The LIM/double zinc-finger motif functions as a protein dimerization domain.

Protein-protein interactions resulting in dimerization and heterodimerization are of central importance in the control of gene expression and cell function. Proteins that share the 52-residue LIM/double zinc-finger domain are involved in a wide range of developmental and cellular controls. Some of these functions have been hypothesized to involve protein dimerization. In the present report we demonstrate, using both in vitro and cell-based studies, that a representative LIM protein, human cysteine-rich protein (hCRP), can efficiently homodimerize. The dimerization ability of hCRP is mapped to the LIM domains, can be transferred to an unrelated protein by fusion of a single minimal LIM/double zinc-finger segment, occurs in the absence as well as the presence of DNA, and appears to depend on coordination of two zinc atoms in the finger doublet. These observations support a specific role for protein dimerization in the function of proteins containing the LIM/double zinc-finger domain and expand the general spectrum of potential interactions mediated by zinc-finger motifs.     

The amino-terminal domain of the prokaryotic enhancer-binding protein XylR is a specific intramolecular repressor.

The mechanism under which the signal-reception amino-terminal portion (A domain) of the prokaryotic enhancer-binding protein XylR controls the activity of the regulator has been investigated through complementation tests in vivo, in which the various protein segments were produced as independent polypeptides. Separate expression of the A domain repressed the otherwise constitutive activity of a truncated derivative of XylR deleted of its A domain (XylR delta A). Such inhibition was not released by m-xylene, the natural inducer of the system. Repression caused by the A domain was specific for XylR because it did not affect activation of the sigma 54 promoter PnifH by a derivative of its cognate regulator, NifA, deleted of its own A domain. The A domain was also unable to repress the activity of a NifA-XylR hybrid protein resulting from fusing two-thirds of the central domain of NifA to the carboxyl-terminal third of XylR, which includes its DNA-binding domain. The inhibitory effect caused by the A domain of XylR on XylR delta A seems, therefore, to result from specific interactions in trans between the two truncated proteins and not from mere hindering of an activating surface.     

The WD40 and FYVE domain containing protein 2 defines a class of early endosomes necessary for endocytosis

The FYVE domain binds with high specificity and avidity to phosphatidylinositol 3-phosphate. It is present in approximately 30 proteins in humans, some of which have been implicated in functions ranging from early endosome fusion to signal transduction through the TGF-beta receptor. To develop a further understanding of the biological roles of this protein family, we turned to the nematode Caenorhabditis elegans, which contains only 12 genes predicted to encode for phosphatidylinositol 3-phosphate binding, FYVE domain-containing proteins, all of which have homologs in the human genome. Each of these proteins was targeted individually by RNA interference. One protein, WDFY2, produced a strong inhibition of endocytosis when silenced. WDFY2 contains WD40 motifs and a FYVE domain, is highly conserved between species, and localizes to a set of small endosomes that reside within 100 nm from the plasma membrane. These endosomes are involved in transferrin uptake but lack the classical endosomal markers Rab5 and EEA1. Silencing of WDFY2 by siRNA in mammalian cells impaired transferrin endocytosis. These studies reveal the important, conserved role of WDFY2 in endocytosis, and the existence of a subset of early endosomes, closely associated with the plasma membrane, that may constitute the first stage of endocytic processing of internalized cargo.     

The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family

Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from ten different phyla. To gain insight to the mechanism and evolution of this repair system, we determined the crystal structures of the ligase domain of Clostridium thermocellum Pnkp in three functional states along the reaction pathway: apoenzyme, ligase•ATP substrate complex, and covalent ligase-AMP intermediate. The tertiary structure is composed of a classical ligase nucleotidyltransferase module that is embellished by a unique α-helical insert module and a unique C-terminal α-helical module. Structure-guided mutational analysis identified active site residues essential for ligase adenylylation. Pnkp defines a new RNA ligase family with signature structural and functional properties.     

