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Peptide Structure (peptide + structure)
Selected AbstractsThe Role of Prion Peptide Structure and Aggregation in Toxicity and Membrane BindingJOURNAL OF NEUROCHEMISTRY, Issue 6 2000Dawn L. Rymer Abstract: Prion diseases are neurodegenerative disorders associatedwith a conformational change in the normal cellular isoform of the prionprotein, PrPC, to an abnormal scrapie isoform, PrPSC.Unlike the ,-helical PrPC, the protease-resistant core ofPrPSC is predominantly ,-sheet and possesses a tendency topolymerize into amyloid fibrils. We performed experiments with two synthetichuman prion peptides, PrP(106-126) and PrP(127-147), to determine how peptidestructure affects neurotoxicity and protein-membrane interactions. Peptidesolutions possessing ,-sheet and amyloid structures were neurotoxic toPC12 cells in vitro and bound with measurable affinities to cholesterol-richphospholipid membranes at ambient conditions, but peptide solutions lackingstable ,-sheet structures and amyloid content were nontoxic and possessedless than one tenth of the binding affinities of the amyloid-containingpeptides. Regardless of structure, the peptide binding affinities tocholesterol-depleted membranes were greatly reduced. These results suggestthat the ,-sheet and amyloid structures of the prion peptides give riseto their toxicity and membrane binding affinities and that membrane bindingaffinity, especially in cholesterol-rich environments, may be related totoxicity. Our results may have significance in understanding the role of thefibrillogenic cerebral deposits associated with some of the prion diseases inneurodegeneration and may have implications for other amyloidoses. [source] Controlling Peptide Structure with Coordination Chemistry: Robust and Reversible Peptide,Dirhodium LigationCHEMISTRY - A EUROPEAN JOURNAL, Issue 36 2009Alexander Mild and reversible: A dirhodium tetracarboxylate reacts with peptides to bridge carboxylate side chains (see scheme). The ligation proceeds under mild aqueous conditions and is readily reversible. Dirhodium adduct formation can be used to control the conformation and supramolecular structure of peptides. [source] Protein tyrosine phosphatase SHP-1 specifically recognizes C-terminal residues of its substrates via helix ,0JOURNAL OF CELLULAR BIOCHEMISTRY, Issue 1 2001Jian Yang Abstract The catalytic domain of protein tyrosine phosphatase SHP-1 possesses distinct substrate specificity. It recognizes the P-3 to P-5 residues of its substrates via the ,5-loop-,6 region. To study the substrate specificity further, we determined the structure of the catalytic domain of SHP-1 (C455S) complexed with a less-favorable-substrate peptide originated from SIRP,. The complex has disordered N-terminal peptide structure and reduced interactions between the N-terminal peptide and the ,5-loop-,6 region. This could be the basis for the lower affinity of peptide pY427 for the catalytic domain of SHP-1. In addition, by comparing the SHP-1/less-favorable peptide complex structure with the SHP-1/substrate complex structures, we identified a novel substrate-recognition site in the catalytic domain of SHP-1. This site was formed by helix ,0 and the ,5-loop-,6 motif of SHP-1, and specifically bound residues at the P,+,4 and further C-terminal positions of peptide substrates. © 2001 Wiley-Liss, Inc. [source] The conformation of fusogenic B18 peptide in surfactant solutions,JOURNAL OF PEPTIDE SCIENCE, Issue 4 2008Sandra Rocha Abstract The interaction of B18 peptide with surfactants has been studied by circular dichroism spectroscopy and fluorescence measurements. B18 is the fusogenic motif of the fertilization sea urchin protein. The peptide forms an ,-helix structure when interacting with positively or negatively charged surfactants below and above the critical micellar concentration (CMC). The ,-helix formation is due to binding of surfactant monomers rather than the formation of surfactant micelles on the peptide. Fluorescence measurements show that the CMC of the negatively charged surfactant increases in the presence of B18, supporting the fact that there is a strong interaction between the peptide and monomers. Nonionic surfactant monomers have no effect on the peptide structure, whereas the micelles induce an ,-helical conformation. In this case the helix stabilization results from the formation of surfactant micelles on the peptide. