title: Folding elastic transmembrane helices to fit in a low-resolution image by electron microscopy.
abstract: Structure prediction of membrane proteins could be constrained and thereby improved by introducing data of the observed molecular shape. We studied a coarse-grained molecular model that relied on residue-based dummy atoms to fold the transmembrane helices of a protein in the observed molecular shape. Based on the inter-residue potential, the α-helices were folded to contact each other in a simulated annealing protocol to search optimized conformation. Fitting the model into a three-dimensional volume was tested for proteins with known structures and resulted in a fairly reasonable arrangement of helices. In addition, the constraint to the packing transmembrane helix with the two-dimensional region was tested and found to work as a very similar folding guide. The obtained models nicely represented α-helices with the desired slight bend. Our structure prediction method for membrane proteins well demonstrated reasonable folding results using a low-resolution structural constraint introduced from recent cell-surface imaging techniques.
authors.affiliation: Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba, 1-1 Umezono Central-2, Tsukuba, Ibaraki, 305-8568, Japan. uenoyt@ni.aist.go.jp
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Ueno
authors.forename: Kazunori
authors.initials: K
authors.lastname: Kawasaki
authors.forename: Osamu
authors.initials: O
authors.lastname: Saito
authors.forename: Masafumi
authors.initials: M
authors.lastname: Arai
authors.forename: Makiko
authors.initials: M
authors.lastname: Suwa
mesh_terms: D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D008854:Microscopy, Electron; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D017433:Protein Structure, Secondary
chemical_list: D008565:Membrane Proteins