Jing-Song Fan

The 8-kDa Dynein Light Chain Binds to Its Targets via a Conserved (K/R)XTQT Motif

Cytoplasmic dynein is a large, multisubunit molecular motor that translocates cargoes toward the minus ends of microtubules. Proper functioning of the dynein motor requires precise assembly of its various subunits. Using purified recombinant proteins, we show that the highly conserved 8-kDa light chain (DLC8) binds to the intermediate chain of the dynein complex. The DLC8-binding region was mapped to a highly conserved 10-residue fragment (amino acid sequence SYSKETQTPL) C-terminal to the second alternative splicing site of dynein intermediate chain. Yeast two-hybrid screening using DLC8 as bait identified numerous additional DLC8-binding proteins. Biochemical and mutational analysis of selected DLC8-binding proteins revealed that DLC8 binds to a consensus sequence containing a (K/R)XTQT motif. The (K/R)XTQT motif interacts with the common target-accepting grooves of DLC8 dimer. The role of each conserved amino acid residue in this pentapeptide motif in supporting complex formation with DLC8 was systematically studied using site-directed mutagenesis.

Supramodular structure and synergistic target binding of the N-terminal tandem PDZ domains of PSD-95

PDZ domain proteins play critical roles in binding, clustering and subcellular targeting of membrane receptors and ion channels. PDZ domains in multi-PDZ proteins often are arranged in groups with highly conserved spacing and intervening sequences; however, the functional significance of such tandem arrangements of PDZs is unclear. We have solved the three-dimensional structure of the first two PDZ domains of postsynaptic density protein-95 (PSD-95 PDZ1 and PDZ2), which are closely linked to each other in the PSD-95 family of scaffold proteins. The two PDZs have limited freedom of rotation and their C-terminal peptide-binding grooves are aligned with each other with an orientation preference for binding to pairs of C termini extending in the same direction. Increasing the spacing between PDZ1 and PDZ2 resulted in decreased binding between PDZ12 and its dimeric targets. The same mutation impaired the functional ability of PSD-95 to cluster Kv1.4 potassium channels in heterologous cells. The data presented provide a molecular basis for preferential binding of PSD-95 to multimeric membrane proteins with appropriate C-terminal sequences.

The tetrameric L27 domain complex as an organization platform for supramolecular assemblies

L27 domain, initially identified in the Caenorhabditis elegans Lin-2 and Lin-7 proteins, is a protein interaction module that exists in a large family of scaffold proteins. The domain can function as an organization center of large protein assemblies required for establishment and maintenance of cell polarity. We have solved the high-resolution NMR structure of a tetrameric complex of L27 domains containing two SAP97–mLin-2 L27 domain heterodimers. Each L27 domain contains three a-helices. The first two helices of each domain are packed together to form a four-helical bundle in the heterodimer. The third helix of each L27 domain forms another four-helical bundle that assembles the two heterodimers into a tetramer. The structure of the complex provides a mechanistic explanation for L27 domain–mediated polymerization of scaffold proteins, a process that is crucial for the assembly of supramolecular complexes in asymmetric cells.

Signaling Complex Organization by PDZ Domain Proteins

As one of the most abundant protein domains in the genomes of metazoans, PDZ domains play important roles in the targeting of proteins to specific cell membranes, as well as assembling proteins into supramolecular signaling complexes. The structures of individual PDZ domains, along with their diverse cooccurrence with a great variety of other protein domains, provide the biochemical basis for the functional diversity of PDZ proteins. In this review, we first briefly summarize the structure and target-binding properties of PDZ domains. After surveying the SMART protein domain database, we attempt to classify PDZ domain proteins into three general categories. We end the review by presenting several recent studies showing some novel features of PDZ domain proteins.

Structure of the Monomeric 8-kDa Dynein Light Chain and Mechanism of the Domain-swapped Dimer Assembly

The 8-kDa light chain of dynein (DLC8) is ubiquitously expressed in various cell types. Other than serving as a light chain of the dynein complexes, this highly conserved protein has been shown to bind a larger number of proteins with diverse biological functions. DLC8 forms a homodimer via three-dimensional domain swapping of an internal β-strand (the β2-strand) at neutral pH. The protein undergoes non-reversible dimer-to-monomer dissociation when the pH value of the protein solution decreases. The three-dimensional structure of the DLC8 monomer determined by NMR spectroscopy at pH 3.0 showed that the protein is well folded. The major conformational change accompanied by dimer dissociation is in the β2-strand of the protein, which undergoes transition from a β-strand to a nascent α-helix. The monomer form of DLC8 is not capable of binding to target proteins. Insertion of two flexible amino acid residues in the tight β1/β2-loop dramatically stabilized the monomer conformation of the protein. NMR studies showed that the mutation altered the conformation as well as the three-dimensional domain swapping-mediated assembly of the DLC8 dimer. The mutant DLC8 was unable to bind to its targets even at physiological pH. The three-dimensional structure of the mutant protein in its monomeric form provides the structural basis of the mutation-induced stabilization of the monomer conformation. Based on the experimental data, we conclude that the formation of the β2-strand swapping-mediated dimer is mandatory for the structure and function of DLC8. We further note that the DLC8 dimer represents a novel mode of three-dimensional domain swapping.

Interdomain Chaperoning between PSD-95, Dlg, and Zo-1 (PDZ) Domains of Glutamate Receptor-interacting Proteins

The multiple PSD-95, Dlg, and Zo-1 (PDZ) domain protein, glutamate receptor-interacting protein (GRIP), is involved in the clustering and trafficking of the α-amino-3-hydroxy-5-methyl-4-isoxazole propionate receptor by directly binding to the cytoplasmic tail of the receptors GluR2 subunit. Both the forth and fifth PDZ domains (PDZ4 and PDZ5) of GRIP are required for effective binding to the receptor. Using NMR and circular dichroism spectroscopic techniques, we show that PDZ5 is completely unstructured in solution. Freshly prepared PDZ4 is largely folded, but the domain can spontaneously unfold. Neither PDZ4 nor PDZ5 binds to GluR2 in solution. Unexpectedly, when PDZ4 and PDZ5 are covalently connected (i.e. PDZ45), both PDZ domains become well folded and stable in solution. The covalent linkage of the two PDZ domains is essential for proper folding of the tandem PDZ domains and its effective binding to GluR2. The interdomain chaperoning effect observed in the PDZ domains of GRIP represents a previously uncharacterized function of PDZ domains.

PDZ7 of Glutamate Receptor Interacting Protein Binds to Its Target via a Novel Hydrophobic Surface Area

Glutamate receptor interacting protein 1 (GRIP1) is a scaffold protein composed of seven PDZ (Postsynaptic synaptic density-95/Discs large/Zona occludens-1) domains. The protein plays important roles in the synaptic targeting of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. The interaction between GRIP1 PDZ7 and a Ras guanine nucleotide exchange factor, GRASP-1, regulates synaptic distribution of AMPA receptors. Here, we describe the three-dimensional structure of GRIP1 PDZ7 determined by NMR spectroscopy. GRIP1 PDZ7 contains a closed carboxyl group-binding pocket and a narrow αB/βB-groove that is not likely to bind to classical PDZ ligands. Unexpectedly, GRIP1 PDZ7 contains a large solvent-exposed hydrophobic surface at a site distinct from the conventional ligand-binding αB/βB-groove. NMR titration experiments show that GRIP1 PDZ7 binds to GRASP-1 via this hydrophobic surface. Our data uncover a novel PDZ domain-mediated protein interaction mode that may be responsible for multimerization of other PDZ domain-containing scaffold proteins.