Comparative Molecular Dynamics Investigation of the Electromotile Hearing Protein Prestin.

Gianfranco Abrusci,Mattia Sturlese,Gianluca Lattanzi,Gabriele Giachin,Thomas Tarenzi,Roberto Battistutta

doi:10.3390/ijms22158318

Abstract

The mammalian protein prestin is expressed in the lateral membrane wall of the cochlear hair outer cells and is responsible for the electromotile response of the basolateral membrane, following hyperpolarisation or depolarisation of the cells. Its impairment marks the onset of severe diseases, like non-syndromic deafness. Several studies have pointed out possible key roles of residues located in the Transmembrane Domain (TMD) that differentiate mammalian prestins as incomplete transporters from the other proteins belonging to the same solute-carrier (SLC) superfamily, which are classified as complete transporters. Here, we exploit the homology of a prototypical incomplete transporter (rat prestin, rPres) and a complete transporter (zebrafish prestin, zPres) with target structures in the outward open and inward open conformations. The resulting models are then embedded in a model membrane and investigated via a rigorous molecular dynamics simulation protocol. The resulting trajectories are analyzed to obtain quantitative descriptors of the equilibration phase and to assess a structural comparison between proteins in different states, and between different proteins in the same state. Our study clearly identifies a network of key residues at the interface between the gate and the core domains of prestin that might be responsible for the conformational change observed in complete transporters and hindered in incomplete transporters. In addition, we study the pathway of Cl ions in the presence of an applied electric field towards their putative binding site in the gate domain. Based on our simulations, we propose a tilt and shift mechanism of the helices surrounding the ion binding cavity as the working principle of the reported conformational changes in complete transporters.

Highlights

Proteins in the solute-carrier (SLC) superfamily are active secondary transporters, whose study has been an active field of research in the last two decades [1,2,3]
Given the lack of experimentally solved structures of prestin proteins, simulations were started from homology models of the Transmembrane Domain (TMD) for both the rat (r) and zebrafish (z) prestins orthologs, in the inward-open (I) and outward-open (O) conformations (Figure 3): SLC26Dg was used as a template for the I states, while the Band 3 transporter was used for the O states
In the case of SLC26Dg, most of these experimental data focus on the structural features and the functional role of the transmembrane domain as a transporter [30], which is the core of the current study; on the other hand, more recent insight on the SLC26A9 protein focused on the dimerization process and on the role played by the sigma factor antagonist (STAS) domain and the N-terminal [28]

Summary

Introduction

Proteins in the solute-carrier (SLC) superfamily are active secondary transporters, whose study has been an active field of research in the last two decades [1,2,3]. Members of the SLC superfamily, which is the second largest family of membrane proteins, play crucial roles in a large number of physiological processes [4]; these range from the transport of amino acids through the cell membrane (SLC1 family [5]), to the regulation of the extracellular concentration of neurotransmitters during synaptic activity (SLC6 family [6]), to the pH regulation of blood [7]. The latter is the case of the SLC4A1 protein, known as band 3, which transports bicarbonate ions through the plasma membrane of erythrocytes in an electroneutral exchange with chloride ions, a process fundamental for respiration [7]. This electromechanical feedback mechanism, called electromotility, was discovered by Brownwell et al in 1985 [20]

Methods

Results

Conclusion