Ptuba: a tool for the visualization of helix surfaces in proteins
| Autor: | Jaime Arce Lopera, James N. Sturgis, Jean-Pierre Duneau |
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| Rok vydání: | 2005 |
| Předmět: |
Models
Molecular Receptor ErbB-2 Protein Structure Secondary Molecular dynamics Projection (mathematics) Materials Chemistry Animals Humans Glycophorin Glycophorins Physical and Theoretical Chemistry Spectroscopy biology Chemistry Membrane Proteins Computer Graphics and Computer-Aided Design Transmembrane protein Visualization Succinate Dehydrogenase Transmembrane domain Crystallography Membrane protein Helix biology.protein Biological system Software |
| Zdroj: | Journal of Molecular Graphics and Modelling. 23:305-315 |
| ISSN: | 1093-3263 |
| DOI: | 10.1016/j.jmgm.2004.10.004 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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