The Det.Belt Server: A Tool to Visualize and Estimate Amphipathic Solvent Belts around Membrane Proteins

Abstract

Detergents wrap around membrane proteins to form a belt covering the hydrophobic part of the protein serving for membrane insertion and interaction with lipids. The number of detergent monomers forming this belt is usually unknown to investigators, unless dedicated detergent quantification is undertaken, which for many projects is difficult to setup. Yet, having an approximate knowledge of the amount of detergent forming the belt is extremely useful, to better grasp the protein of interest in interaction with its direct environment rather than picturing the membrane protein “naked”. We created the Det.Belt server to dress up membrane proteins and represent in 3D the bulk made by detergent molecules wrapping in a belt. Many detergents are included in a database, allowing investigators to screen in silico the effect of different detergents around their membrane protein. The input number of detergents is changeable with fast recomputation of the belt for interactive usage. Metrics representing the belt are readily available together with scripts to render quality 3D images for publication. The Det.Belt server is a tool for biochemists to better grasp their sample.

Hydrogen/deuterium exchange-mass spectrometry of integral membrane proteins in native-like environments: current scenario and the way forward

“…Another key feature was the 93% sequence coverage in nanodiscs achieved using a C4 ultra-performance liquid chromatography (UPLC) column that potentially helped in the elution of more hydrophobic peptides. In addition, DDM/cholate, in a ratio shown to significantly reduce the estimated detergent-belt size, was used to disassemble the nanodiscs at the quench step [ 34 ]. Pre-equilibrated magnetic zirconium beads were then used to remove the phospholipids.…”

The non-Newtonian behavior of detergents during concentration is increased by macromolecules, in trans, and results in their over-concentration

“…With the later we were able to track and quantify detergents during purification of various membrane proteins, thereby bringing light on their behavior around their cognate protein. This allowed for a web server to be created to represent detergent belts around membrane proteins [15]. Overall, these tools allow rationalization of their use.…”