Home About us Contact
|
Home About us Contact | ||
|
|
||
Sheet Conformation (sheet + conformation)
Selected AbstractsStructural studies and model membrane interactions of two peptides derived from bovine lactoferricinJOURNAL OF PEPTIDE SCIENCE, Issue 7 2005Leonard T. Nguyen Abstract The powerful antimicrobial properties of bovine lactoferricin (LfcinB) make it attractive for the development of new antimicrobial agents. An 11-residue linear peptide portion of LfcinB has been reported to have similar antimicrobial activity to lactoferricin itself, but with lower hemolytic activity. The membrane-binding and membrane-perturbing properties of this peptide were studied together with an amidated synthetic version with an added disulfide bond, which was designed to confer increased stability and possibly activity. The antimicrobial and cytotoxic properties of the peptides were measured against Staphylococcus aureus and Escherichia coli and by hemolysis assays. The peptides were also tested in an anti-cancer assay against neuroblastoma cell lines. Vesicle disruption caused by these LfcinB derivatives was studied using the fluorescent reporter molecule calcein. The extent of burial of the two Trp residues in membrane mimetic environments were quantitated by fluorescence. Finally, the solution NMR structures of the peptides bound to SDS micelles were determined to provide insight into their membrane bound state. The cyclic peptide was found to have greater antimicrobial potency than its linear counterpart. Consistent with this property, the two Trp residues of the modified peptide were suggested to be embedded deeper into the membrane. Although both peptides adopt an amphipathic structure without any regular ,-helical or ß-sheet conformation, the 3D-structures revealed a clearer partitioning of the cationic and hydrophobic faces for the cyclic peptide. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd. [source] Nociceptin and its natural and specifically-modified fragments: Structural studiesBIOPOLYMERS, Issue 12 2010E. Podstawka-Proniewicz Abstract The vibrational structures of Nociceptin (FQ), its short bioactive fragments, and specifically-modified [Tyr1]FQ (1-6), [His1]FQ (1-6), and [His1,4]FQ (1-6) fragments were characterized. We showed that in the solid state, all of the aforementioned peptides except FQ adopt mainly turn and disordered secondary structures with a small contribution from an antiparallel ,-sheet conformation. FQ (1-11), FQ (7-17) [His1]FQ (1-6), and [His1,4]FQ (1-6) have an ,-helical backbone arrangement that could also slightly influence their secondary structure. The adsorption behavior of these peptides on a colloidal silver surface in an aqueous solution (pH = ,8.3) was investigated by means of surface-enhanced Raman scattering (SERS). All of the peptides, excluding FQ (7-17), chemisorbed on the colloidal silver surfaces through a Phe4 residue, which for FQ, FQ (1-11), FQ (1-6), [Tyr1]FQ (1-6), and [His1]FQ (1-6) lies almost flat on this surface, while for FQ (1-13) and FQ (1-13)NH2 adopts a slightly tilted orientation with respect to the surface. The Tyr1 residue in [Tyr1]FQ (1-6) does not interact with the colloidal silver surface, suggesting that the Tyr1 and Phe4 side chains are located on the opposite sides of the peptide backbone, which can be also true for His1 and Phe4 in [His1]FQ (1-6). The lone pair of electrons on the oxygen atom of the ionized carbonyl group of FQ (1-13) and FQ (7-17) appears to be coordinated to the colloidal silver nanoparticles, whereas in the case of the remaining peptides, it only assists in the adsorption process, similar to the NH2 group. We also showed that upon adsorption, the secondary structure of these peptides is altered. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 1039,1054, 2010. 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] Dense-core and diffuse A, plaques in TgCRND8 mice studied with synchrotron FTIR microspectroscopyBIOPOLYMERS, Issue 4 2007Margaret Rak Abstract Plaques composed of the A, peptide are the main pathological feature of Alzheimer's disease. Dense-core plaques are fibrillar deposits of A,, showing all the classical properties of amyloid including ,-sheet secondary structure, while diffuse plaques are amorphous deposits. We studied both plaque types, using synchrotron infrared (IR) microspectroscopy, a technique that allows the chemical composition and average protein secondary structure to be investigated in situ. We examined plaques in hippocampal, cortical and caudal tissue from 5- to 21-month-old TgCRND8 mice, a transgenic model