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Secondary Structure Content (secondary + structure_content)
Selected AbstractsPar j 1 and Par j 2, the two major allergens in Parietaria judaica, bind preferentially to monoacylated negative lipidsFEBS JOURNAL, Issue 6 2009Roberto González-Rioja Par j 1 and Par j 2 proteins are the two major allergens in Parietaria judaica pollen, one of the main causes of allergic diseases in the Mediterranean area. Each of them contains eight cysteine residues organized in a pattern identical to that found in plant nonspecific lipid transfer proteins. The 139- and 102-residue recombinant allergens, corresponding respectively to Par j 1 and Par j 2, refold properly to fully functional forms, whose immunological properties resemble those of the molecules purified from the natural source. Molecular modeling shows that, despite the lack of extensive primary structure homology with nonspecific lipid transfer proteins, both allergens contain a hydrophobic cavity suited to accommodate a lipid ligand. In the present study, we present novel evidence for the formation of complexes of these natural and recombinant proteins from Parietaria pollen with lipidic molecules. The dissociation constant of oleyl-lyso-phosphatidylcholine is 9.1 ± 1.2 ,m for recombinant Par j 1, whereas pyrenedodecanoic acid shows a much higher affinity, with a dissociation constant of approximately 1 ,m for both recombinant proteins, as well as for the natural mixture. Lipid binding does not alter the secondary structure content of the protein but is very efficient in protecting disulfide bonds from reduction by dithiothreitol. We show that Par j 1 and Par j 2 not only bind lipids from micellar dispersions, but also are able to extract and transfer negative phospholipids from bilayers. [source] Conformational and functional analysis of the lipid binding protein Ag-NPA-1 from the parasitic nematode Ascaridia galliFEBS JOURNAL, Issue 1 2005Rositsa Jordanova Ag-NPA-1 (AgFABP), a 15 kDa lipid binding protein (LBP) from Ascaridia galli, is a member of the nematode polyprotein allergen/antigen (NPA) family. Spectroscopic analysis shows that Ag-NPA-1 is a highly ordered, ,-helical protein and that ligand binding slightly increases the ordered secondary structure content. The conserved, single Trp residue (Trp17) and three Tyr residues determine the fluorescence properties of Ag-NPA-1. Analysis of the efficiency of the energy transfer between these chromophores shows a high degree of Tyr-Trp dipole-dipole coupling. Binding of fatty acids and retinol was accompanied by enhancement of the Trp emission, which allowed calculation of the affinity constants of the binary complexes. The distance between the single Trp of Ag-NPA-1 and the fluorescent fatty acid analogue 11-[(5-dimethylaminonaphthalene-1- sulfonyl)amino]undecanoic acid (DAUDA) from the protein binding site is 1.41 nm as estimated by fluorescence resonance energy transfer. A chemical modification of the Cys residues of Ag-NPA-1 (Cys66 and Cys122) with the thiol reactive probes 5-({[(2-iodoacetyl)amino]ethyl}amino) naphthalene-1-sulfonic acid (IAEDANS) and N,N,-dimethyl- N -(iodoacetyl)- N,-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)ethylenediamine (IANBD), followed by MALDI-TOF analysis showed that only Cys66 was labeled. The observed similar affinities for fatty acids of the modified and native Ag-NPA-1 suggest that Cys66 is not a part of the protein binding pocket but is located close to it. Ag-NPA-1 is one of the most abundant proteins in A. galli and it is distributed extracellularly mainly as shown by immunohistology and immunogold electron microscopy. This suggests that Ag-NPA-1 plays an important role in the transport of fatty acids and retinoids. [source] Protein secondary structure from deep-UV resonance Raman spectroscopy,JOURNAL OF RAMAN SPECTROSCOPY, Issue 1-3 2006Cheng-Yen Huang Abstract Raman spectra of proteins that are obtained with deep ultraviolet excitation contain resonance-enhanced amide bands of the polypeptide backbone, as well as aromatic side chain bands. The amide bands are sensitive to conformation, and can be used to estimate the backbone secondary structure. UV Raman spectra are reported at 206.5 and 197 nm, for a set of 12 proteins with varied secondary structure content, and are used to establish quantitative signatures of secondary structure via least-squares fitting. Amide band enhancement is greater at 197 nm, where basis spectra are established for ,-turn, as well as ,-helix, ,-sheet and unordered structures; the lower signal strength at 206.5 nm does not provide a reliable spectrum for the first