Insights into mechanism kinematics for protein motion simulation

Background: The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations. On the other hand, less accurate procedures such as interpolation methods, do not generate realistic morphs from the kinematic point of view. Analyzing a protein's movement is very similar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composed of rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen, based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmap method, which discretizes the protein configurational space against a scoring function, or the kinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulate protein motion with a reduced computational cost. Results: In this paper a new viewpoint for protein motion simulation, based on mechanism kinematics is presented. The paper describes a set of methodologies, combining different techniques such as structure normalization normalization processes, simulation algorithms and secondary structure detection procedures. The combination of all these procedures allows to obtain kinematic morphs of proteins achieving a very good computational cost-error rate, while maintaining the biological meaning of the obtained structures and the kinematic viability of the obtained motion. Conclusions: The procedure presented in this paper, implements different modules to perform the simulation of the conformational change suffered by a protein when exerting its function. The combination of a main simulation procedure assisted by a secondary structure process, and a side chain orientation strategy, allows to obtain a fast and reliable simulations of protein motion.

Abordagem informacional da política externa brasileira : a participação da CREDN (1995-2011)

O estudo a ser apresentado tem como objetivo analisar a influência dos deputados federais na política externa brasileira, mais especificamente dos deputados da Comissão de Relação Exteriores e Defesa Nacional. A idéia não é criar um novo paradigma de inserção, mas levantar pistas sobre diferentes formas de participação que o legislativo pode ter na condução dessa política no país. Contrariamos as análises que atribuem ao legislativo pouca participação ao processo decisório e focalizam a atuação na aprovação (ou não), dos acordos internacionais enviados pelo Executivo. Nesse sentido, procuramos ir além dessa abordagem tradicional abrindo o leque para outras formas de participação dos deputados federais na política externa brasileira. A politização da política externa e o papel mais ativo da Comissão de Relações Exteriores e Defesa Nacional (CREDN) têm levado a uma maior atuação do legislativo nessas questões. Principalmente a partir da maior atenção da oposição para as questões de política externa. A política externa foi considerada a política pública mais insulada do debate político-partidário. Mas, agora, os legisladores têm participado e se interessado cada vez mais por estas questões. O Congresso tem utilizado mais seus instrumentos institucionais de fiscalização para monitorar a condução da política externa. Assim, foi analisado o papel da CREDN como mecanismo de aquisição de informação, com o intuito de informar o legislador mediano em termos de política externa. O estudo parte do modelo informacional para encontrar respostas sobre o incentivo que os legisladores teriam em coletar informações (custosas) sobre política externa. Desse modo, procura-se analisar o incentivo dos legisladores em ativar tal política no plenário (Santos e Almeida, 2009; Martin, 2000). De forma cada vez mais extensiva e fiscalizadora, acrescentando informações às políticas formuladas pelo Executivo (Almeida & Santos, 2008)

Thermodynamic damage mechanism of transparent films caused by a low-power laser

A new model for analyzing the laser-induced damage process is provided. In many damage pits, the melted residue can been found. This is evidence of the phase change of materials. Therefore the phase change of materials is incorporated into the mechanical damage mechanism of films. Three sequential stages are discussed: no phase change, liquid phase change, and gas phase change. To study the damage mechanism and process, two kinds of stress have been considered: thermal stress and deformation stress. The former is caused by the temperature gradient and the latter is caused by high-pressure drive deformation. The theory described can determine the size of the damage pit. (c) 2006 Optical Society of America.

Development in laser induced extrinsic absorption damage mechanism of dielectric films

Absorption of host and the temperature-dependence of absorption coefficient have been considered in evaluating temperatures distribution in films, when laser pulse irradiates on films. Absorption of dielectric materials experience three stages with the increase of temperature: multi-photon absorption; single photon absorption; metallic absorption. These different absorption mechanisms correspond to different band gap energies of materials, which will decrease when the temperature of materials increases. evaluating results indicate that absorption of host increases rapidly when the laser pulse will be over. If absorption of host and the temperature-dependence of absorption are considered, the material temperatures in films will be increased by a factor of four.

Study on the activation mechanism of BCL-2 related ovarian killer (BOK)

BCL-2 family proteins are key regulators of the mitochondrial apoptotic machinery, controlling the mitochondrial outer membrane (MOM) permeabilization (MOMP). BCL-2 related Ovarian Killer (BOK) is a poorly understood pro-apoptotic member of this protein family. It has been reported that BOK localizes predominantly (although not exclusively) at membranes of the endoplasmic reticulum and of the Golgi apparatus. However, it is unclear whether BOK also operates at the MOM to promote apoptosis, as other pro-apoptotic BCL-2 family members do. Basing on the fact that the other two BAX-like pro-apoptotic members have been reported to oligomerize in order to induce MOMP, site-directed mutagenesis was used to generate two point mutations that predictably eliminated BOK’s oligomerization capacity. Then, the effect of such mutations on BOK’s membrane activity was examined using fluorescence spectroscopy.