Biomedical subjects

Jan Seebacher

Publications and source records attributed to Jan Seebacher.

4 recordsLinked to original sources

PubMed2006

Zn-OH2 and Zn-OH complexes with hydroborate-derived tripod ligands: a comprehensive study.

The complete array of those hydrotris(pyrazolyl/thioimidazolyl)borate ligands that were developed and used in the author's laboratories, with N3, N2S, NS2, and S3 donor sets, was scanned for their ability to form Zn-OH2 and Zn-OH complexes. The coordination motifs found were Zn-OH2, Zn-OH, Zn-OH-Zn, and Zn-O2H3-Zn. Of these, the well-established Zn-OH motif was complemented with novel species bearing N3, NS2, and S3 tripods. The Zn-OH2 motif was observed only with pyrazolylborate ligands and only in unusual situations with coordination numbers higher than 4 for zinc. The new Zn-OH-Zn motif was realized for three different pyrazolylborates, for one NS2 tripod, and for two S3 tripods. Finally, it was verified that the Zn-O2H3-Zn motif again occurs only with pyrazolylborate ligands. The new complexes were identified by a total of 11 structure determinations.

Borates↗

PubMed2006

Thiolate alkylation in tripod zinc complexes: a comparative kinetic study.

The biologically relevant alkylations of the thiolate ligands in tripod zinc thiolates by methyl iodide were studied kinetically. Five tripod ligands of the pyrazolyl/thioimidazolyl borate type were employed, offering N3, N2S, NS2, and S3 donor sets. For each of them, the ethyl-, benzyl-, phenyl-, and p-nitrophenylthiolate zinc complexes were investigated, yielding a total of 20 second-order rate constants. The comparison of these rate constants shows three effects: (1) the electronic effect among the thiolates, i.e., the ethanethiolates react about 3 orders of magnitude faster than the p-nitrophenylthiolates; (2) the steric effect among the pyrazolylborates, i.e., the phenyl-substituted ones react about 2 orders of magnitude faster than the tert-butyl-substituted ones; and (3) the strong acceleration by the sulfur donors in the tripods, reaching 4 orders of magnitude between the reaction times of the (N3)Zn-SR and (S3)Zn-SR complexes.

Alkylation↗

PubMed2006

Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing.

Distance constraints in proteins and protein complexes provide invaluable information for calculation of 3D structures, identification of protein binding partners and localization of protein-protein contact sites. We have developed an integrative approach to identify and characterize such sites through the analysis of proteolytic products derived from proteins chemically cross-linked by isotopically coded cross-linkers using LC-MALDI tandem mass spectrometry and computer software. This method is specifically tailored toward the rapid analysis of low microgram amounts of proteins or multimeric protein complexes cross-linked with nonlabeled and deuterium-labeled bis-NHS ester cross-linking reagents (both commercially available and readily synthesized). Through labeling with [18O]water solvent and LC-MALDI analysis, the method further allows the possible distinction between Type 0 and Type 1 or Type 2 modified peptides (monolinks and looplinks or cross-links), although such a distinction is more readily made from analysis of tandem mass spectrometry data. When applied to the bacterial Colicin E7 DNAse/Im7 heterodimeric protein complex, 23 cross-links were identified including six intersubunit cross-links, all between residues that are close in space when examined in the context of the X-ray structure of the heterodimer. In addition, cross-links were successfully identified in five single subunit proteins, beta-lactoglobulin, cytochrome c, lysozyme, myoglobin, and ribonuclease A, establishing the generality of the approach.

Chromatography, Liquid↗

PubMed2005

Tris(thioimidazolyl)borate-zinc-thiolate complexes for the modeling of biological thiolate alkylations.

The S3Zn-SR coordination of thiolate-alkylating enzymes such as the Ada DNA repair protein was reproduced in tris(thioimidazolyl)borate-zinc-thiolate complexes Tti(R)Zn-SR'. Four different Tti(R) ligands and nine different thiolates were employed, yielding a total of 12 new complexes. In addition, one Tti(R)Zn-SH complex and two thiolate-bridged [Tti(R)-SEt-Tti(R)]+ complexes were obtained. A selection of six thiolate complexes was converted with methyl iodide to the corresponding methyl thioethers and Tti(R)Zn-I. According to a kinetic analysis these reactions are second-order processes, which implies that the alkylations are likely to occur at the zinc-bound thiolates. They are much faster than the alkylations of zinc thiolates with N3 or N2S tripod ligands. The most reactive thiolate, Tti(Xyl)Zn-SEt, reacts slowly with trimethyl phosphate in a nonpolar medium at room temperature, yielding methyl-ethyl-thioether and Tti(Xyl)Zn-OPO(OMe)2 which can be converted back to the thiolate complex with NaSEt. This is the closest reproduction of the Ada repair process so far.

Alkylation↗