of these. Application of these basis spectra is illustrated for the melting of apo-myoglobin. The amide band positions and cross sections are discussed. Copyright © 2006 John Wiley & Sons, Ltd. [source] Trifluoroethanol and binding to model membranes stabilize a predicted turn in a peptide corresponding to the first extracellular loop of the angiotensin II AT1A receptorBIOPOLYMERS, Issue 1 2002Roberto K. Salinas Abstract Homology modeling of the angiotensin II AT1A receptor based on rhodopsin,s crystal structure has assigned the 92,100 (YRWPFGNHL) sequence of the receptor to its first extracellular loop. Solution and membrane-bound conformational properties of a peptide containing this sequence (EL1) were examined by CD, fluorescence, and 1H-NMR. CD spectra in aqueous solution revealed an equilibrium between less organized and folded conformers. NMR spectra indicated the coexistence of trans and cis isomers of the Trp3,Pro4 bond. A positive band at 226 nm in the CD spectra suggested aromatic ring stacking, modulated by EL1's ionization degree. CD spectra showed that trifluoroethanol (TFE), or binding to detergent micelles and phospholipid bilayers, shifted the equilibrium toward conformers with higher secondary structure content. Different media gave rise to spectra suggestive of different ,-turns. Chemical shift changes in the NMR spectra corroborated the stabilization of different conformations. Thus, environments of lower polarity or binding to interfaces probably favored the formation of hydrogen bonds, stabilizing ,-turns, predicted for this sequence in the whole receptor. Increases in Trp3 fluorescence intensity and anisotropy, blue shifts of the maximum emission wavelength, and pK changes also evinced the interaction between EL1 and model membranes. Binding was seen to depend on both hydrophobic and electrostatic interactions, as well as lipid phase packing. Studies with water-soluble and membrane-bound fluorescence quenchers demonstrated that Trp3 is located close to the water,membrane interface. The results are discussed with regard to possible implications in receptor folding and function. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 21,31, 2002 [source] Structural and Thermal Stability Characterization of Escherichia colid -Galactose/d -Glucose-Binding ProteinBIOTECHNOLOGY PROGRESS, Issue 1 2004Sabato d'Auria The effect of temperature and glucose binding on the structure of the galactose/glucose-binding protein from Escherichia coli was investigated by circular dichroism, Fourier transform infrared spectroscopy, and steady-state and time-resolved fluorescence. The data showed that the glucose binding induces a moderate change of the secondary structure content of the protein and increases the protein thermal stability. The infrared spectroscopy data showed that some protein stretches, involved in ,-helices and , strand conformations, are particularly sensitive to temperature. The fluorescence studies showed that the intrinsic tryptophanyl fluorescence of the protein is well represented by a three-exponential model and that in the presence of glucose the protein adopts a structure less accessible to the solvent. The new insights on the structural properties of the galactose/glucose-binding protein can contribute to a better understanding of the protein functions and represent fundamental information for the development of biotechnological applications of the protein. [source] Secondary structural formation of ,-synuclein amyloids as revealed by g -factor of solid-state circular dichroismBIOPOLYMERS, Issue 3 2006Xiao-Jing Lin Abstract ,-Synuclein (,-Syn) has been identified as a component of intracellular fibrillar deposits in Parkinson's disease. Though the real pathogenesis is still unknown, many investigations have revealed that conformational alteration and fibril formation of ,-Syn protein have an important role in causing the disease. In this work, we introduced the g -factor spectra of solid-state circular dichroism to estimate the secondary structure contents of ,-Syn fragments in amyloids. Fourier-transform infrared (FTIR) was also applied to confirm the structural formation. The results suggest that the central hydrophobic region is critical for ,-sheet formation and the conformational alteration is the foundation of protein abnormal aggregation. The research provides a practical approach to estimate the secondary structure contents of protein amyloids and further insight into the relevance of structural transformation and amyloidogenesis. © 2006 Wiley Periodicals, Inc. Biopolymers 83: 226,232, 2006 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] | ||||||||||