MENSADB: A Thorough Structural Analysis of Membrane Protein Dimers

TL;DR

MENSADB is a comprehensive web-based database providing detailed structural features of membrane protein dimers, aiding research despite limited experimental data due to their membrane localization.

Contribution

This work introduces MENSADB, a novel real-time web application that offers extensive structural analysis tools for membrane protein dimers, including conservation and interaction descriptors.

Findings

Provides detailed interfacial and surface features of MPs

Enables comparison of residue classes in membrane proteins

Accessible online for broad scientific use

Abstract

Membrane Proteins (MPs) account for around 15-39% of the human proteome and assume a critical role in a vast set of cellular and physiological mechanisms, including molecular transport, nutrient uptake, toxin and waste product clearance, respiration, and signaling. While roughly 60% of all FDA-approved drugs target MPs, there is a shortage of structural and biochemical data on them mainly hindered by their localization in the lipid bilayer. We present here MEmbrane protein dimer Novel Structure Analyser database (MENSAdb), a real time web-application exposing a broad array of fundamental features about MPs surface and their interfacial regions. In particular, we present conservation, four distinctive Accessible Solvent Area (ASA) descriptors, average and environment-specific B-factors, intermolecular contacts at 2.5 and 4.0 angstroms distance cutoffs, salt-bridges, hydrogen-bonds, hydrophobic, pi-pi interactions, t-stacking and cation-pi interactions. Additionally, users can closely inspect differences in values between three distinctive residues classes: i) non-surface, ii) surface and non-interfacial and iii) interfacial. The database is freely available at www.moreiralab.com/resources/mensadb.