Sim-xl: A Powerful And User-friendly Tool For Peptide Cross-linking Analysis.

Chemical cross-linking has emerged as a powerful approach for the structural characterization of proteins and protein complexes. However, the correct identification of covalently linked (cross-linked or XL) peptides analyzed by tandem mass spectrometry is still an open challenge. Here we present SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). Our software introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. Moreover, our search engine is the first to capitalize on reporter ions for selecting tandem mass spectra derived from cross-linked peptides. It also makes available a 2D interaction map and a spectrum-annotation tool unmatched by any of its kind. We show SIM-XL to be more sensitive and faster than a competing tool when analyzing a data set obtained from the human HSP90. The software is freely available for academic use at http://patternlabforproteomics.org/sim-xl. A video demonstrating the tool is available at http://patternlabforproteomics.org/sim-xl/video. SIM-XL is the first tool to support XL data in the mzIdentML format; all data are thus available from the ProteomeXchange consortium (identifier PXD001677).

Estudo teórico da interação existente entre a artemisinina e o heme

The purpose of this work is to study theoretically stereoelectronic aspects of the interaction between heme and artemisinin in the transitional heme-artemisinin complex. Through semi-empirical calculations using the PM3 method, the potential energy barrier of artemisinin rotation relative to heme in the heme-artemisinin complex was studied in vacuum and in the partially solvated state. The minimum heat of formation obtained for the complex with and without water molecules is -702.39 and -100.86 kcal mol-1, respectively, which corresponds to the dihedral angle C-Fe-O1-O2 of 43.93º and 51.90º around the iron-oxygen O1 bond, respectively. The water molecules bind to heme via 13 hydrogen bonds and O-H O and 6 C-H O interactions, which accounts for -67.23 kcal mol-1. It is observed that the inclusion of water molecules does not affect significantly the stability of the heme-artemisinin complex.

A valoração de traços de concordância dentro do DP

This paper argues in favor of a concord features valuing within the DP in terms of the Agree operation (Chomsky, 1999), with no recourse to any other mechanism. I show that Agree accounts for feature valuing both in the sentence level as well as in the DP, contrary to Chomsky's (1999) suggestion that concord in DP should involve some other checking mechanism.

Juventude, lazer e uso abusivo de alcool

Universidade Estadual de Campinas . Faculdade de Educação Física

Jogando com o psicodrama : uma contribuição para a psicologia do esporte

Universidade Estadual de Campinas . Faculdade de Educação Física