The use of hydrolytic enzymes and multi-stage tandem mass spectrometry to analyze pyridoxal phosphate-modified peptides.

A previous approach was established that allowed direct identification of pyridoxal-5'-phosphate (PLP) bonding sites in proteins using mass spectrometry after tryptic proteolysis. The approach required peptide mass fingerprinting owing to suppressed amide backbone fragmentation in favor of side-chain elimination of diagnostic product ions from PLP-derivatized lysyl residues. While sufficient for purified proteins, unambiguous sequence determination is needed to assign PLP bonding sites in unknown proteins in complex mixtures. Here, we describe the use of hydrolytic enzymes and multi-stage tandem mass spectrometry to elucidate the amino acid sequence and PLP bonding site in PLP-modified peptides.

Evaluation of dispersion type metal···π arene interaction in arylbismuth compounds - an experimental and theoretical study.

The dispersion type Bi···π arene interaction is one of the important structural features in the assembly process of arylbismuth compounds. Several triarylbismuth compounds and polymorphs are discussed and compared based on the analysis of single crystal X-ray diffraction data and computational studies. First, the crystal structures of polymorphs of Ph3Bi (1) are described emphasizing on the description of London dispersion type bismuth···π arene interactions and other van der Waals interactions in the solid state and the effect of it on polymorphism. For comparison we have chosen the substituted arylbismuth compounds (C6H4-CH═CH2-4)3Bi (2), (C6H4-OMe-4)3Bi (3), (C6H3-t-Bu2-3,5)3Bi (4) and (C6H3-t-Bu2-3,5)2BiCl (5). The structural analyses revealed that only two of them show London dispersion type bismuth···π arene interactions. One of them is the styryl derivative 2, for which two polymorphs were isolated. Polymorph 2a crystallizes in the orthorhombic space group P212121, while polymorph 2b exhibits the monoclinic space group P21/c. The general structure of 2a is similar to the monoclinic C2/c modification of Ph3Bi (1a), which leads to the formation of zig-zag Bi-arenecentroid ribbons formed as a result of bismuth···π arene interactions and π···π intermolecular contacts. In the crystal structures of the polymorph 2b as well as for 4 bismuth···π arene interactions are not observed, but both compounds revealed C-HPh···π intermolecular contacts, as likewise observed in all of the three described polymorphs of Ph3Bi. For compound 3 intermolecular contacts as a result of coordination of the methoxy group to neighboring bismuth atoms are observed overruling Bi···π arene contacts. Compound 5 shows a combination of donor acceptor Bi···Cl and Bi···π arene interactions, resulting in an intermolecular pincer-type coordination at the bismuth atom. A detailed analysis of three polymorphs of Ph3Bi (1), which were chosen as model systems, at the DFT-D level of theory supported by DLPNO-CCSD(T) calculations reveals how van der Waals interactions between different structural features balance in order to stabilize molecular arrangements present in the crystal structure. Furthermore, the computational results allow to group this class of compounds into the range of heavy main group element compounds which have been characterized as dispersion energy donors in previous work.

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.

Policies supporting the rapid and open sharing of genomic data have directly fueled the accelerated pace of discovery in large-scale genomics research. The proteomics community is starting to implement analogous policies and infrastructure for making large-scale proteomics data widely available on a precompetitive basis. On August 14, 2008, the National Cancer Institute (NCI) convened the "International Summit on Proteomics Data Release and Sharing Policy" in Amsterdam, The Netherlands, to identify and address potential roadblocks to rapid and open access to data. The six principles agreed upon by key stakeholders at the summit addressed issues surrounding (1) timing, (2) comprehensiveness, (3) format, (4) deposition to repositories, (5) quality metrics, and (6) responsibility for proteomics data release. This summit report explores various approaches to develop a framework of data release and sharing principles that will most effectively fulfill the needs of the funding agencies and the research community.