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] Temperature dependence and resonance assignment of 13C NMR spectra of selectively and uniformly labeled fusion peptides associated with membranesMAGNETIC RESONANCE IN CHEMISTRY, Issue 2 2004Michele L. Bodner Abstract HIV-1 and influenza viral fusion peptides are biologically relevant model fusion systems and, in this study, their membrane-associated structures were probed by solid-state NMR 13C chemical shift measurements. The influenza peptide IFP-L2CF3N contained a 13C carbonyl label at Leu-2 and a 15N label at Phe-3 while the HIV-1 peptide HFP-UF8L9G10 was uniformly 13C and 15N labeled at Phe-8, Leu-9 and Gly-10. The membrane composition of the IFP-L2CF3N sample was POPC,POPG (4:1) and the membrane composition of the HFP-UF8L9G10 sample was a mixture of lipids and cholesterol which approximately reflects the lipid headgroup and cholesterol composition of host cells of the HIV-1 virus. In one-dimensional magic angle spinning spectra, labeled backbone 13C were selectively observed using a REDOR filter of the 13C,15N dipolar coupling. Backbone chemical shifts were very similar at ,50 and 20°C, which suggests that low temperature does not appreciably change the peptide structure. Relative to ,50°C, the 20°C spectra had narrower signals with lower integrated intensity, which is consistent with greater motion at the higher temperature. The Leu-2 chemical shift in the IFP-L2CF3N sample correlates with a helical structure at this residue and is consistent with detection of helical structure by other biophysical techniques. Two-dimensional 13C,13C correlation spectra were obtained for the HFP-UF8L9G10 sample and were used to assign the chemical shifts of all of the 13C labels in the peptide. Secondary shift analysis was consistent with a ,-strand structure over these three residues. The high signal-to-noise ratio of the 2D spectra suggests that membrane-associated fusion peptides with longer sequences of labeled amino acids can also be assigned with 2D and 3D methods. Copyright © 2004 John Wiley & Sons, Ltd. [source] Boom in the development of non-peptidic ,-secretase (BACE1) inhibitors for the treatment of Alzheimer's diseaseMEDICINAL RESEARCH REVIEWS, Issue 2 2009Romano Silvestri Abstract ,-Amyloid cleaving enzyme-1 (BACE1) has become a significant target for the therapy of Alzheimer's disease. After the discovery of the first non-peptidomimetic ,-secretase inhibitors by Takeda Chemicals in 2001, several research teams focused on SAR development of these agents. The non-peptidic BACE1 inhibitors may potentially overcome the classical problems associated with the peptide structure of first generation, such as blood,brain barrier crossing, poor oral bioavailability and susceptibility to P-glycoprotein transport. In the past 6 years a boom in research of non-peptidic BACE1 inhibitors has disseminated findings over hundreds of publications and patents. The rapidly growing literature has been reviewed with particular emphasis on literature of pharmaceutical companies. © 2008 Wiley Periodicals, Inc. Med Res Rev, 29, No. 2, 295,338, 2009 [source] De novo sequencing of peptides by MS/MSPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2010Joerg Seidler Abstract The current status of de novo sequencing of peptides by MS/MS is reviewed with focus on collision cell MS/MS spectra. The relation between peptide structure and observed fragment ion series is discussed and the exhaustive extraction of sequence information from CID spectra of protonated peptide ions is described. The partial redundancy of the extracted sequence information and a high mass accuracy are recognized as key parameters for dependable de novo sequencing by MS. In addition, the benefits of special techniques enhancing the generation of long uninterrupted fragment ion series for de novo peptide sequencing are highlighted. Among these are terminal 18O labeling, MSn of sodiated peptide ions, N-terminal derivatization, the use of special proteases, and time-delayed fragmentation. The emerging electron transfer dissociation technique and the recent progress of MALDI techniques for intact protein sequencing are covered. Finally, the integration of bioinformatic tools into peptide de novo sequencing is demonstrated. [source] Photocontrollable Peptide-Based Switches Target the Anti-Apoptotic Protein Bcl-xLCHEMBIOCHEM, Issue 18 2008Sabine Kneissl Abstract Photocontrol of Bcl-xL binding affinity has been achieved by using short BH3 domain peptides for Bak72,87 and Bid91,111 alkylated with an azobenzene crosslinker through two cysteine residues with different sequence spacings. The power to control the conformation of the