Histidine residue in the zinc-binding motif of aminopeptidase A is critical for enzymatic activity.

The murine BP-1 antigen (also called 6C3) is a homodimeric, phosphorylated cell surface glycoprotein that is expressed on immature B-lineage cells, bone marrow stromal cell lines, thymic cortical epithelial cells, endothelial cells, enterocytes, and renal proximal tubular cells. The amino acid sequence deduced from a BP-1 cDNA predicted a type II integral membrane protein with a zinc-binding motif (His-Glu-Xaa-Xaa-His) found in zinc-dependent metallopeptidases, and functional analysis suggested that BP-1 is aminopeptidase A [APA; L-alpha-aspartyl(L-alpha-glutamyl)-peptide hydrolase, EC 3.4.11.7]. Here we constructed an expression vector in which the BP-1 cDNA was placed downstream from the SR alpha promoter and used this construct to transfect COS-7 and Ltk- cells. Both transfectants expressed the BP-1 antigen on the cell surface and APA activity. The enzymatic activity of recombinant APA was increased by Ca2+ and inhibited by Zn2+, consistent with previous reports with purified APA. Point mutation of one of the histidine residues in the zinc-binding motif to phenylalanine completely abolished APA enzymatic activity, suggesting the structure of the zinc-binding motif of APA is critical for catalytic activity. Both wild-type and mutant BP-1 were glycosylated, transported to the cell surface, and possessed molecular weights similar to native BP-1 molecules on the murine 18.81 pre-B-cell line. The successful expression of both wild-type and mutant APA should allow more precise analysis of the diverse physiological roles of this ectoenzyme.     

Ceramide-binding and activation defines protein kinase c-Raf as a ceramide-activated protein kinase.

Interleukin 1 is the prototype of an inflammatory cytokine, and evidence suggests that it uses the sphingomyelin pathway and ceramide production to trigger mitogen-activated protein kinase (MAPK) activation and subsequent gene expression required for acute inflammatory processes. To identify downstream signaling targets of ceramide, a radioiodinated photoaffinity labeling analog of ceramide ([125I] 3-trifluoromethyl-3-(m-iodophenyl)diazirine-ceramide) was employed. It is observed that ceramide specifically binds to and activates protein kinase c-Raf, leading to a subsequent activation of the MAPK cascade. Ceramide does not bind to any other member of the MAPK module nor does it bind to protein kinase C-zeta. These data identify protein kinase c-Raf as a specific molecular target for interleukin 1 beta-stimulated ceramide formation and demonstrate that ceramide is a lipid cofactor participating in regulation of c-Raf activity.     

Cardiac-enriched LIM domain protein fhl2 is required to generate I(Ks) in a heterologous system

OBJECTIVE: Co-expression of the KvLQT1 and minK potassium channel subunits is required to recapitulate I(Ks), the slow component of the cardiac delayed rectifier current, and mutations in either gene cause the congenital Long QT syndrome. It is becoming increasingly well-recognized that multiprotein channel complexes containing proteins capable of modulating channel function assemble at the plasma membrane. Thus, the aim of our study was to identify proteins involved in I(Ks) modulation. METHODS AND RESULTS: Using a yeast-two-hybrid screen with the intracytoplasmic C-terminus of minK as bait, we identified the cardiac-enriched four-and-a-half LIM domain-containing protein (fhl2) as a potential minK partner. We show interaction between the two proteins in GST pulldown assays and demonstrate overlapping subcellular localization using immunocytochemistry of transfected cells supporting a potential interaction. At the functional level, expression of KvLQT1and minK in HEK cells, which lack endogenous fhl2 protein, generated I(Ks) only when fhl2 was co-expressed. By contrast, in CHO-K1 cells, which express fhl2 endogenously, I(Ks) was suppressed by anti-fhl2 antisense which did not affect the currents generated by KvLQT1alone. CONCLUSION: These data indicate that at least in heterologous cells, the generation of I(Ks) requires fhl2 as an additional protein component.     

