF PEPTIDE SCIENCE, Issue 7 2006Paolo Ruzza Abstract Eukaryotic signal transduction involves the assembly of transient protein,protein complexes mediated by modular interaction domains. Specific Pro-rich sequences with the consensus core motif PxxP adopt the PPII helix conformation upon binding to SH3 domains. For short Pro-rich peptides, little or no ordered secondary structure is usually observed before binding interactions. The association of a Pro-rich peptide with the SH3 domain involves unfavorable binding entropy due to the loss of rotational freedom on forming the PPII helix. With the aim of stabilizing the PPII helix conformation in the Pro-rich HPK1 decapeptide PPPLPPKPKF (P2), a series of P2 analogues was prepared, in which specific Pro positions were alternatively occupied by 4(S)- or 4(R)-4-fluoro- L -proline. The interactions of these peptides with the SH3 domain of the HPK1-binding partner HS1 were quantitatively analyzed by the NILIA-CD approach. A CD thermal analysis of the P2 analogues was performed to assess their propensity to adopt the PPII helix conformation. Contrary to our expectations, the Kd values of the analogues were lower than that of the parent peptide P2. These results clearly show that the induction of a stable PPII helix conformation in short Pro-rich peptides is not sufficient to increase their affinity toward the SH3 domain and that the effect of 4-fluoroproline strongly depends on the position of this residue in the sequence and the chirality of the substituent in the pyrrolidine ring. Copyright © 2006 European Peptide Society and John Wiley & Sons, Ltd. [source] Processing of a Strong Biodegradable Poly[(R)-3-hydroxybutyrate] Fiber and a New Fiber Structure Revealed by Micro-Beam X-Ray Diffraction with Synchrotron RadiationMACROMOLECULAR RAPID COMMUNICATIONS, Issue 11 2004Tadahisa Iwata Abstract Summary: Biodegradable poly[(R)-3-hydroxybutyrate] (P(3HB)) fibers with high tensile strength of 1.32 GPa were processed from ultra-high-molecular-weight P(3HB) by a method combining cold-drawing and two-step-drawing procedures at room temperature. The distribution of molecular structures in a mono-filament was analyzed by micro-beam X-ray diffraction with synchrotron radiation. It was revealed that the P(3HB) fiber has a new core-sheath structure consistent with two types of molecular conformations: a 21 helix conformation in the sheath region and a planar zigzag conformation in the core region. P(3HB) fiber processed by cold-drawing in ice water and two-step drawing at room temperature, and subsequently annealing at 50,°C. [source] Solution structure determination of oligoureas using methylene spin state selective NMR at 13C natural abundanceMAGNETIC RESONANCE IN CHEMISTRY, Issue 10 2008Gilles Guichard Abstract Ability of N,N,-linked oligoureas containing proteinogenic side chains to adopt a stable helix conformation in solution has been described recently. NMR as well as circular dichroism (CD) spectroscopies were employed to gain insight into their specific fold. It is herein proposed to extend the structural information available on these peptidomimetics by an advantageous use of a methylene spin state selective NMR experiment. Homodecoupling provided by the pulse scheme made it possible to readily measure conformation-dependent 3JHH constants that are difficult if not impossible to obtain with standard NMR experiments. Adding those couplings to the NMR restraints improved the quality of the structure calculations significantly, as judged by a ca 30% decrease of the root mean square deviation (RMSD) obtained over an ensemble of 20 structures. Moreover, accurate determination of individual 1JCH couplings within each methylene group revealed uniform values throughout the oligourea sequence, with 1JCH systematically slightly larger for the pro-S hydrogen than for the pro-R. As shown in this study, the methylene spin state selective NMR experiment displays a good intrinsic sensitivity and could therefore provide valuable structural information at 13C natural abundance for peptidomimetic molecules and foldamers bearing diastereotopic methylene protons. Copyright © 2008 John Wiley & Sons, Ltd. [source] Tightly winding structure of sequential model peptide for repeated helical region in Samia cynthia ricini silk fibroin studied with solid-state NMRPROTEIN SCIENCE, Issue 4 2003Yasumoto Nakazawa Abstract There are many kinds of silks from silkworms and spiders with different structures and properties, and thus, silks are suitable to study the structure-property relationship of fibrous proteins. Silk fibroin from a wild silkworm, Samia cynthia ricini, mainly