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.

A linha que contorna a crônica: a obra de Tarsila do Amaral

A proposta desta dissertação é investigar o trabalho artístico de Tarsila do Amaral, sua obra plástica como também sua obra escrita. Esta pesquisa se propõe a compreender de que maneira sua pintura, elaborada como um desenho, com cores delimitadas por fios e imagens geometrizadas adquire uma dependência a uma narrativa de cunho literário. Tarsila do Amaral, pintora modernista, parece organizar os espaços em suas pinturas ao construir linhas, elaboradas cuidadosamente, imprimindo um aspecto aparentemente cerebral ao seu trabalho. Assim, partindo dessas duas formas de arte, imagem e texto, que dialogam entre si na obra da pintora, surgiu a necessidade de escrever a dissertação em forma de crônica. Ao longo da pesquisa este gênero literário demonstrou ser a forma mais adequada para lidar com o objeto de estudo, pois, escrever crônicas tendo como ponto de partida os quadros e textos de Tarsila do Amaral permitiu um olhar mais detalhado e demorado sobre sua obra, possibilitando também lidar com todos os aspectos de sua vida que tangenciaram sua arte. Parece importante perceber as influências estrangeiras em sua formação como pintora e sua busca por uma identidade como artista. Ressaltando o aspecto lúdico de sua obra, as crônicas a seguir buscam compreender como uma pintura racional pode gerar um resultado próximo a uma imagem infantil, especialmente no período Pau-Brasil. Já na fase Antropofágica, o foco de estudo se concentrou na tela Abaporu, em sua elaboração, inspiração e desdobramentos como movimento literário e artístico. Assim, vinte e uma crônicas proporcionam um panorama de aspectos relevantes na obra de Tarsila do Amaral desde o início de seus estudos de desenho até o período em que já recebia o devido reconhecimento por sua obra artística

Length-weight relationship of small pelagic fish species of the southeast and South Brazilian Exclusive Economic Zone

The length-weight relationship (LWR) parameters of 23 small pelagic fish species (belonging to 13 families) from the south-southeast Brazilian Exclusive Economic Zone in 1996 and 1997 are presented. The b values varied between 2.72 and 3.53. The samples for this study were collected during hydroacoustic surveys covering an area of 700 000 square km.

Length-weight relationships of marine fishes from the central Brazilian coast

Parameters of the length-weight relationship are presented for 85 fish species from the marine and estuarine regions of the central Brazilian coast (latitude 13° to 23° S). Three different methods were used. A non-linear iterative process using the quasi-Newton algorithm yielded a better fit for all data sets analyzed. The length-weight allometry coefficient b estimated from standard length data tended to be lower than from total length data. The difference between these estimates was significant for some species.

Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.