title: LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins.
abstract: Crystallographic studies have shown that the coiled-coil motif occurs in several viral membrane-fusion proteins, including HIV-1 gp41 and influenza virus hemagglutinin. Here, the LearnCoil-VMF program was designed as a specialized program for identifying coiled-coil-like regions in viral membrane-fusion proteins. Based upon the use of LearnCoil-VMF, as well as other computational tools, we report detailed sequence analyses of coiled-coil-like regions in retrovirus, paramyxovirus and filovirus membrane-fusion proteins. Additionally, sequence analyses of these proteins outside their putative coiled-coil domains illustrate some structural differences between them. Complementing previous crystallographic studies, the coiled-coil-like regions detected by LearnCoil-VMF provide further evidence that the three-stranded coiled coil is a common motif found in many diverse viral membrane-fusion proteins. The abundance and structural conservation of this motif, even in the absence of sequence homology, suggests that it is critical for viral-cellular membrane fusion. The LearnCoil-VMF program is available at http://web.wi.mit.edu/kim
authors.affiliation: Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: M
authors.initials: M
authors.lastname: Singh
authors.forename: B
authors.initials: B
authors.lastname: Berger
authors.forename: P S
authors.initials: PS
authors.lastname: Kim
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D017124:Conserved Sequence; D016208:Databases, Factual; D016563:Filoviridae / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D018108:Respirovirus / Q000737:chemistry; D012190:Retroviridae / Q000737:chemistry; D017421:Sequence Analysis; D012984:Software; D014760:Viral Fusion Proteins / Q000737:chemistry* / Q000235:genetics
chemical_list: D014760:Viral Fusion Proteins