crosslinker and hence peptide structure was demonstrated by CD and UV/Vis spectroscopy. The binding affinity of the alkylated peptides with Bcl-xL was determined in their dark-adapted and irradiated states by fluorescence anisotropy measurements, and use of different cysteine spacings allowed either activation or deactivation of the binding activities of these peptide-based switches by application of light pulses. Helix-stabilized peptides exhibited high Bcl-xL binding affinity with dissociation constants of 42±9, 21±1, and 55±4 nM for Bak, Bak, and Bid, respectively (superscript numbers refer to the spacing between cysteine residues), and up to 20-fold enhancements in affinity in relation to their helix-destabilized forms. Bak, Bak, and Bid each displayed more than 200-fold selectivity for binding to Bcl-xL over Hdm2, which is targeted by the N-terminal helix of the tumor suppressor p53. Structural studies by NMR spectroscopy demonstrated that the peptides bind to the same cleft in Bcl-xL as the wild-type peptide regardless of their structure. This work opens the possibility of using such photocontrollable peptide-based switches to interfere reversibly and specifically with biomacromolecular interactions to study and modulate cellular function. [source] Ultra-Stable Peptide Scaffolds for Protein Engineering,Synthesis and Folding of the Circular Cystine Knotted Cyclotide Cycloviolacin O2CHEMBIOCHEM, Issue 1 2008Teshome Leta Aboye Abstract The cyclic cystine knot motif, as defined by the cyclotide peptide family, is an attractive scaffold for protein engineering. To date, however, the utilisation of this scaffold has been limited by the inability to synthesise members of the most diverse and biologically active subfamily, the bracelet cyclotides. This study describes the synthesis and first direct oxidative folding of a bracelet cyclotide,cycloviolacin O2,and thus provides an efficient method for exploring the most potent cyclic cystine knot peptides. The linear chain of cycloviolacin O2 was assembled by solid-phase Fmoc peptide synthesis and cyclised by thioester-mediated native chemical ligation, and the inherent difficulties of folding bracelet cyclotides were successfully overcome in a single-step reaction. The folding pathway was characterised and was found to include predominating fully oxidised intermediates that slowly converted to the native peptide structure. [source] A Novel Heavy-Atom Label for Side-Specific Peptide Iodination: Synthesis, Membrane Incorporation and X-ray ReflectivityCHEMPHYSCHEM, Issue 9-10 2009Philipp E. Schneggenburger Abstract A novel iodine peptide label for X-ray analysis of membrane-active peptide structures is applied to solid-phase peptide synthesis. The resulting pore-structured labeled peptide as well as a non-labeled reference were reconstituted in lipid bilayer stacks (see scheme). The results indicate the exhibition of a membrane-spanning ,5.6 -double helical peptide structure and illustrate the quality of the new label. Structural parameters, such as conformation, orientation and penetration depth of membrane-bound peptides and proteins that may function as channels, pores or biocatalysts, are of persistent interest and have to be probed in the native fluid state of a membrane. X-ray scattering in combination with heavy-atom labeling is a powerful and highly appropriate method to reveal the position of a certain amino acid residue within a lipid bilayer with respect to the membrane normal axis up to a resolution of several Ångstrøm. Herein, we report the synthesis of a new iodine-labeled amino acid building block. This building block is intended for peptide incorporation to provide high intensities for electron density difference analysis of X-ray reflectivity data and improve the labeling potential for the lipid bilayer head-group and water region. The novel building block as well as the commercially available non-iodinated analogue, required for X-ray scattering, was implemented in a transmembrane peptide motif via manual solid-phase peptide synthesis (SPPS) following the fluorenylmethyloxycarbonyl (Fmoc)-strategy. The derived peptides were reconstituted in lipid vesicles as well as in highly aligned multilamellar lipid stacks and investigated via circular dichroism (CD) and X-ray reflectivity. Thereby, it has been revealed that the bulky iodine probe neither causes conformational change of the peptide structure nor lamellar disordering of the membrane complexes. [source] The expansion of mechanistic and organismic diversity associated with non-ribosomal