Identification of calreticulin as ligand of GABARAP by phage display screening of a peptide library

4-Aminobutyrate type A (GABA(A)) receptor-associated protein (GABARAP) is a ubiquitin-like modifier implicated in the intracellular trafficking of GABA(A) receptors, and belongs to a family of proteins involved in intracellular vesicular transport processes, such as autophagy and intra-Golgi transport. In this article, it is demonstrated that calreticulin is a high affinity ligand of GABARAP. Calreticulin, although best known for its functions as a Ca(2+) -dependent chaperone and a Ca(2+) -buffering protein in the endoplasmic reticulum, is also localized to the cytosol and exerts a variety of extra-endoplasmic reticulum functions. By phage display screening of a randomized peptide library, peptides that specifically bind GABARAP were identified. Their amino acid sequences allowed us to identify calreticulin as a potential GABARAP binding protein. GABARAP binding to calreticulin was confirmed by pull-down experiments with brain lysate and colocalization studies in N2a cells. Calreticulin and GABARAP interact with a dissociation constant K(d) = 64 nm and a mean lifetime of the complex of 20 min. Thus, the interaction between GABARAP and calreticulin is the strongest so far reported for each protein

Structural characterization of GABARAP-ligand interactions

The GABA(A) receptor-associated protein (GABARAP) plays an important role in intracellular trafficking of several proteins. It undergoes a C-terminal lipidation process that enables anchoring in the cytosolic leaflet of cellular membranes. While the three-dimensional structure of GABARAP itself has been determined, structural investigation of complexes with its interaction partners has just commenced. Studies with indole derivatives revealed that GABARAP features two hydrophobic binding sites (hp1 and hp2). These also play an essential role in complex formation with the native ligand calreticulin. Furthermore, a model of hexameric N-ethylmaleimide-sensitive factor (NSF) suggests that binding of GABARAP to this molecular machine may involve a similar site. Since hp1 and hp2 are highly conserved throughout the GABARAP family, the relevance of the structural data presented here is likely to extend to GABARAP homologues

Solution structure of Atg8 reveals conformational polymorphism of the N-terminal domain

During autophagy a crescent shaped like membrane is formed, which engulfs the material that is to be degraded. This membrane grows further until its edges fuse to form the double membrane covered autophagosome. Atg8 is a protein, which is required for this initial step of autophagy. Therefore, a multistage conjugation process of newly synthesized Atg8 to phosphatidylethanolamine is of critical importance. Here we present the high resolution structure of unprocessed Atg8 determined by nuclear magnetic resonance spectroscopy. Its C-terminal subdomain shows a well-defined ubiquitin-like fold with slightly elevated mobility in the pico- to nanosecond timescale as determined by heteronuclear NOE data. In comparison to unprocessed Atg8, cleaved Atg8(G116) shows a decreased mobility behaviour. The N-terminal domain adopts different conformations within the micro- to millisecond timescale. The possible biological relevance of the differences in dynamic behaviours between both subdomains as well as between the cleaved and uncleaved forms is discussed

Sequence-specific 1H, 13C and 15N resonance assignment of the autophagy-related protein Atg 8.

The autophagy-related protein Atg8 is important for the formation of autophagosomes as it mediates membrane fusion. To elucidate the solution structure of Atg8 backbone and side chain chemical shifts of Atg8 were assigned as far as possible

Identification of clathrin heavy chain as a direct binding partner for the GABA type A receptor associated protein GABARAP

Gamma-aminobutyric acid type A receptors (GABAA receptors) are the major sites of GABA-mediated fast synaptic inhibition in the central nervous system. Variation of the cell surface receptor count is postulated to be of importance in modulating inhibitory synaptic transmission. The GABAA receptor associated protein (GABARAP) is a ubiquitin-like modifier, implicated in GABAA receptor clustering, trafficking, and turnover. GABARAP pull-down experiments with brain lysate identified clathrin heavy chain to be GABARAP-associated. Phage display screening of a randomized peptide library for GABARAP ligands yielded a sequence motif which characterizes the peptide binding specificity of GABARAP. Sequence database searches with this motif revealed clathrin heavy chain as a protein containing the identified sequence motif within its residues 510-522, supporting the result of the pull-down experiments. Calreticulin, which was identified recently as a GABARAP ligand, contains a very similar sequence motif. We demonstrate that calreticulin indeed competes with clathrin heavy chain for GABARAP binding. Finally, employing nuclear magnetic resonance spectroscopy, we mapped the GABARAP residues responsible for binding to clathrin. The hereby mapped GABARAP regions overlap very well with the homologue residues in yeast Atg8 that were recently shown to be important for autophagy. Together with the knowledge that GABARAP and clathrin are known to be involved in GABAA receptor trafficking within the cell, this strongly suggests a clear physiological relevance of the direct interaction of GABARAP with clathrin heavy chain

