title: Ptuba: a tool for the visualization of helix surfaces in proteins.
abstract: 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.
authors.affiliation: Laboratoire d'ingénierie des Systèmes Macromoléculaires (UPR 9027), Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. arce@ibsm.cnrs-mrs.fr
authors.forename: Jaime Arce
authors.initials: JA
authors.lastname: Lopera
authors.forename: James N
authors.initials: JN
authors.lastname: Sturgis
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Duneau
mesh_terms: D000818:Animals; D006021:Glycophorins / Q000737:chemistry; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000737:chemistry; D012984:Software; D013385:Succinate Dehydrogenase / Q000737:chemistry
chemical_list: D006021:Glycophorins; D008565:Membrane Proteins; D018719:Erb-b2 Receptor Tyrosine Kinases; D013385:Succinate Dehydrogenase