title: Strategies for the Analysis of Bam Recognition Motifs in Outer Membrane Proteins.
abstract: Well-structured proteins interact with other proteins through surface-surface interactions. In such cases, the residues that form the interacting surface are not necessarily neighboring residues on the level of protein sequence. In contrast, unfolded or partially unfolded proteins can interact with other proteins through defined linear motifs. In the case of the β-barrel assembly machinery (BAM) in the outer membrane of Gram-negative bacteria, unfolded β-barrel proteins are recognized through a C-terminal linear motif, and are inserted into the membrane. While the exact mechanism of recognition is still under investigation, it has been shown that mutations in the recognition motif can partially or completely abolish membrane insertion. In this chapter, we demonstrate the workflow for motif discovery, motif extraction, and motif visualization on the example of the C-terminal motifs in transmembrane β-barrel proteins.
authors.affiliation: Department 1, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076, Tübingen, Germany.|Computational Oncology, Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
authors.forename: Nagarajan
authors.initials: N
authors.lastname: Paramasivam
authors.affiliation: Department 1, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076, Tübingen, Germany. dirk.linke@ibv.uio.no.|Department of Biosciences, University of Oslo, 1066 Blindern, 0316 Oslo, Blindern, 0316, Oslo, Norway. dirk.linke@ibv.uio.no.
authors.forename: Dirk
authors.initials: D
authors.lastname: Linke
mesh_terms: D020816:Amino Acid Motifs; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D001425:Bacterial Outer Membrane Proteins
keywords: BAM recognition; C-terminal motif; Linear motif; Motif extraction; Protein−protein interaction