peptidesFEMS MICROBIOLOGY LETTERS, Issue 2 2000Michelle C Moffitt Abstract Non-ribosomal peptides are a group of secondary metabolites with a wide range of bioactivities, produced by prokaryotes and lower eukaryotes. Recently, non-ribosomal synthesis has been detected in diverse microorganisms, including the myxobacteria and cyanobacteria. Peptides biosynthesized non-ribosomally may often play a primary or secondary role in the producing organism. Non-ribosomal peptides are often small in size and contain unusual or modified amino acids. Biosynthesis occurs via large modular enzyme complexes, with each module responsible for the activation and thiolation of each amino acid, followed by peptide bond formation between activated amino acids. Modules may also be responsible for the enzymatic modification of the substrate amino acid. Recent analysis of biosynthetic gene clusters has identified novel integrated, mixed and hybrid enzyme systems. These diverse mechanisms of biosynthesis result in the wide variety of non-ribosomal peptide structures and bioactivities seen today. Knowledge of these biosynthetic systems is rapidly increasing and methods of genetically engineering these systems are being developed. In the future, this may lead to rational drug design through combinatorial biosynthesis of these enzyme systems. [source] Time-averaged predictions of folded and misfolded peptides using a reduced physicochemical modelJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2008Oliver J. Clarke Abstract Energy-based methods for calculating time-averaged peptide structures are important for rational peptide design, for defining local structure propensities in large protein chains, and for exploring the sequence determinants of amyloid formation. High-end methods are currently too slow to be practicable, and will remain so for the foreseeable future. The challenge is to create a method that runs quickly on limited computer resources and emulates reality sufficiently well. We have developed a simplified off-lattice protein model, incorporating semi-empirical physicochemical potentials, and combined it with an efficient Monte Carlo method for calculating time-averaged peptide structures. Reasonably accurate predictions are found for a set of small ,-helical and ,-hairpin peptides, and we demonstrate a potential application in measuring local structure propensities in protein chains. Time-averaged structures have also been calculated for a set of small peptides known to form ,-amyloid fibrils. The simulations were of three interacting peptides, and in each case the time-averaged structure describes a three-stranded ,-sheet. The performance of our method in measuring the propensities of small peptides to self-associate into possible prefibrillar species compares favorably with more detailed and CPU-intensive approaches. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Modeling an active conformation for linear peptides and design of a competitive inhibitor for HMG-CoA reductaseJOURNAL OF MOLECULAR RECOGNITION, Issue 4 2008Valeriy V. Pak Abstract This study presents an approach that can be used to search for lead peptide candidates, including unconstrained structures in a recognized sequence. This approach was performed using the design of a competitive inhibitor for 3-hydroxy-3-methylglutaryl CoA reductase (HMGR). In a previous design for constrained peptides, a head-to-tail cyclic structure of peptide was used as a model of linear analog in searches for lead peptides with a structure close to an active conformation. Analysis of the conformational space occupied by the peptides suggests that an analogical approach can be applied for finding a lead peptide with an unconstrained structure in a recognized sequence via modeling a cycle using fixed residues of the peptide backbone. Using the space obtained by an analysis of the bioactive conformations of statins, eight cyclic peptides were selected for a peptide library based on the YVAE sequence as a recognized motif. For each cycle, the four models were assessed according to the design criterion ("V" parameter) applied for constrained peptides. Three cyclic peptides (FGYVAE, FPYVAE, and FFYVAE) were selected as lead cycles from the library. The linear FGYVAE peptide (IC50,=,0.4,µM) showed a 1200-fold increase the inhibitory activity compared to the first isolated LPYP peptide (IC50,=,484,µM) from soybean. Experimental analysis of the modeled peptide structures confirms the appropriateness of the proposed approach for the modeling of active conformations of