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High energy irradiation to the hydrogen bonded system is important in relevance with the initial process of DNA and enzyme damages. In the present study, the effects of radiation to catalytic triad have been investigated by means of direct ab-initio molecular dynamics (AIMD) calculation. As a model of the catalytic triad, Ser-His-Glu residue, which is one of the important enzymes in the acylation reaction, was examined. The ionization and electron attachment processes in Ser-His- Glu were investigated as the radiation effects. The direct AIMD calculation showed that a proton of His is spontaneously transferred to carbonyl oxygen of Glu after the ionization. However, the whole structure of catalytic triad was essentially kept after the ionization. On the other hand, in the case of the electron capture in the model catalytic triad Ser-His-Glu, the dissociation of Glu residue from [Ser-His]- was found as a product channel. The mechanism of ionization and electron capture process in the catalytic triad was discussed on the basis of theoretical results. [ABSTRACT FROM AUTHOR]

Apoptosis proteins play an essential role in the development and homeostasis of an organism. The accurate prediction of subcellular location for apoptosis proteins is helpful for understanding the mechanism of programmed cell death and their biological functions. In this article, a new apoptosis proteins localization algorithm, named PSSP, is proposed based on the predicted cleavage sites of primary protein sequences. First, protein chains are divided into N-terminal signal parts and mature protein parts according to their predicted cleavage sites by SignalP. Then, amino acid composition (ACC) of the individual subsequence together with pseudo-ACC and stereochemical properties of whole chain were extracted to represent a given protein sequence. Jackknife test by support vector machine on three broadly used datasets (ZD98, ZW225, and CL317 datasets) of apoptosis proteins demonstrated that the total accuracies by this approach are 93.9, 87.6, and 91.5%, respectively. In addition, an independent nonapoptosis benchmark dataset (NNPSL) was also used to evaluate the performance of this method, and predictive accuracies for eukaryotic and prokaryotic proteins are also comparable to existing methods. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Here, we present some highlights of our recent study [Malhado et al. J. Phys. Chem. A 115, 3729 (2011)] of the photoisomerization involving a conical intersection for a model protonated Schiff base (PSB) in modeled water and acetonitrile solvents, in which the inclusion of energy- and momentum-transfer effects is described via a generalized Langevin equation (GLE) frictional approach and surface-hopping dynamics. Short-time GLE frictional effects on the model's three coordinates, the intramolecular bond length alternation, and torsional PSB coordinates and a solvent coordinate, have a number of important features. Among these are the general feature of accelerating nonadiabatic transitions to the ground electronic state and a predicted preferential higher proportion of ground-state trans isomer, that is, a successful cis to trans photoreaction. This preference is solvent-dependent and is enhanced in water solvent with its higher friction intensity and short time scales. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]