A biokinematic approach for the computational simulation of proteins molecular mechanism |
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Authors: | Mikel Diez,Ví ctor Petuya,Luis Alfonso Martí nez-Cruz,Alfonso Herná ndez |
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Affiliation: | aFaculty of Engineering in Bilbao, University of the Basque Country, Department of Mechanical Engineering, Alameda de Urquijo s/n 48013 Bilbao, Spain;bCIC bioGUNE Research Centre, Ed. 800 Parque Tecnolgico de Bizkaia, 48160 Derio, Spain |
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Abstract: | Proteins play an essential role in the biological processes that take place in the human body. For this reason, it is very important to understand the molecular mechanisms involved. Recently a new approach, based on the parallelism between proteins and spatial mechanisms, has allowed methods to be developed to obtain atomic trajectories for protein motion using concepts from the kinematics of mechanisms. This paper presents a method for simulating protein motion, based on the evaluation of the potential energy during the motion, thereby avoiding the need to perform a minimization procedure. This approach constitutes a good compromise between computational effort and accuracy of the results. In addition, in order to efficiently simulate the motion, a new algorithm for normalization of the structure of the protein is presented. Finally, we illustrate the results of applying this method to an inorganic pyrophosphatase (family II) from Streptococcus gordonii evaluating geometric accuracy, energetic evolution and biological indicators. |
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Keywords: | Protein chain Serial robot Biokinematics Normalization |
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