peptides. Copyright © 2008 John Wiley & Sons, Ltd. [source] Peptide conformational changes induced by tryptophan,phosphocholine interactions in a micelleBIOPOLYMERS, Issue 5 2002Jonathan W. Neidigh Abstract Sodium dodecylsulfate (SDS) and dodecylphosphocholine (DPC) micelles are often used to mimic the membrane- or receptor-bound states of peptides in NMR studies. From the present examination of a 26-residue analog of exendin-4 (TrEX4) by NMR and CD in water, aqueous 30% trifluoroethanol (TFE), and bound to both SDS and DPC micelles, it is clear that these two lipid micelles can yield very different peptide structures. The Trp-cage fold (also observed in 30% TFE) is present when TrEX4 is bound to SDS micelles; however, tertiary structure is absent in the presence of DPC micelles. The loss of tertiary structure is attributed to an energetically favorable interaction (estimated as 2,3 kcal/mol) of the tryptophan side chain with the phosphocholine head groups. These dramatic structural differences suggest that care must be taken when using either SDS or DPC to mimic the membrane- or receptor-bound states. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 354,361, 2002 [source] DNA and RNA-Controlled Switching of Protein Kinase ActivityCHEMBIOCHEM, Issue 4 2009Lars Röglin Dr. Abstract Constrained: The readily programmable nucleic acid mediated recognition is used to constrain a phosphopeptide that was flanked by PNA segments. RNA-based switching allows control over the activity of target enzymes such as the protein kinase Src. It might thus be feasible to transduce changes of the concentration of selected RNA molecules to changes of the activity of signal transduction proteins. Protein switches use the binding energy gained upon recognition of ligands to modulate the conformation and binding properties of protein segments. We explored whether the programmable nucleic acid mediated recognition might be used to design or mimic constraints that limit the conformational freedom of peptide segments. The aim was to design nucleic acid,peptide conjugates in which the peptide portion of the conjugate would change the affinity for a protein target upon hybridization. This approach was used to control the affinity of a PNA,phosphopeptide conjugate for the signal transduction protein Src kinase, which binds the cognate phosphopeptides in a linear conformation. Peptide,nucleic acid arms were attached to known peptide binders. The chimeric molecules were studied in three modes: 1) as single strands, 2) constrained by intermolecular hybridization (duplex formation) and 3) constrained by intramolecular hybridization (hairpin formation). Of note, duplexes that were designed to accommodate bulged peptide structures (for example, in hairpins or bulges) had lower binding affinities than duplexes in which the peptide was allowed to adopt a more relaxed conformation. Greater than 90-fold differences in binding affinities were observed. It was, thus, feasible to make use of DNA hybridization to reversibly switch from no to almost complete inhibition of Src-SH2,peptide binding, and vice versa. A series of DNA and PNA-based hybridization experiments revealed the importance of charges and conformational effects. Nucleic acid mediated switching was extended to the use of RNA; this enabled a regulation of the enzymatic activity of the Src kinase. The proof-of-principle results demonstrate for the first time that PNA,peptide chimeras can transduce changes of the concentration of a given RNA molecule to changes of the activity of a signal transduction enzyme. [source] Nuclear magnetic resonance studies of CXC chemokine receptor 4 allosteric peptide agonists in solutionCHEMICAL BIOLOGY & DRUG DESIGN, Issue 2005O.K. Baryshnikova Abstract:, CXC chemokine receptor 4 (CXCR4) is an important pharmacological target due to its involvement in HIV-1 pathogenesis and cancer metastasis. Two recently discovered allosteric agonists that bind and activate CXCR4, the ASLW and RSVM peptides, were analyzed using solution nuclear magnetic resonance spectroscopy. Both peptides assumed an extended backbone conformation with several well-defined local motifs in the regions from residues 5 to 8 and 9 to 12. The local structures in the region of residues 5,8 were different for agonists studied here and natural ligands. The local structure in the region 9,12 was adopted by the entire ensemble of the ASLW peptide structures and by the subset of conformations for the RSVM peptide. The same turn was found in full-length stromal derived factor (SDF)-1 and in the