Ptuba: a tool for the visualization of helix surfaces in proteins

Projection of transmembrane helices using a Uniform B-spline Algorithm is a tool for the visualization of interactions between helices in membrane proteins. It allows the user to generate projections of 3D helices, no matter what their deviations from a canonical helix might be. When associated with...

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Bibliographic Details
Published in:Journal of molecular graphics & modelling 2005, Vol.23 (4), p.305-315
Main Authors: Lopera, Jaime Arce, Sturgis, James N., Duneau, Jean-Pierre
Format: Article
Language:English
Subjects:
Animals
Glycophorin - chemistry
Helical interactions
Humans
Membrane protein
Membrane Proteins - chemistry
Models, Molecular
Projection
Protein Structure, Secondary
Receptor, ErbB-2 - chemistry
Software
Succinate Dehydrogenase - chemistry
Transmembrane
Visualization
α Helix
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Summary:Projection of transmembrane helices using a Uniform B-spline Algorithm is a tool for the visualization of interactions between helices in membrane proteins. It allows the user to generate projections of 3D helices, no matter what their deviations from a canonical helix might be. When associated with adapted coloring schemes it facilitates the comprehension of helix-helix interactions. Examples of transmembrane proteins were chosen to illustrate the advantages that this method provides. In the glycophorin A dimer we can easily appreciate the structural features behind homodimerisation. Using the structure of the fumarate reductase we analyze the contact surfaces inside a helical bundle and thanks to structures from a molecular dynamics simulation we see how modifications in structure and electrostatics relate to their interaction. We propose the use of this tool as an aid to the visualization and analysis of transmembrane helix surfaces and properties.
ISSN:1093-3263
1873-4243
DOI:10.1016/j.jmgm.2004.10.004