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Molecular dynamics investigation of the human epithelial sodium channel behaviour in salty taste recognition

Alessandro Leoni

Molecular dynamics investigation of the human epithelial sodium channel behaviour in salty taste recognition.

Rel. Marco Agostino Deriu, Lorenzo Pallante. Politecnico di Torino, Corso di laurea magistrale in Ingegneria Biomedica, 2021

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Sodium and water homeostasis is regulated by the activity of the epithelial sodium channel (ENaC), a crucial factor for the physiology and well-being of the human body. In particular the ENaC is the main receptor candidate for salty taste. Nowadays, the mechanisms and behaviour of this receptor are not fully known, and their transmembrane and cytosolic domains have not been resolved yet. Despite reduced knowledge of the molecular mechanisms of receptor activation, one of the most accredited hypotheses relates the so-called cleavage mechanism with a more active state of ENaC, representing, nowadays, the main actor in the gating mechanism of the receptor. Computational Molecular Modelling is an elective tool to study nanoscale level biological systems with an atomistic resolution, allowing to model the 3D structure and study the dynamics of proteins to shed light on the molecular mechanisms linked to protein function. In the present work, the ENaC experimental model found in literature was firstly refined through traditional homology modelling and other modelling methods such as Threading based methods and ML-based methods. A rational confront across the various models obtained was performed through the application of several validation tools. Then, the obtained model was studied through Molecular Dynamics in order to, first, demonstrate that it was possible to simulate the refined system and, once ascertained the reliability and stability of the model, investigate its behaviour. Two types of systems have been simulated in parallel, one about the uncleaved state of ENaC and the other about the cleaved state of ENaC. The main focus was first to support and confirm the hypothesis found in literature, and then to characterize the similarities and differences between the two ENaC’s states, aiming to demonstrate that cleavage is the key process that leads to the opening of the sodium channel and, eventually, to the recognition of the salty taste. The performed studies used computational methods to characterize conformational changes of the receptor both in the cleaved and uncleaved states remarking major differences related to receptor activity and function. This work represents the first deep computational investigation of the human ENaC and it paves the way towards future computational works. For instance, deeper investigations about the cation-receptor interaction or extensions in the simulations time to capture conformational changes occurring in the receptor on longer times will be pivotal to improve the understanding of the molecular mechanisms underlying the functioning of this receptor.

Relators: Marco Agostino Deriu, Lorenzo Pallante
Academic year: 2021/22
Publication type: Electronic
Number of Pages: 73
Corso di laurea: Corso di laurea magistrale in Ingegneria Biomedica
Classe di laurea: New organization > Master science > LM-21 - BIOMEDICAL ENGINEERING
Aziende collaboratrici: Politecnico di Torino
URI: http://webthesis.biblio.polito.it/id/eprint/21690
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