MeMotif: a database of linear motifs in alpha-helical transmembrane proteins

Abstract

Membrane proteins are important for many processes in the cell and used as main drug targets. The increasing number of high-resolution structures available makes for the first time a characterization of local structural and functional motifs in alpha-helical transmembrane proteins possible. MeMotif (http://projects.biotec.tu-dresden.de/memotif) is a database and wiki which collects more than 2000 known and novel computationally predicted linear motifs in alpha-helical transmembrane proteins. Motifs are fully described in terms of several structural and functional features and editable. Motifs contained in MeMotif can be used in different biological applications, from the identification of biochemically important functional residues which are candidates for mutagenesis experiments to the improvement of tools for transmembrane protein modeling.

Figure 1.

Typical entry of a fully annotated motif. Entry of a fully annotated motif in MeMotif with emphasis on the manually curated description.

Figure 2.

Results from the search: proteinmane: ‘cytochrome b’. Result page from the search by means of the keyword cytochrome b. Four significant matching motifs are highlighted on the cytochrome b protein structure (PDB ID: 2a06). Motifs are highlighted in violet on the PDB structure.

Figure 3.

Structural motifs. (a) Reentrant loop; (b) Helix kink; (c) Interface helix; (d) Cardiolipin-binding motif. The motifs are highlighted in green on the corresponding PDB structures and the stigmatellin molecule is shown in red on (d).