small family of the SDF-1 N-terminal 17-mer. Similar examples in literature suggest the relevance of nascent structures in peptides to their biologically relevant conformations. The significance of found local structures and implications for further drug design are discussed. [source] Design of peptides with branched ,-carbon dehydro-residues: syntheses, crystal structures and molecular conformations of two peptides, (I) N -Carbobenzoxy-,Val-Ala-Leu-OCH3 and (II) N -Carbobenzoxy-,Ile-Ala-Leu-OCH3CHEMICAL BIOLOGY & DRUG DESIGN, Issue 2 2003R. Vijayaraghavan Abstract: Highly specific structures can be designed by inserting dehydro-residues into peptide sequences. The conformational preferences of branched , -carbon residues are known to be different from other residues. As an implication it was expected that the branched , -carbon dehydro-residues would also induce different conformations when substituted in peptides. So far, the design of peptides with branched , -carbon dehydro-residues at (i + 1) position has not been reported. It may be recalled that the nonbranched , -carbon residues induced , -turn II conformation when placed at (i + 2) position while branched , -carbon residues induced , -turn III conformation. However, the conformation of a peptide with a nonbranched , -carbon residue when placed at (i + 1) position was not found to be unique as it depended on the stereochemical nature of its neighbouring residues. Therefore, in order to induce predictably unique structures with dehydro-residues at (i + 1) position, we have introduced branched , -carbon dehydro-residues instead of nonbranched , -carbon residues and synthesized two peptides: (I) N -Carbobenzoxy-,Val-Ala-Leu-OCH3 and (II) N -Carbobenzoxy-,Ile-Ala-Leu-OCH3 with ,Val and ,Ile, respectively. The crystal structures of peptides (I) and (II) have been determined and refined to R-factors of 0.065 and 0.063, respectively. The structures of both peptides were essentially similar. Both peptides adopted type II , -turn conformations with torsion angles; (I): ,1 = ,38.7 (4)°, ,1 = 126.0 (3)°; ,2 = 91.6 (3)°, ,2 = ,9.5 (4)° and (II): ,1 = ,37.0 (6)°, ,1 = 123.6 (4)°, ,2 = 93.4 (4), ,2 = ,11.0(4)° respectively. Both peptide structures were stabilized by intramolecular 4,1 hydrogen bonds. The molecular packing in both crystal structures were stabilized in each by two identical hydrogen bonds N1,O1, (,x, y + 1/2, ,z) and N2,O2, (,x + 1, y + 1/2, ,z) and van der Waals interactions. [source] A Novel Heavy-Atom Label for Side-Specific Peptide Iodination: Synthesis, Membrane Incorporation and X-ray ReflectivityCHEMPHYSCHEM, Issue 9-10 2009Philipp E. Schneggenburger Abstract A novel iodine peptide label for X-ray analysis of membrane-active peptide structures is applied to solid-phase peptide synthesis. The resulting pore-structured labeled peptide as well as a non-labeled reference were reconstituted in lipid bilayer stacks (see scheme). The results indicate the exhibition of a membrane-spanning ,5.6 -double helical peptide structure and illustrate the quality of the new label. Structural parameters, such as conformation, orientation and penetration depth of membrane-bound peptides and proteins that may function as channels, pores or biocatalysts, are of persistent interest and have to be probed in the native fluid state of a membrane. X-ray scattering in combination with heavy-atom labeling is a powerful and highly appropriate method to reveal the position of a certain amino acid residue within a lipid bilayer with respect to the membrane normal axis up to a resolution of several Ångstrøm. Herein, we report the synthesis of a new iodine-labeled amino acid building block. This building block is intended for peptide incorporation to provide high intensities for electron density difference analysis of X-ray reflectivity data and improve the labeling potential for the lipid bilayer head-group and water region. The novel building block as well as the commercially available non-iodinated analogue, required for X-ray scattering, was implemented in a transmembrane peptide motif via manual solid-phase peptide synthesis (SPPS) following the fluorenylmethyloxycarbonyl (Fmoc)-strategy. The derived peptides were reconstituted in lipid vesicles as well as in highly aligned multilamellar lipid stacks and investigated via circular dichroism (CD) and X-ray reflectivity. Thereby, it has been revealed that the bulky iodine probe neither causes conformational change of the peptide structure nor lamellar disordering of the membrane complexes. [source] | |||||||||||||