The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila.

The Polycomb (Pc) gene of Drosophila melanogaster is a member of a large class of genes (Pc group) required for the segment-specific repression of homeotic selector genes. Mutations in Pc-group genes show strong posterior transformations in homozygous embryos resulting from an ectopic expression of homeotic genes in segments where they are not supposed to be active. Genetic evidence suggests that Pc is part of a cellular memory mechanism responsible for the transmission of the homeotic expression pattern through developmental time. We have determined the nucleotide sequence for the genomic DNA of the Pc gene and for cDNAs corresponding to the 2.5-kilobase Pc mRNA. The deduced sequence of the Pc protein exhibits a homology to the heterochromatin-associated protein HP1 encoded by the suppressor of position effect variegation gene Su(var) 205. The homology is confined to a 37-amino acid domain in the N-terminal part of the two proteins. Our findings extend to the molecule level the genetically identified parallels between the Pc-group genes and the modifiers of position effect variegation. This suggests that Pc could use analogous mechanisms at the level of the higher order chromatin structure for the stable transmission of a determined state, as has been proposed for the clonal propagation of heterochromatin domains.     

Muscle-specific trk-related receptor with a kringle domain defines a distinct class of receptor tyrosine kinases.

Little is known about the signaling pathways by which motoneurons induce synapses on muscle fibers, and no receptors for synapse-inducing signals have yet been identified. Because several other inductive events in development are mediated by receptor tyrosine kinases (RTKs), and because phosphotyrosine staining within muscle fibers is concentrated at synaptic sites, one possibility is that synapse-inducing signals are transduced by a RTK within the muscle fiber. We have used PCR to search for tyrosine kinases within the electric organ of the electric ray Torpedo californica, since this tissue is homologous to muscle but is much more densely innervated and is therefore a rich source of synaptic molecules. We have isolated a RTK that is specifically expressed in electric organ and skeletal muscle. The kinase domain of this receptor is related to the trk family of neurotrophin receptors, but unlike any previously described receptor, the extracellular region of this Torpedo RTK contains a kringle domain close to the transmembrane domain.     

A conserved retina-specific gene encodes a basic motif/leucine zipper domain.

Using subtraction cloning, we have isolated a human cDNA, AS321, which is expressed in retina and retinoblastoma cell lines but not in any other tissue or cell line tested. AS321 mRNA is detected in all cells of neural retina, with a high level of expression in photoreceptors. The polypeptide sequence deduced from the cDNA reveals consensus phosphorylation sites for protein kinase A and proline-directed protein kinase. Its C-terminal region contains a basic motif and a leucine zipper domain similar to the DNA binding proteins of the jun and fos oncoprotein family, and it shows a strong similarity to the product of an avian retroviral oncogene, v-maf. The gene for AS321 is conserved during evolution and is expressed in vertebrate retina. We propose to name the gene NRL (neural retina leucine zipper.     

The vitelliform macular dystrophy protein defines a new family of chloride channels

Vitelliform macular dystrophy (VMD/Best disease; MIM*153700) is an early-onset autosomal dominant disorder in which accumulation of lipofuscin-like material within and beneath the retinal pigment epithelium is associated with a progressive loss of central vision. Bestrophin, the protein product of the VMD gene, has four predicted transmembrane domains. There are multiple bestrophin homologues in the human, Drosophila, and Caenorhabditis elegans genomes, but no function has previously been ascribed to these proteins, and they show no detectable homology to other proteins of known function. Using heterologous expression, we show here that human, Drosophila, and C. elegans bestrophins form oligomeric chloride channels, and that human bestrophin is sensitive to intracellular calcium. Each of 15 missense mutations asscociated with VMD greatly reduces or abolishes the membrane current. Four of these mutant bestrophins were coexpressed with the wild type and each dominantly inhibited the wild-type membrane current, consistent with the dominant nature of the disease. These experiments establish the existence of a new chloride channel family and VMD as a channelopathy.     

