Home About us Contact
|
Home About us Contact | ||
|
|
||
Random Coil Conformation (random + coil_conformation)
Selected AbstractsThe Alzheimer ,-peptide shows temperature-dependent transitions between left-handed 31 -helix, ,-strand and random coil secondary structuresFEBS JOURNAL, Issue 15 2005Jens Danielsson The temperature-induced structural transitions of the full length Alzheimer amyloid ,-peptide [A,(1,40) peptide] and fragments of it were studied using CD and 1H NMR spectroscopy. The full length peptide undergoes an overall transition from a state with a prominent population of left-handed 31 (polyproline II; PII)-helix at 0 °C to a random coil state at 60 °C, with an average ,H of 6.8 ± 1.4 kJ·mol,1 per residue, obtained by fitting a Zimm,Bragg model to the CD data. The transition is noncooperative for the shortest N-terminal fragment A,(1,9) and weakly cooperative for A,(1,40) and the longer fragments. By analysing the temperature-dependent 3JHNH, couplings and hydrodynamic radii obtained by NMR for A,(1,9) and A,(12,28), we found that the structure transition includes more than two states. The N-terminal hydrophilic A,(1,9) populates PII-like conformations at 0 °C, then when the temperature increases, conformations with dihedral angles moving towards ,-strand at 20 °C, and approaches random coil at 60 °C. The residues in the central hydrophobic (18,28) segment show varying behaviour, but there is a significant contribution of ,-strand-like conformations at all temperatures below 20 °C. The C-terminal (29,40) segment was not studied by NMR, but from CD difference spectra we concluded that it is mainly in a random coil conformation at all studied temperatures. These results on structural preferences and transitions of the segments in the monomeric form of A, may be related to the processes leading to the aggregation and formation of fibrils in the Alzheimer plaques. [source] Phage display selection of efficient glutamine-donor substrate peptides for transglutaminase 2PROTEIN SCIENCE, Issue 11 2006Zsolt Keresztessy Abstract Understanding substrate specificity and identification of natural targets of transglutaminase 2 (TG2), the ubiquitous multifunctional cross-linking enzyme, which forms isopeptide bonds between protein-linked glutamine and lysine residues, is crucial in the elucidation of its physiological role. As a novel means of specificity analysis, we adapted the phage display technique to select glutamine-donor substrates from a random heptapeptide library via binding to recombinant TG2 and elution with a synthetic amine-donor substrate. Twenty-six Gln-containing sequences from the second and third biopanning rounds were susceptible for TG2-mediated incorporation of 5-(biotinamido)penthylamine, and the peptides GQQQTPY, GLQQASV, and WQTPMNS were modified most efficiently. A consensus around glutamines was established as pQX(P,T,S)l, which is consistent with identified substrates listed in the TRANSDAB database. Database searches showed that several proteins contain peptides similar to the phage-selected sequences, and the N-terminal glutamine-rich domain of SWI1/SNF1-related chromatin remodeling proteins was chosen for detailed analysis. MALDI/TOF and tandem mass spectrometry-based studies of a representative part of the domain, SGYGQQGQTPYYNQQSPHPQQQQPPYS (SnQ1), revealed that Q6, Q8, and Q22 are modified by TG2. Kinetic parameters of SnQ1 transamidation (KMapp = 250 ,M, kcat = 18.3 sec,1, and kcat/KMapp = 73,200) classify it as an efficient TG2 substrate. Circular dichroism spectra indicated that SnQ1 has a random coil conformation, supporting its accessibility in the full-length parental protein. Added together, here we report a novel use of the phage display technology with great potential in transglutaminase research. [source] Conformational transition and liquid crystalline state of regenerated silk fibroin in waterBIOPOLYMERS, Issue 6 2008Xin-Gui Li Abstract The conformational transition of molecular chains of regenerated silk fibroin (SF) aqueous solution is systematically investigated by circular dichroism, Raman, IR, and UV,vis spectroscopies. It is found that an initial random coil conformation of the SF can be readily changed into an ordered ,-sheet structure by optimizing the solution conditions, such as the SF concentration, pH, temperature, or metal-ion content. Circular dichroic spectra quantitatively confirm a steadily decreased content of the random coil conformation but a significantly increased ,-sheet content after an ultrasonic or extruding treatment. Furthermore, the extrusion is more powerful to achieve high ,-sheet content than the ultrasonic. It is interesting that the polarized optical micrographs of the SF aqueous solution extruded by injection illustrate the formation and existence of liquid crystalline state. A study of extrusion in vitro could be used as a model system to understand the natural silk spinning process in silkworm. © 2007 Wiley Periodicals, Inc. Biopolymers 89: 497,505, 2008. 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] Vibrational 13C-cross-polarization/magic angle spinning NMR spectroscopic and thermal characterization of poly(alanine-glycine) as model for silk I Bombyx mori fibroinBIOPOLYMERS, Issue 5 2003Patrizia Monti Abstract This study focuses on the conformational characterization of poly(alanine-glycine) II (pAG II) as a model for a Bombyx mori fibroin silk I structure. Raman, IR, and 13C-cross-polarization/magic angle spinning NMR spectra of pAG II are discussed in comparison with those of the crystalline fraction of B. mori silk fibroin (chymotryptic precipitate, Cp) with a silk I (silk I-Cp) structure. The spectral data give evidence that silk I-Cp and the synthetic copolypeptide pAG II have similar conformations. Moreover, the spectral findings reveal that silk I-Cp is more crystalline than pAG II; consequently, the latter contains a larger amount of the random coil conformation. Differential scanning calorimetry measurements confirm this result. N-Deuteration experiments on pAG II allow us to attribute the Raman component at 1320 cm,1 to the amide III mode of a ,-turn type II conformation, thus confirming the results of those who propose a repeated ,-turn type II structure for silk I. The analysis of the Raman spectra in the ,NH region confirms that the silk I structure is characterized by the presence of different types of H-bonding arrangements, in agreement with the above model. © 2003 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 72: 329,338, 2003 [source] Inhibition Mechanism of TbIII on Horseradish Peroxidase ActivityCHEMISTRY & BIODIVERSITY, Issue 10 2008Shaofen Guo Abstract The inhibition mechanism of TbIII on horseradish peroxidase (HRP) in vitro was discussed. The results from MALDI-TOF/MS and X-ray photoelectron spectroscopy (XPS) showed that TbIII mainly interacts with the O-containing groups of the amides in the polypeptide chains of the HRP molecules and forms the complex of TbIII,HRP, and, in the complex, the molar ratio TbIII/HRP is 2,:,1. The results from CD and atomic force microscopy (AFM) indicated that the coordination effect between TbIII and HRP can lead to the conformation change in the HRP molecule, in which the contents of , -helix and , -sheet conformation in the peptide of the HRP molecules is decreased, and the content of the random coil conformation is increased. Meanwhile, the coordination effect also leads to the decrease in the content of inter- and intrapeptide-chain H-bonds in the HRP molecules, resulting in the HRP molecular looseness and/or aggregation. Thus, the conformation change in the HRP molecules can significantly decrease the electrochemical reaction of HRP and its electrocatalytic activity for the reduction of H2O2. [source] | ||||||||||