Simulation of Post-translational Conformations in the Ribosomal Polypeptide Synthesis

L. Znamirowski (Poland) and E. Zukowska (USA)


Conformations, Parallel Computations, Protein Folding, Message-Passing Interface, Ribosome, Translation.


In this paper the paradigm for simulation of post-translational conformations of the polypeptide chain in a dynamic of the protein torsion angles aspect is discussed. The polypeptide synthesized in the ribosome is modeled using torsion angles as a degrees of freedom. The model construction paradigm for dynamics modeling of the translation processes performed in a ribosome and post translational modifications (conformations) is discussed in general, and the modeling of the translation process and post-translational conformations in a static sense is presented in details. A model using the concept of process communicating through messages paradigm is discussed. The computer network structure contains a workstation fulfilling the needs of Graphic User Interface, and a supercomputer working under control of the workstation to fulfill the tasks of time-consuming, interdependent numerical computations performed in the Message-Passing Interface environment on a UNIX platform. The model introductory implementation is illustrated through the examples.

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