Short linear motif

In molecular biology Short Linear Motifs (also known as SLiMs, Linear Motifs or minimotifs) are short stretches of protein sequence that mediate protein protein interaction.

The first definition was given by Tim Hunt:

“The sequences of many proteins contain short, conserved motifs that are involved in recognition and targeting activities, often separate from other functional properties of the molecule in which they occur. These motifs are linear, in the sense that three-dimensional organization is not required to bring distant segments of the molecule together to make the recognizable unit. The conservation of these motifs varies: some are highly conserved while others, for example, allow substitutions that retain only a certain pattern of charge across the motif.”

SLiMs are generally situated in intrinsically disordered regions (over 80% of known SLiMs), however, upon interaction with a structured partner secondary structure is often induced. The majority of annotated SLiMs consist of 3 to 11 contiguous amino acids, with an average of just over 6 residues. However, only few hotspot residues (on average 1 hotspot for each 3 residues in the motif) contribute the majority of the free energy of binding and determine most of the affinity and specificity of the interaction. Although most motifs have no positional preference, several of them are required to be localized at the protein termini in order to be functional. The key defining attribute of SLiMs, having a limited number of residues that directly contact the binding partner, has two major consequences. First, only few or even a single mutation can result in the generation of a functional motif, with further mutations of flanking residues allowing tuning affinity and specificity. This results in SLiMs having an increased propensity to evolve convergently, which facilitates their proliferation, as is evidenced by their conservation and increased incidence in higher Eukaryotes. It has been hypothesized that this might increase and restructure the connectivity of the interactome. Second, SLiMs have relatively low affinity for their interaction partners (generally between 1 and 150 μM), which makes these interactions transient and reversible, and thus ideal to mediate dynamic processes such as cell signaling. In addition, this means that these interactions can be easily modulated by post-translational modifications that change the structural and physicochemical properties of the motif. Also, regions of high functional density can mediate molecular switching by means of overlapping motifs (e.g. the C-terminal tails of integrin beta subunits), or they can allow high avidity interactions by multiple low affinity motifs (e.g. multiple AP2-binding motifs in Eps15).

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