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Peptide Recognition (peptide + recognition)
Selected AbstractsSequence-Selective Peptide Recognition with Designed ModulesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 1 2006Mark Wehner Abstract A concept for the rational design of sequence-selective peptide receptors has been extended: in addition to recognition modules for polar, aromatic and basic amino acids, the series has now been completed with new receptor units for apolar and acidic amino acids. The underlying strategy uses the intermolecular ,-sheet stabilization of a dipeptide as a prerequisite to bind its N-terminal amino acid side chain through a strategically placed recognition tip at the end of a U-turn protruding from the receptor moiety. Thus, a diaminopyrazole has been covalently attached to Kemp's triacid by way of a cyclic imide, while a meta -substituted aniline was coupled as an amide to the pendant third carboxylate arm, bringing the two aromatic units into a sub-van der Waals distance in a tight conformational lock. NMR titrations, Karplus analyses and Monte-Carlo simulations demonstrate the effective sequence-selective recognition of alanine-containing dipeptides. No example of such a rationally designed set of peptide receptors had existed previously. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Peptide Recognition: Encapsulation and ,-Helical Folding of a Nine-Residue Peptide within a Hydrophobic Dimeric Capsule of a Bowl-Shaped HostCHEMISTRY - A EUROPEAN JOURNAL, Issue 12 2006Shohei Tashiro Abstract A dimeric capsule of coordination bowl 1 encapsulated a nine-residue peptide (Trp-Ala-Glu-Ala-Ala-Ala-Glu-Ala-Trp; 2) within the large hydrophobic cavity in water, and stabilized the ,-helical conformation of bound 2. An NMR titration experiment revealed that monomeric bowl 1 recognized two Trp residues at the both terminals of 2 through 1/2=1:1 to 2:1 complexation. The 1:1 and 2:1 species exist in equilibrium even in the presence of excess 1. It was found that the formation of the 2:1 complex, in which two bowls of 1 wrapped the whole of 2, became dominant by the addition of NaNO3 due to the fact that the enhanced ion strength increased the hydrophobic interaction between Trp residues and the cavity of 1. The ,-helical conformation of 2 within the dimeric capsule of 1 was elucidated from detailed NOESY analysis. [source] Use of peptide for selective and sensitive detection of an Anthrax biomarker via peptide recognition and surface-enhanced Raman scatteringJOURNAL OF RAMAN SPECTROSCOPY, Issue 2 2010Kyungtag Ryu Abstract A short 16-amino acid peptide has been used in place of an antibody to selectively detect the specific Anthrax biomarker, protective antigen (PA), using surface-enhanced Raman scattering (SERS). Peptides are more stable than antibodies under various biological conditions and are easily synthesized for a specific target. A peptide that has high affinity to PA was conjugated onto gold nanoparticles along with a Raman reporter and then incubated in various concentrations of PA. Parallel studies in which the peptide sequence was replaced with an antibody were performed to compare the performance of the two methodologies. Both the peptide and antibody functionalized nanoparticles were able to specifically detect PA concentrations down to 6.1 fM. These results demonstrate that these short, robust peptides can be used in the place of traditional antibodies to specifically recognize target biomarkers in the field for the potential diagnosis of disease. Copyright © 2010 John Wiley & Sons, Ltd. [source] The identification of conserved interactions within the SH3 domain by alignment of sequences and structuresPROTEIN SCIENCE, Issue 11 2000Stefan M. Larson Abstract The SH3 domain, comprised of approximately 60 residues, is found within a wide variety of proteins, and is a mediator of protein,protein interactions. Due to the large number of SH3 domain sequences and structures in the databases, this domain provides one of the best available systems for the examination of sequence and structural conservation within a protein family. In this study, a large and diverse alignment of SH3 domain sequences was constructed, and the pattern of conservation within this alignment was compared to conserved structural features, as deduced from analysis of eighteen different SH3 domain structures. Seventeen SH3 domain structures solved in the presence of bound peptide were also examined to identify positions that are consistently most important in mediating the peptide-binding function of this domain. Although residues at the two most conserved positions in the alignment are directly involved in peptide binding, residues at most other conserved positions play structural roles, such as stabilizing turns or comprising the hydrophobic core. Surprisingly, several highly conserved side-chain to main-chain hydrogen bonds were observed in the functionally crucial RT-Src loop between residues with little direct involvement in peptide binding. These hydrogen bonds may be important for maintaining this region in the precise conformation necessary for specific peptide recognition. In addition, a previously unrecognized yet highly conserved ,-bulge was identified in the second ,-strand of the domain, which appears to provide a necessary kink in this strand, allowing it to hydrogen bond to both sheets comprising the fold. [source] Structure of human TSG101 UEV domainACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2006Pedro L. Mateo The UEV domain of the TSG101 protein functions in the vacuolar protein-sorting pathway and in the budding process of HIV-1 and other retroviruses by recognizing ubiquitin in proteins tagged for degradation and short sequences in viral proteins containing an essential and well conserved PTAP motif, respectively. A deep understanding of these interactions is key to the rational design of much-needed novel antivirals. Here, the crystal structure of the TSG101 UEV domain (TSG101-UEV) is presented. TSG101-UEV was crystallized in the presence of PEG 4000 and ammonium sulfate. Under these conditions, crystals were obtained in space group R3, with unit-cell parameters a = b = 97.9, c = 110.6,Å, , = , = 90, , = 120°. Phases were solved by molecular replacement and the crystal structure of TSG101-UEV was refined to an R factor of 18.8% at 2.2,Å resolution. A comparison between the crystal structure and previously reported NMR structures has revealed significant differences in the conformation of one of the loops implicated in ubiquitin recognition. Also, the resulting structure has provided information about the presence of water molecules at the binding interface that could be of relevance for peptide recognition. [source] | ||||||||||