Ligand binding mode of GABA(A) receptor-associated protein

The gamma-aminobutyric acid type A (GABA(A)) receptor-associated protein is a versatile adaptor protein playing an important role in intracellular vesicle trafficking, particularly in neuronal cells. We present the X-ray structure of the soluble form of human GABA(A) receptor-associated protein complexed with a high-affinity synthetic peptide at 1.3 A resolution. The data shed light on the probable binding modes of key interaction partners, including the GABA(A) receptor and the cysteine protease Atg4. The resulting models provide a structural background for further investigation of the unique biological properties of this protein

Assessment of GABARAP self-association by its diffusion properties.

Gamma-aminobutyric acid type A receptor-associated protein (GABARAP) belongs to a family of small ubiquitin-like adaptor proteins implicated in intracellular vesicle trafficking and autophagy. We have used diffusion-ordered nuclear magnetic resonance spectroscopy to study the temperature and concentration dependence of the diffusion properties of GABARAP. Our data suggest the presence of distinct conformational states and provide support for self-association of GABARAP molecules. Assuming a monomer-dimer equilibrium, a temperature-dependent dissociation constant could be derived. Based on a temperature series of (1)H(15)N heteronuclear single quantum coherence nuclear magnetic resonance spectra, we propose residues potentially involved in GABARAP self-interaction. The possible biological significance of these observations is discussed with respect to alternative scenarios of oligomerization

Author Correction: The highly GABARAP specific rat monoclonal antibody 8H5 visualizes GABARAP in immunofluorescence imaging at endogenous levels (Scientific Reports, (2019), 9, 1, (526), 10.1038/s41598-018-36717-1).

This Article contains typographical errors in the Acknowledgements section. “This study was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Projektnummer 190586431 – SFB 974, project B02 (D.W., I.M.S.), and project WE5343/1–1 (T.Z.), and by a grant from the Jürgen Manchot Foundation, Molecules of Infection Graduate School (MOI III) (D.W. and J.D.).” should read: “This study was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Projektnummer 267205415 – SFB 1208, project B02 (D.W., I.M.S.), and project WE5343/1–1 (T.Z.), and by a grant from the Jürgen Manchot Foundation, Molecules of Infection Graduate School (MOI III) (D.W. and J.D.).”

Structural characterization of intracellular C-terminal domains of group III metabotropic glutamate receptors

Metabotropic glutamate receptors (mGluRs) are regulated by interacting proteins that mostly bind to their intracellular C-termini. Here, we investigated if mGluR6, mGluR7a and mGluR8a C-termini form predefined binding surfaces or if they were rather unstructured. Limited tryptic digest of purified peptides argued against the formation of stable globular folds. Circular dichroism, (1)H NMR and (1)H(15)N HSQC spectra indicated the absence of rigid secondary structure elements. Furthermore, we localized short linear binding motifs in the unstructured receptor domains. Our data provide evidence that protein interactions of the analyzed mGluR C-termini are mediated rather by short linear motifs than by preformed folds

An indole binding site is a major determinant of the ligand specificity of the GABA type A receptor-associated protein GABARAP

The role of tryptophan as a key residue for ligand binding to the ubiquitin-like modifier GABA(A) receptor associated protein (GABARAP) was investigated. Two tryptophan-binding hydrophobic patches were identified on the conserved face of the GABARAP structure by NMR spectroscopy and molecular docking. GABARAP binding of indole and indole derivatives, including the free amino acid tryptophan was quantified. The two tryptophan binding sites can be clearly distinguished by mapping the NMR spectroscopy-derived residue-specific apparent dissociation constant, K(d), onto the three-dimensional structure of GABARAP. The biological relevance of tryptophan-binding pockets of GABARAP was supported by a highly conserved tryptophan residue in the GABARAP binding region of calreticulin, clathrin heavy chain, and the gamma2 subunit of the GABA(A) receptor. Replacement of tryptophan by alanine abolished ligand binding to GABARAP