Membrane Protein Explorer (MPEx)

MPEx is a tool for explaining membrane proteins. The first version of MPEx was born to aid the studies of the role of peptide bonds in the energetics of transmembrane helix stability, but evolved over time to serve other research needs, such as studies of the relative contribution of hydrophobic moment to translocon recognition of transmembrane segments and peptide partitioning into membrane interfaces. MPEx is a now a highly refined implementation of the sliding-window method that utilizes primarily experiment-derived physical and biological hydrophobicity scales, although other scales can be us.

  MPEx is a tool that provides an extendable framework not only for physical and biological hydropathy analyses, but β-barrel identification screening as well. MPEx also calculates and displays hydrophobic moment data, generates helical wheel displays, and allows direct comparison of different sliding-window plots.

   The graphical user interface of MPEx is divided into a plot window and a control panel, used for setting the plot parameters for the analysis mode. MPEx has three analysis modes of operation and two utility modes that are available from a convenient tabbed interface. The analysis modes include:

1. physical-scale hydropathy analysis

2. translocon-scale hydropathy analysis

3. beta-barrel analysis.

In the above shown fig,

(A) MPEx in translocon TM analysis mode. 

(B) Results window for translocon TM analysis, displaying control settings, analysis results, and working amino acid sequence. 

(C) MPEx in totalizer mode

HYDROPATHY ANALYSIS MODE:

Hydropathy plots allow for the visualization of hydrophobicity over the length of a peptide sequence. In hydropathy analysis mode, hydropathy plots are generated using the augmented Wimley–White (WW) experiment-based whole-residue hydrophobicity scale described by Jayasinghe et al.

TRANSLOCAN TM ANALYSIS MODE:

Translocon TM analysis mode is a hydropathy analysis of transmembrane proteins based on the molecular code for transmembrane-helix recognition by the Sec61 translocon. This code not only provided measurements of the apparent hydrophobicity scale used by the translocon, it established that the apparent hydrophobicity value of a residue depends on its location within the TM segment.

BETA-BARREL ANALYSIS MODE:

The beta-barrel analysis mode does a screening analysis for the identification of beta-barrel membrane proteins based on the analysis algorithm of Wimley. The algorithm uses amino acid composition and architecture of beta-barrel proteins of known structure to make predictions of TM beta-strands, connecting beta-hairpin loops, and the number of likely TM beta-strands.