expressing doubly mutant amyloid precursor protein, and displaying impaired hippocampal function and robust pathology from an early age. Spectral analysis confirmed that the congophilic plaque cores were composed of protein in a ,-sheet conformation. The amide I maximum of plaque cores was at 1623 cm,1, and unlike for in vitro A, fibrils, the high-frequency (1680,1690 cm,1) component attributed to antiparallel ,-sheet was not observed. A significant elevation in phospholipids was found around dense-core plaques in TgCRND8 mice ranging in age from 5 to 21 months. In contrast, diffuse plaques were not associated with IR detectable changes in protein secondary structure or relative concentrations of any other tissue components. © 2007 Wiley Periodicals, Inc. Biopolymers 87: 207,217, 2007. 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] ,-sheet folding of 11-kDa fibrillogenic polypeptide is completely aggregation drivenBIOPOLYMERS, Issue 4 2007Natalya I. Topilina Abstract A de novo polypeptide GH6[(GA)3GY(GA)3GE]8GAH6 (YE8) was designed and genetically engineered to form antiparallel ,-strands of GAGAGA repeats. Modulation of pH enables control of solubility, folding, and aggregation of YE8 by control of the overall polypeptide charge, a consequence of the protonation or deprotonation of the glutamic acid and histidine residues. YE8 exhibits all the major properties of a fibrillogenic protein providing an excellent model for detailed study of the fibrillation. At neutral pH, YE8 is soluble in disordered form, yet at pH 3.5 folds into a predominantly ,-sheet conformation that is fibrillogenic. Atomic force microscopy and transmission electron microscopy indicated the formation of fibrillar aggregates on well-defined, hydrophobic surfaces. The ,-sheet folding of YE8 exhibited a lag phase that could be eliminated by seeding or stirring. The strong dependence of lag time on polypeptide concentration established the limiting step in aggregation as initiation of ,-sheet folding. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 261,264, 2007. 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] Aggregation characteristics of ovalbumin in ,-sheet conformation determined by spectroscopyBIOPOLYMERS, Issue 2 2002Raimon Sabaté Abstract Protein misfolding and aggregation are involved in a number of the so-called "conformational" diseases (e.g., transmissible spongiform encephalopathies and Alzheimer disease). The development of rational strategies to interfere with aggregation is a potential therapeutic approach that requires complete knowledge of the aggregation process. We studied the aggregation of ovalbumin in ,-sheet conformation using mainly the spectral changes in the spectra of two dyes (Congo Red and pinacyanol) caused by the aggregates. We assumed a linear model of polymerization that fit to the experimental data. The critical aggregation constant, concentration of half-aggregation, nucleation parameter, growth parameter, and number of aggregation and free energy changes (total and per residue) were determined as aggregation-related parameters. ,-Ovalbumin aggregates in a cooperative way. Moreover, the differences between such parameters obtained with Congo Red and pinacyanol suggest that each dye interacts with the protein in its own way. © 2002 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 67: 113,120, 2002 [source] NMR solution structure of the isolated Apo Pin1 WW domain: Comparison to the x-ray crystal structures of Pin1BIOPOLYMERS, Issue 2 2002Jennifer A. Kowalski Abstract The NMR solution structure of the isolated Apo Pin1 WW domain (6,39) reveals that it adopts a twisted three-stranded antiparallel ,-sheet conformation, very similar to the structure exhibited by the crystal of this domain in the context of the two domain Pin1 protein. While the B factors in the apo x-ray crystal structure indicate that loop 1 and loop 2 are conformationally well defined, the solution NMR data suggest that loop 1 is quite flexible, at least in the absence of the ligand. The NMR chemical shift and nuclear Overhauser effect pattern exhibited by the 6,39 Pin1 WW domain has proven to be diagnostic for demonstrating that single site variants of this domain adopt a normally folded structure. Knowledge of this type is critical before embarking on time-consuming kinetic and thermodynamic studies required for a detailed understanding of ,-sheet folding. © 2002 John Wiley & Sons, Inc. Biopolymers 63: 111,121, 2002 [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] 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] | ||||||||||