Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

Abstract

ABSTRACT:Short Linear Motifs (SLiMs) contribute to almost every cellular function by connecting appropriate protein partners. Accurate prediction of SLiMs is difficult due to their shortness and sequence degeneracy. Leucine-aspartic acid (LD) motifs are SLiMs that link paxillin family proteins to factors controlling (cancer) cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. To enable a proteome-wide assessment of these motifs, we developed an active-learning based framework that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome identified a dozen proteins that contain LD motifs, all being involved in cell adhesion and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter-species comparison revealed a conserved LD signalling core, and reveals the emergence of species-specific adaptive connections, while maintaining a strong functional focus of the LD motif interactome. Collectively, our data elucidate the mechanisms underlying the origin and adaptation of an ancestral SLiM.

Endogenous Control Mechanisms of FAK and PYK2 and Their Relevance to Cancer Development

“…Focal Adhesion Kinase (FAK) is a multi-domain non-receptor protein tyrosine kinase (PTK) found in metazoans and also in the unicellular eukaryote Capsaspora owczarzaki [ 1 , 2 ]. FAK is a multifunctional protein that integrates and transduces signals perceived through integrin or growth-factor receptors into cytoplasmic and nuclear responses.…”

Recognition of LD motifs by the focal adhesion targeting domains of focal adhesion kinase and proline‐rich tyrosine kinase 2‐beta: Insights from molecular dynamics simulations

“…X‐ray crystallography and NMR studies have shown that peptides with the Paxillin, Leupaxin, and other LD motifs adopt a helical fold in the complexes 7‐9,15,17,20‐23,25,57,59 . Due to the placement of hydrophobic residues (mainly leucines) at 3‐residue intervals (positions 0, +3, +4, +7) along the peptide sequence, and polar or charged residues at other positions, these helices are amphipathic.…”

“…The mechanisms of Paxillin and Leupaxin binding to FAT domains display differences: PYK2‐FAT:Leupaxin and FAK‐FAT:Paxillin complexes are stable, whereas the PYK2‐FAT:Paxillin complex is more dynamic, possibly due to differences in the binding affinities of the Paxillin and Leupaxin LD motifs for the FAK and PYK2 binding sites 8 . Also, the experimental comparison of the relative strength of LD complexes and the classification of LD motifs into binders and non‐binders is challenging 17 : The measured affinities are in the order of μ M, but can display significant variations, depending on the experimental method and conditions and the peptide length 8,9,15,17,20,22,23,25,55‐60 . The up‐to‐date experimental binding affinities are collected in Supplementary Table S11.…”

Endogenous Control Mechanisms of FAK and PYK2 and Their Relevance to Cancer Development and Therapy

“…The FAT domain is sufficient to localize to focal adhesions, through interactions mainly with paxillin, but also with cofactors or alternative ligands, such as talin or Rgnef/p190RhoGef [50][51][52]. Alternative interactions can also localize FAT to other structures, such as the T-cell receptor complex [1,38,53], or the growth cone of developing axons [54]. FRNK and PRNK maintain these functions, although without any regulatory influence from the other FAK/PYK2 regions.…”

“…Focal Adhesion Kinase (FAK) is a multi-domain non-receptor protein tyrosine kinase (PTK) found in metazoan, but also the unicellular eukaryote Capsaspora owczarzaki [1,2]. FAK is a multifunctional protein that integrates and transduces signals perceived through integrin or growth factor receptors into adapted cytoplasmic and nuclear responses.…”