APPL1表达与结直肠癌发生发展的关系及意义

目的:研究APPL1蛋白在人结直肠癌组织中的表达情况与临床病理参数的关系.方法:收集35例新鲜结直肠癌及27例正常直肠黏膜组织,采用免疫组织化学SP法和RT-PCR法检测APPL1在结直肠癌组织及正常直肠黏膜组织中的表达.采用半定量积分分级对该蛋白的表达强弱进行评分.结果:免疫组织化学和RT-PCR结果显示,APPL1蛋白在结直肠癌组织以及正常直肠黏膜组织中普遍表达,但该蛋白和相应的mRNA在癌组织中的表达高于对照组(P<0.05).在35例结直肠癌组织中,APPL1表达与分化程度、淋巴结转移、TNM分期相关(P<0.05),与性别、年龄、肿瘤大小、组织学类型无明显相关(P>0.05).结论:APPL1蛋白在结直肠癌组织中的表达上调,且该蛋白表达与患者肿瘤的分化程度、淋巴结转移情况以及TNM分期有关.APPL1有可能成为结直肠癌治疗的一个新靶点.     

The HDQVH-motif in domain E of the estradiol receptor alpha is responsible for zinc-binding and zinc-induced hormone release.

The estradiol receptor alpha and proteolytic fragments thereof which contain the entire ligand-binding domain E, bind 65Zn with high affinity. Four putative double-histidine zinc-binding sequences can be identified within the hormone-binding domain E: HDQVH [amino acid (aa) 373-377], HIH (aa 474-476), HFRH (aa 513-516) and HRLH (aa 547-550). Only the HDQVH-motif is responsible for the 1:1 zinc-binding to domain E because the proteolytic (endo-Lys-C) 17 kDa fragment (aa 303-467) from porcine estradiol receptor alpha possesses the zinc-binding ability but none of the fragments containing the other motifs. In addition, H373A- and H377A-mutants lack the metal-binding capacity. Moreover, divalent metal ions are able to release estradiol out of the binding-niche. The order for this feature parallels the competition pattern of 65Zn-binding: Mg2+ < Ni2+ < Zn2+ < or = Cu2+. Mutant estradiol receptor alpha fragments (H373A and H377A) lack the zinc-induced hormone release.     

Minimizing a binding domain from protein A.

We present a systematic approach to minimizing the Z-domain of protein A, a three-helix bundle (59 residues total) that binds tightly (Kd = 10 nM) to the Fc portion of an immunoglobin IgG1. Despite the fact that all the contacts seen in the x-ray structure of the complex with the IgG are derived from residues in the first two helices, when helix 3 is deleted, binding affinity is reduced > 10(5)-fold (Kd > 1 mM). By using structure-based design and phage display methods, we have iteratively improved the stability and binding affinity for a two-helix derivative, 33 residues in length, such that it binds IgG1, with a Kd of 43 nM. This was accomplished by stepwise selection of random mutations from three regions of the truncated Z-peptide: the 4 hydrophobic residues from helix 1 and helix 2 that contacted helix 3 (the exoface), followed by 5 residues between helix 1 and helix 2 (the intraface), and lastly by 19 residues at or near the interface that interacts with Fc (the interface). As selected mutations from each region were compiled (12 in total), they led to progressive increases in affinity for IgG, and concomitant increases in alpha-helical content reflecting increased stabilization of the two-helix scaffold. Thus, by sequential increases in the stability of the structure and improvements in the quality of the intermolecular contacts, one can reduce larger binding domains to smaller ones. Such mini-protein binding domains are more amenable to synthetic chemistry and thus may be useful starting points for the design of smaller organic mimics. Smaller binding motifs also provide simplified and more tractable models for understanding determinants of protein function and stability.