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Updated: Jul 14, 2026
12:19
Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing (MTT)
Published on: May 27, 2012
TMM@: a web application for the analysis of transmembrane helix mobility
Lars Skjaerven1, Inge Jonassen, Nathalie Reuter
1Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway. slars@ii.uib.no <slars@ii.uib.no>
BMC Bioinformatics
|July 3, 2007
Summary
A new web tool, TMM@, analyzes transmembrane protein flexibility using Normal Mode Analysis (NMA). It identifies mobile alpha-helices, crucial for understanding protein signaling and transport across cell membranes.
Area of Science:
- Structural Biology
- Biophysics
- Computational Biology
Background:
- Understanding protein signaling across cell membranes requires knowledge of transmembrane (TM) region flexibility.
- Normal Mode Analysis (NMA) is a key method for studying slow, functionally relevant protein motions.
- Previous limitations existed in applying NMA to TM regions for non-expert users.
Purpose of the Study:
- To develop an accessible tool for analyzing the mobility of transmembrane alpha-helices.
- To enable researchers to investigate protein dynamics and signal transduction mechanisms.
Main Methods:
- Developed TMM@ (TransMembrane alpha-helical Mobility analyzer), a web application.
- Utilizes NMA to compute protein normal modes from PDB structure files.
- Identifies the most mobile alpha-helices within protein bundles.
Main Results:
- TMM@ characterizes the propensity of transmembrane alpha-helices to undergo displacement.
- The web server provides visualization of mobile helices directly in a web browser.
- Raw analysis data is available for download for further investigation.
Conclusions:
- TMM@ is a unique tool for studying transmembrane alpha-helix mobility.
- Facilitates research on membrane transporters and other transmembrane proteins.
- Helps identify helices involved in molecular transport and cellular signaling.
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