Mapping of possible prion protein self-interaction domains using peptide arrays

Background  

The common event in transmissible spongiform encephalopathies (TSEs) or prion diseases is the conversion of host-encoded protease sensitive cellular prion protein (PrP^C) into strain dependent isoforms of scrapie associated protease resistant isoform (PrP^Sc) of prion protein (PrP). These processes are determined by similarities as well as strain dependent variations in the PrP structure. Selective self-interaction between PrP molecules is the most probable basis for initiation of these processes, potentially influenced by chaperone molecules, however the mechanisms behind these processes are far from understood. We previously determined that polymorphisms do not affect initial PrP^C to PrP^Sc binding but rather modulate a subsequent step in the conversion process. Determining possible sites of self-interaction could elucidate which amino acid(s) or amino acid sequences contribute to binding and further conversion into other isoforms. To this end, ovine – and bovine PrP peptide-arrays consisting of 15-mer overlapping peptides were probed with recombinant sheep PrP^C fused to maltose binding protein (MBP-PrP).     

An improved method for the synthesis of cellulose membrane-bound peptides with free C termini is useful for PDZ domain binding studies

SPOT synthesis permits parallel synthesis and screening of thousands of cellulose membrane-bound peptides to study protein-protein interactions in a proteomic context. Recognition of C-terminal residues is one of the most common binding features of PDZ domains. Unfortunately, most solid support-bound peptide libraries lack a free C terminus due to C-terminal fixation on the solid support. To overcome this restriction, we developed a robust methodology based on our previous strategy for generating peptides with authentic C termini. To validate this improved method, we screened a human peptide library of 6223 C termini with the syntrophin PDZ domain. Furthermore, using the same library, new peptide ligands derived from membrane proteins and receptors were found for the ERBIN PDZ domain. Finally, we identified the protein kinase breakpoint cluster region, which is known as a negative regulator of cell proliferation and oncogenic transformation, as an ERBIN ligand.     

The solid state and solution chemistry of dichlorobis(pyridine)cobalt(II)

The thermal decomposition of dichlorobisquinolinecobalt(II) was investigated. Kinetic analyses were performed on the dynamic and isothermal curves. The dynamic and d.s.c. studies revealed two simultaneously reactions while the isothermal reactions represented single processes. The scheme of thermal decomposition is:

Kristallstruktur von Hexamincyclotriphosphazen,P3N3(NH2)6

Crystal Structure of Hexamine Cyclotriphosphazene, P₃N₃(NH₂)₆ In the presence of KNH₂ hexamine cyclotriphosphazene semi ammoniate (molar ratio 12:1) in NH₃ gives crystals of solvent free P₃N₃(NH₂)₆ within 5 d at 130°C and p(NH₃) = 110 bar. The structure was solved by X-rax methods: P₃N₃(NH₂)₆: P2₁/c, Z = 4, a = 10.889(6) Å, b = 5.9531(6) Å, c = 13.744(8) Å, β = 97.83(3)°, Z(F_o) = 1 721 with (F_o)² ≥ 3σ(F_o)², Z(var.) = 157, R/R_w = 0,036/0,041 The structure contains columns of molecules P₃N₃(NH₂)₆ all in the same orientation. The six-membered rings within one molecule have boat conformation. The columns are stacked together in a way that one is surrounded by four others shifted by half a lattice constant in direction [010]. Strong hydrogen bridge-bonds N? H…?N connect molecules within the columns and between them.     

CsMoO2(HO3P–CH2–PO3): a new metallodiphosphonate with a hybrid framework

Crystals of caesium molybdeno­methyl­enedi­phospho­nate, [CsMoO₂(CH₃O₆P₂)], were hydro­thermally synthesized at 473 K. The monoclinic structure, as determined from single‐crystal X‐ray diffraction, is two‐dimensional and consists of stacked mixed layers of corner‐sharing tetrahedral di­phosphon­ate groups and MoO₆ octahedra, between which Cs⁺ cations are intercalated.     

Recognition of G-1:C73 atomic groups by Escherichia coli histidyl-tRNA synthetase

This work focuses on the RNA-protein interactions necessary for efficient aminoacylation of tRNAHis by Escherichia coli histidyl-tRNA synthetase (HisRS). The E. coli tRNAHis acceptor stem is characterized by a unique "extra" G-1:C73 base pair. Previous in vivo and in vitro studies showed that G-1:C73 is a major recognition element for E. coli HisRS. To further probe the role of the G-1:C73 base pair in specific aminoacylation, we carried out atomic group "mutagenesis" studies. Systematic base analogue substitutions at the -1:73 position of chemically synthesized microhelixHis substrates suggest that the G-1 base serves to position the 5'-monophosphate, which is critical for aminoacylation. Additionally, the C73 and G-1 bases contain major groove exocyclic atomic groups that contribute to HisRS recognition.     

