Application of mixed peptide arrays to study combinatorial readout of chromatin modifications.

The N-terminal tails of histone proteins are massively decorated with post-translational modifications (PTMs), which play important roles in the regulation of gene expression. Several highly conserved chromatin interacting proteins can bind to histone modifications in a sequence and modification specific manner employing specific reading domains. These proteins often contain several reading domains, which can cooperate in the readout of different PTMs.

From spots to beads-PTM-peptide bead arrays for the characterization of anti-histone antibodies.

Antibodies that recognize PTMs of histones play a central role in epigenetic proteomic research. Modification-specific antibodies are employed in chromatin immunoprecipitation, for Western blotting and during the immunoprecipitation steps for MS-based global proteomic analyses. Knowledge about the antibodies' off-target binding is essential for the interpretation of experimental data.

Peptide arrays for development of PDGFRβ Affine molecules.

Purpose: Peptide arrays represent an attractive method for identification of amino acid motifs that bind to target structures. Spotting derivatives of the linear peptide platelet-derived growth factor receptor (PDGFR)-P1, which has been identified to bind the extracellular domain of the platelet-derived growth factor receptor beta, allows the synchronous investigation of the target affinity of numerous ligands.

Procedures: A peptide array randomizing PDGFR-P1 was constructed by replacement of each amino acid by all 20 natural amino acids.

Chemical labeling strategy with (R)- and (S)-trifluoromethylalanine for solid state 19F NMR analysis of peptaibols in membranes.

Substitution of a single Aib-residue in a peptaibol with (R)- and (S)-trifluoromethylalanine yields two local orientational constraints theta by solid state (19)F NMR. The structure of the membrane-perturbing antibiotic alamethicin in DMPC bilayers was analyzed in terms of two angles tau and rho from six such constraints, showing that the N-terminus (up to a kink at Pro14) is folded as an alpha-helix, tilted away from the membrane normal by 8 degrees, and assembled as an oligomer. The new (19)F NMR label CF(3)-Ala has thus been demonstrated to be highly sensitive, virtually unperturbing, and ideally suited to characterize peptaibols in membranes.