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Coil Conformation (coil + conformation)
Kinds of 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] Molecular dynamic simulations of nanomechanic chaperone peptide and effects of in silico His mutations on nanostructured functionJOURNAL OF PEPTIDE SCIENCE, Issue 11 2008Abolfazl Barzegar Abstract The nanoscale peptide YSGVCHTDLHAWHGDWPLPVK exhibits molecular chaperone activity and prevents protein aggregation under chemical and/or thermal stress. Here, His mutations of this peptide and their impact on chaperone activity were evaluated using theoretical techniques. Molecular dynamic (MD) simulations with simulated annealing (SA) of different mutant nanopeptides were employed to determine the contribution of the scaffolding His residues (H45, H49, H52), when mutated to Pro, on chaperone action in vitro. The in silico mutations of His residues to Pro (H45P, H49P, H52P) revealed loss of secondary ordered strand structure. However, a small part of the strand conformation was formed in the middle region of the native chaperone peptide. The His-to-Pro mutations resulted in decreased gyration radius (Rg) values and surface accessibility of the mutant peptides under the simulation times. The invariant dihedral angle (,) values and the disrupting effects of the Pro residues indicated the coil conformation of mutant peptides. The failure of the chaperone-like action in the Pro mutant peptides was consistent with their decreased effective accessible surfaces. The high variation of , value for His residues in native chaperone peptide leads to high flexibility, such as a minichaperone acting as a nanomachine at the molecular level. Our findings demonstrate that the peptide strand conformation motif with high flexibility at nanoscale is critical for chaperone activity. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] Synthesis and Characterization of Novel Mesogen-Jacketed Liquid Crystalline Miktoarm Star Rod-Coil Block CopolymerMACROMOLECULAR RAPID COMMUNICATIONS, Issue 1 2006Jianfang Chen Abstract Summary: A series of novel mesogen-jacketed liquid crystal miktoarm star rod-coil block copolymers were synthesized via atom transfer radical polymerization (ATRP). Their architectures {coil conformation of styrene segment and rigid rod conformation of {2,5-bis[(4-methoxyphenyl)oxycarbonyl]styrene} (MPCS) segment} were confirmed by GPC, 1H NMR, and MALDI-TOF studies. The liquid crystalline behaviors of the synthesized copolymers are evidenced from POM observation. The liquid crystalline phase depends on the molecular weights of the rigid rod arm of miktoarm star copolymers. Miktoarm star rod-coil block copolymer. [source] Synthesis, static, and dynamic light scattering studies of soluble aromatic polyamidePOLYMERS FOR ADVANCED TECHNOLOGIES, Issue 9 2008Sonia Zulfiqar Abstract Aromatic polyamide was synthesized via condensation polymerization of 4-aminophenyl sulfone (APS) with isophthaloyl chloride (IPC) using N,N -dimethyl acetamide (DMAc) as a solvent under anhydrous conditions. The purified aramid was studied by laser light scattering (LLS) in dimethyl sulfoxide (DMSO), a thermodynamically good solvent at 20°C. Static and dynamic light scattering studies permitted to determine the weight average molecular weight , radius of gyration , second virial coefficient A2, the hydrodynamic radius RH, and the diffusion coefficient D. Light scattering experiments were conducted at five concentrations ranging from 0.27 to 2.5,g/L. LLS measurement is also a very useful technique to study the aggregation or association in a polymer system as long as the large "clusters" are reasonably stable in time. The intensity autocorrelation function obtained on the quasi-elastically scattered light showed a simple diffusive relaxation mode. The ratio of radius of gyration to the hydrodynamic radius, i.e. ,,,1.3 indicates that the polyamide chain has coil conformation in DMSO at 20°C. Copyright © 2008 John Wiley & Sons, Ltd. [source] The hydrodynamic and conformational properties of denatured proteins in dilute solutionsPROTEIN SCIENCE, Issue 1 2010Guy C. Berry Abstract Published data on the characterization of unfolded proteins in dilute solutions in aqueous guanidine hydrochloride are analyzed to show that the data are not fit by either the random flight or wormlike chain models for linear chains. The analysis includes data on the intrinsic viscosity, root-mean-square radius of gyration, from small-angle X-ray scattering, and hydrodynamic radius, from the translational diffusion coefficient. It is concluded that residual structure consistent with that deduced from nuclear magnetic resonance on these solutions can explain the dilute solution results in a consistent manner through the presence of ring structures, which otherwise have an essentially flexible coil conformation. The ring structures could be in a state of continual flux and rearrangement. Calculation of the radius of gyration for the random-flight model gives a similar reduction of this measure for chains joined at their endpoints, or those containing loop with two dangling ends, each one-fourth the total length of the chain. This relative insensitivity to the details of the ring structure is taken to support the behavior observed across a range of proteins. [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] Physical,chemical determinants of coil conformations in globular proteinsPROTEIN SCIENCE, Issue 6 2010Lauren L. Perskie Abstract We present a method with the potential to generate a library of coil segments from first principles. Proteins are built from ,-helices and/or ,-strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two-, three-, and four-residue turns from X-ray,elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash-free conformers in which no backbone polar group lacks a hydrogen-bond partner. Further, at least 90% of longer coil segments, ranging from 5- to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or abinitio methods. Empirical methods use database-derived information; abinitio methods rely on physical,chemical principles exclusively. Replacing the database-derived coil library with one generated from first principles would transform any empirically based method into its corresponding abinitio homologue. [source] | |||||||||||||