β-Lactam Derivatives as Enzyme Inhibitors: Peptidic Derivatives of ( RS )-2-Oxo-4-phenylazetidine-1-alkanoic Acids

4-Phenylazetidine-2-one was transformed into 4-phenylazetidine-1-alkanoic acids, which were reacted in the presence of diphenylphosphoroazidate with amino acid esters and dipeptide esters yielding β-lactam peptides with different spacers between the lactam ring and the peptide moiety. All structures were established by elementary analyses, HPLC, optical rotation, and spectroscopic data and all new compounds were tested as inhibitors of PPE using standard procedures. Four compounds exhibited a weak activity compared with the standard inhibitor trifluoroacetyl-l-val-l-tyr-l-val.     

Dynamics and energetics of the self-assembly of a hydrophobically modified polyelectrolyte: Naphthalene-labeled poly(acrylic acid)

Steady-state and time-resolved fluorescence studies were performed on aqueous solutions of poly(acrylic acid) hydrophobically modified with two very different levels of naphthalene (Np). It is demonstrated that unique information on association phenomena involving hydrophobe-modifed polymers can be obtained from an extended fluorescence study by using data for a less-modified polymer as a reference. For the more highly modified polymer, the presence of excited-state (as well as ground-state) dimers in addition to monomer emission due to locally excited naphthalene gives evidence for hydrophobic association between naphthalene groups. This association becomes, as expected, much less important at higher pH due to the electrostatic repulsion between different chain segments. However, it is noted that even at high pH there is a significant self-association. The coexistence of static and dynamic quenching phenomena of the Np monomer label was also revealed in the time-resolved fluorescence data. The data are compatible with the existence of two types of monomers and one excimer and suggest that the essential contribution to the monomer emission comes from isolated chromophores, whereas excimer formation arises from both a dynamic route (excited Np chromophores able to produce a dynamic excimer) and a static route (excitation of ground-state Np dimers). At room temperature, the dissociative reaction, excimer-to-monomer, can be neglected, and thus the rate constant for excimer formation and decay could be obtained with and without considering the influence of preformed dimers. Temperature has shown to induce different behavior in the polymer photophysics. In the case of the less-labeled polymer, the decays were found to be single-exponential with the fluorescence lifetime decreasing with increasing temperature. From the temperature dependence of the steady-state fluorescence data, the activation energy for excimer formation and the binding energy of the excimer were evaluated at different pH values, through the Stevens-Ban-type plots of the excimer-to-monomer intensity ratio. With the time-resolved data, measured in the temperature range of 5-60 degrees C, it was possible to extract the intrinsic activation energies for excimer formation. The thermodynamic driving force for the intrapolymeric association was found to be dependent on a balance between hydrophobic and electrostatic interactions, which are dependent on the pH, temperature, and hydrophobic content of the polymer.     

Synthesis of (±)-Desmarestene and (±)-Viridiene,the Two Sperm Releasing and Attracting Pheromones from the Brown Algae Desmarestia aculeata and Desmarestia viridis

Desmarestene 1 6-(1Z,3-butadienyl)-1,4-cycloheptadiene and viridiene 3 cis-3-(1Z, 3-butadienyl)-4-vinylcyclopentene are chemical messengers for male gametes of the brown algae Desmarestia aculeate and Desmarestia viridis. Total syntheses of 1 , 3 and their stereoisomers 1a , 3a - c are reported. Gas-chromatographic comparison of synthetic 1 and 3 with the corresponding natural products has established their structural identity.     

Carbohydrate chain of ganglioside GM1 as a ligand: identification of the binding strategies of three 15 mer peptides and their divergence from the binding modes of growth-regulatory galectin-1 and cholera toxin

The branched pentasaccharide chain of ganglioside GM1 is a prominent cell surface ligand, for example, for cholera toxin or tumor growth-regulatory homodimeric galectins. This activity profile via protein recognition prompted us to examine the binding properties of peptides with this specificity. Our study provides insights into the mechanism of molecular interaction of this thus far unexplored size limit of the protein part. We used three pentadecapeptides in a combined approach of mass spectrometry, NMR spectroscopy and molecular modelling to analyze the ligand binding in solution. Availability of charged and hydrophobic functionalities affected the intramolecular flexibility of the peptides differently. Backfolding led to restrictions in two cases; the flexibility was not reduced significantly by association of the ligand in its energetically privileged conformations. Major contributions to the interaction energy arise from the sialic acid moiety contacting Arg/Lys residues and the N-terminal charge. Considerable involvement of stacking between the monovalent ligand and aromatic rings could not be detected. This carbohydrate binding strategy is similar to how an adenoviral fiber knob targets sialylated glycans. Rational manipulation for an affinity enhancement can now be directed to reduce the flexibility, exploit the potential for stacking and acquire the cross-linking capacity of the natural lectins by peptide attachment to a suitable scaffold.