consists of the repeated similar sequences by about 100 times where there are alternative appearances of the polyalanine (Ala)12,13 region and the Gly-rich region. In this paper, a sequential model peptide, GGAGGGYGGDGG(A)12GGAGDGYGAG, which is a typical sequence of the silk fibroin, was synthesized, and the atomic-level conformations of Gly residues at the N- and C-terminal ends of the polyalanine region were determined as well as that of the central Ala residue using 13C 2D spin diffusion solid-state nuclear magnetic resonance (NMR) under off-magic angle spinning. In the model peptide with ,-helical conformation, the torsion angle of the central Ala residue, the 19th Ala, was determined to be (,, ,) = (,60°, ,50°), which was a typical ,-helical structure, but the torsion angles of two Gly residues, the 12th and 25th Gly residues, which are located at the N- and C-terminal ends of the polyalanine region, were determined to be (,,,) = (,70°, ,30°) and (,,,) = (,70°, ,20°), respectively. Thus, it was observed that the turns at both ends of polyalanine with ,-helix conformation in the model peptide are tightly wound. [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] Insight Into the Kinetic of Amyloid , (1,42) Peptide Self-Aggregation: Elucidation of Inhibitors' Mechanism of ActionCHEMBIOCHEM, Issue 17 2007Manuela Bartolini Dr. Abstract The initial transition of amyloid , (1,42) (A,42) soluble monomers/small oligomers from unordered/,-helix to a ,-sheet-rich conformation represents a suitable target to design new potent inhibitors and to obtain effective therapeutics for Alzheimer's disease. Under optimized conditions, this reliable and reproducible CD kinetic study showed a three-step sigmoid profile that was characterized by a lag phase (prevailing unordered/,-helix conformation), an exponential growth phase (increasing ,-sheet secondary structure) and a plateau phase (prevailing ,-sheet secondary structure). This kinetic analysis brought insight into the inhibitors' mechanism of action. In fact, an increase in the duration of the lag phase can be related to the formation of an inhibitor,A, complex, in which the non-amyloidogenic conformation is stabilized. When the exponential rate is affected exclusively, such as in the case of Congo red and tetracycline, then the inhibitor affinity might be higher for the pleated ,-sheet structure. Finally, by adding the inhibitor at the end of the exponential phase, the soluble protofibrils can be disrupted and the A, amyloidogenic structure can revert into monomers/small oligomers. Congo red and tetracycline preferentially bind to amyloid in the ,-sheet conformation because both decreased the slope of the exponential growth, even if to a different extent, whereas no effect was observed for tacrine and galantamine. Some very preliminary indications can be derived about the structural requirements for binding to nonamyloidogenic or ,-sheet amyloid secondary structure for the development of potent antiaggregating agents. On these premises, memoquin, a multifunctional molecule that was designed to become a drug candidate for the treatment of Alzheimer's disease, was investigated under the reported circular dichroism assay and its anti-amyloidogenic mechanism of action was elucidated. [source] Synthesis and self-assembly of helical polypeptide-random coil amphiphilic diblock copolymerJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 9 2008Shiao-Wei Kuo Abstract Three amphiphilic rod-coil diblock copolymers, poly(2-ethyl-2-oxazoline- b -,-benzyl- L -glutamate) (PEOz- b -PBLG), incorporating the same-length PEOz block length and various lengths of their PBLG blocks, were synthesized through a combining of living cationic and N -carboxyanhydride (NCA) ring-opening polymerizations. In the bulk, these block copolymers display thermotropic liquid crystalline behavior. The self-assembled aggregates that formed from these diblock copolymers in aqueous solution exhibited morphologies that differed from those obtained in ,-helicogenic solvents, that is, solvents in which the PBLG blocks adopt rigid ,-helix conformations. In aqueous solution, the block copolymers self-assembled into spherical micelles and vesicular aggregates because of their amphiphilic structures. In helicogenic solvents (in this case, toluene and benzyl alcohol), the PEOz- b -PBLG copolymers exhibited rod-coil chain properties, which result in a diverse array of aggregate morphologies (spheres, vesicles, ribbons, and tube nanostructures) and thermoreversible gelation behavior. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 3108,3119, 2008 [source] | |||||||||||||