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Modelization of Thermal Fluctuations in G Protein-Coupled Receptors

C. Pennetta·V. Akimov·E. Alfinito·L. Reggiani·G. Gomila·G. Ferrari·L. Fumagalli·M. Sampietro
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Abstract

We simulate the electrical properties of a device realized by a G protein coupled receptor (GPCR), embedded in its membrane and in contact with two metallic electrodes through which an external voltage is applied. To this purpose, recently, we have proposed a model based on a coarse graining description, which describes the protein as a network of elementary impedances. The network is built from the knowledge of the positions of the C-alpha atoms of the amino acids, which represent the nodes of the network. Since the elementary impedances are taken depending of the inter-nodes distance, the conformational change of the receptor induced by the capture of the ligand results in a variation of the network impedance. On the other hand, the fluctuations of the atomic positions due to thermal motion imply an impedance noise, whose level is crucial to the purpose of an electrical detection of the ligand capture by the GPCR. Here, in particular, we address this issue by presenting a computational study of the impedance noise due to thermal fluctuations of the atomic positions within a rhodopsin molecule. In our model, the C-alpha atoms are treated as independent, isotropic, harmonic oscillators, with amplitude depending on the temperature and on the position within the protein (alpha-helix or loop). The relative fluctuation of the impedance is then calculated for different temperatures.

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C. Pennetta, V. Akimov, E. Alfinito, L. Reggiani, G. Gomila, G. Ferrari, L. Fumagalli, M. Sampietro. 2005-06-30. Modelization of Thermal Fluctuations in G Protein-Coupled Receptors. https://doi.org/10.1063/1.2036827

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