Conserved region of human TDP-43 is structurally similar to membrane binding protein FARP1 and protein chaperons BAG6 and CYP33.

Transactive response DNA-binding protein of 43 KDa (TDP-43) is important for RNA metabolism in all animals and in humans is involved in neuromuscular diseases. Full-length TDP-43 is prone to oligomerization and misfolding what renders difficult its characterization. We report that TDP-43 domains are structurally similar to lipid binding protein FARP1 and protein chaperons BAG6 and CYP33.

tRNA binds TDP-43 RNA recognition motifs and ligand of Ate1 protein LIAT1.

Transactive response DNA-binding protein 43 (TDP-43) is important for RNA metabolism in all animals and its malfunctions are linked to neurodegenerative and myodegenerative diseases in humans. Arginyl transferase Ate1 transfers an arginyl group from arginylated tRNA to proteolytic fragments of the C-terminal region of TDP-43, prompting their degradation by the ubiquitin proteasome system, thus contributing to TDP-43 proteostasis. To gain more insight into the molecular basis of TDP-43 arginylation, we tested if tRNA could bind to a panel of recombinant multidomain constructs of human TDP-43 or to the arginylation cofactor protein LIAT1.

Biochemical and structural characterization of the flavodoxin-like domain of the putative tRNA 4-demethylwyosine synthase Tyw1 in complex with FMN.

The S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 catalyzes biosynthesis of 4-demethylwyosine (imG-14), the precursor for wyosine, the hypermodified guanine-derived nucleotide present at position 37 of phenylalanine tRNAs of archaea and eukarya. Eukaryotic TYW1 enzymes contain N-terminal flavodoxin-like and C-terminal radical-SAM domains. We determined co-crystal structures of the flavodoxin-like domain of the putative Tyw1 from in complex with flavin mononucleotide (FMN), exploiting an unexpected anomalous scatterer present in the recombinant protein.

Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence.

Thioflavin T (ThT) is widely used for the detection of amyloids. Many unrelated DNAs and RNAs that contain G-quadruplex motifs also bind ThT and strongly activate its fluorescence. To elucidate the structural basis of ThT binding to G quadruplexes and its fluorescence turn-on, we determined its co-crystal structure with the homodimeric RNA Corn, which contains two G quadruplexes.

A homodimer interface without base pairs in an RNA mimic of red fluorescent protein.

Corn, a 28-nucleotide RNA, increases yellow fluorescence of its cognate ligand 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO) by >400-fold. Corn was selected in vitro to overcome limitations of other fluorogenic RNAs, particularly rapid photobleaching. We now report the Corn-DFHO co-crystal structure, discovering that the functional species is a quasisymmetric homodimer.

Selective microRNA uridylation by Zcchc6 (TUT7) and Zcchc11 (TUT4).

Recent small RNA sequencing data has uncovered 3' end modification of mature microRNAs (miRNAs). This non-templated nucleotide addition can impact miRNA gene regulatory networks through the control of miRNA stability or by interfering with the repression of target mRNAs. The miRNA modifying enzymes responsible for this regulation remain largely uncharacterized.

On the aggregation properties of FMRP--a link with the FXTAS syndrome?

Fragile X mental retardation protein (FMRP) is an RNA binding protein necessary for correct spatiotemporal control of neuronal gene expression in humans. Lack of functional FMRP causes fragile X mental retardation, which is the most common inherited neurodevelopmental disorder in humans. In a previous study, we described the biochemical and biophysical aggregation properties of constructs spanning the conserved region of FMRP and of two other human fragile X related (FXR) proteins, FXR1P and FXR2P.

A study of the ultrastructure of fragile-X-related proteins.

Fragile-X-related proteins form a family implicated in RNA metabolism. Their sequence is composed of conserved N-terminal and central regions which contain Tudor and KH domains and of a divergent C-terminus with motifs rich in arginine and glycine residues. The most widely studied member of the family is probably FMRP (fragile X mental retardation protein), since absence or mutation of this protein in humans causes fragile X syndrome, the most common cause of inherited mental retardation.

Crystal structure of human filamin C domain 23 and small angle scattering model for filamin C 23-24 dimer.

Filamin C is a dimeric, actin-binding protein involved in organization of cortical cytoskeleton and of the sarcomere. We performed crystallographic, small-angle X-ray scattering and analytical ultracentrifugation experiments on the constructs containing carboxy-terminal domains of the protein (domains 23-24 and 19-21). The crystal structure of domain 23 of filamin C showed that the protein adopts the expected immunoglobulin (Ig)-like fold.

Cloning, expression, purification, crystallization and preliminary crystallographic analysis of gamma-filamin repeat 23.

Human gamma-filamin is a protein of 2705 amino-acid residues that localizes mainly in the myofibrillar Z-disc and to smaller extent in the subsarcolemmal region of striated muscle cells. gamma-Filamin consists of an N-terminal actin-binding domain followed by a long rod-shaped region. The rod-shaped region consists of 24 immunoglobulin-like domains that form a platform for interaction with different transmembrane, cell-signalling and cytoskeletal proteins.