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Proceedings of the National Academy of Sciences of... 104건

  1. [해외논문]   Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.  

    Pellegrini, M , Marcotte, E M , Thompson, M J , Eisenberg, D , Yeates, T O
    Proceedings of the National Academy of Sciences of the United States of America v.96 no.8 ,pp. 4285 - 4288 , 1999 , 0027-8424 ,

    초록

    Determining protein functions from genomic sequences is a central goal of bioinformatics. We present a method based on the assumption that proteins that function together in a pathway or structural complex are likely to evolve in a correlated fashion. During evolution, all such functionally linked proteins tend to be either preserved or eliminated in a new species. We describe this property of correlated evolution by characterizing each protein by its phylogenetic profile, a string that encodes the presence or absence of a protein in every known genome. We show that proteins having matching or similar profiles strongly tend to be functionally linked. This method of phylogenetic profiling allows us to predict the function of uncharacterized proteins.

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  2. [해외논문]   Crystal structure of the CD2-binding domain of CD58 (lymphocyte function-associated antigen 3) at 1.8-A resolution.  

    Ikemizu, S , Sparks, L M , van der Merwe, P A , Harlos, K , Stuart, D I , Jones, E Y , Davis, S J
    Proceedings of the National Academy of Sciences of the United States of America v.96 no.8 ,pp. 4289 - 4294 , 1999 , 0027-8424 ,

    초록

    The binding of the cell surface molecule CD58 (formerly lymphocyte function-associated antigen 3) to its ligand, CD2, significantly increases the sensitivity of antigen recognition by T cells. This was the first heterophilic cell adhesion interaction to be discovered and is now an important paradigm for analyzing the structural basis of cell-cell recognition. The crystal structure of a CD2-binding chimeric form of CD58, solved to 1.8-A resolution, reveals that the ligand binding domain of CD58 has the expected Ig superfamily V-set topology and shares several of the hitherto unique structural features of CD2, consistent with previous speculation that the genes encoding these molecules arose via duplication of a common precursor. Nevertheless, evidence for considerable divergence of CD2 and CD58 is also implicit in the structures. Mutations that disrupt CD2 binding map to the highly acidic surface of the AGFCC'C" beta-sheet of CD58, which, unexpectedly, lacks marked shape complementarity to the equivalent, rather more basic CD58-binding face of human CD2. The specificity of the very weak interactions of proteins mediating cell-cell recognition may often derive largely from electrostatic complementarity, with shape matching at the protein-protein interface being less exact than for interactions that combine specificity with high affinity, such as those involving antibodies.

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  3. [해외논문]   The Cys4 zinc finger of bacteriophage T7 primase in sequence-specific single-stranded DNA recognition.  

    Kusakabe, T , Hine, A V , Hyberts, S G , Richardson, C C
    Proceedings of the National Academy of Sciences of the United States of America v.96 no.8 ,pp. 4295 - 4300 , 1999 , 0027-8424 ,

    초록

    Bacteriophage T7 DNA primase recognizes 5'-GTC-3' in single-stranded DNA. The primase contains a single Cys4 zinc-binding motif that is essential for recognition. Biochemical and mutagenic analyses suggest that the Cys4 motif contacts cytosine of 5'-GTC-3' and may also contribute to thymine recognition. Residues His33 and Asp31 are critical for these interactions. Biochemical analysis also reveals that T7 primase selectively binds CTP in the absence of DNA. We propose that bound CTP selects the remaining base G, of 5'-GTC-3', by base pairing. Our deduced mechanism for recognition of ssDNA by Cys4 motifs bears little resemblance to the recognition of trinucleotides of double-stranded DNA by Cys2His2 zinc fingers.

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  4. [해외논문]   Location of translational initiation factor IF3 on the small ribosomal subunit.  

    McCutcheon, J P , Agrawal, R K , Philips, S M , Grassucci, R A , Gerchman, S E , Clemons, W M , Ramakrishnan, V , Frank, J
    Proceedings of the National Academy of Sciences of the United States of America v.96 no.8 ,pp. 4301 - 4306 , 1999 , 0027-8424 ,

    초록

    The location of translational initiation factor IF3 bound to the 30S subunit of the Thermus thermophilus ribosome has been determined by cryoelectron microscopy. Both the 30S.IF3 complex and control 30S subunit structures were determined to 27-A resolution. The difference map calculated from the two reconstructions reveals three prominent lobes of positive density. The previously solved crystal structure of IF3 fits very well into two of these lobes, whereas the third lobe probably arises from conformational changes induced in the 30S subunit as a result of IF3 binding. Our placement of IF3 on the 30S subunit allows an understanding in structural terms of the biochemical functions of this initiation factor, namely its ability to dissociate 70S ribosomes into 30S and 50S subunits and the preferential selection of initiator tRNA by IF3 during initiation.

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  5. [해외논문]   DRONC, an ecdysone-inducible Drosophila caspase.  

    Dorstyn, L , Colussi, P A , Quinn, L M , Richardson, H , Kumar, S
    Proceedings of the National Academy of Sciences of the United States of America v.96 no.8 ,pp. 4307 - 4312 , 1999 , 0027-8424 ,

    초록

    Caspases play an essential role in the execution of programmed cell death in metazoans. Although 14 caspases are known in mammals, only a few have been described in other organisms. Here we describe the identification and characterization of a Drosophila caspase, DRONC, that contains an amino terminal caspase recruitment domain. Ectopic expression of DRONC in cultured cells resulted in apoptosis, which was inhibited by the caspase inhibitors p35 and MIHA. DRONC exhibited a substrate specificity similar to mammalian caspase-2. DRONC is ubiquitously expressed in Drosophila embryos during early stages of development. In late third instar larvae, dronc mRNA is dramatically up-regulated in salivary glands and midgut before histolysis of these tissues. Exposure of salivary glands and midgut isolated from second instar larvae to ecdysone resulted in a massive increase in dronc mRNA levels. These results suggest that DRONC is an effector of steroid-mediated apoptosis during insect metamorphosis.

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  6. [해외논문]   A MHC-encoded ubiquitin-like protein (FAT10) binds noncovalently to the spindle assembly checkpoint protein MAD2.  

    Liu, Y C , Pan, J , Zhang, C , Fan, W , Collinge, M , Bender, J R , Weissman, S M
    Proceedings of the National Academy of Sciences of the United States of America v.96 no.8 ,pp. 4313 - 4318 , 1999 , 0027-8424 ,

    초록

    Recently a number of nonclass I genes were discovered in the human MHC class I region. One of these, FAT10, encodes a protein consisting of two domains with homology to ubiquitin. FAT10 mRNA is expressed constitutively in some lymphoblastoid lines and dendritic cells and in certain other cells after gamma-interferon induction. FAT10 protein expression is controlled at several levels including transcription, translation, and protein stability. Yeast two-hybrid screening of a human lymphocyte library and immunoprecipitation studies revealed that FAT10 noncovalently associated with MAD2, a protein implicated in a cell-cycle checkpoint for spindle assembly during anaphase. Thus, FAT10 may modulate cell growth during B cell or dendritic cell development and activation.

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  7. [해외논문]   Crystal structure of human T cell leukemia virus type 1 gp21 ectodomain crystallized as a maltose-binding protein chimera reveals structural evolution of retroviral transmembrane proteins.  

    Kobe, B , Center, R J , Kemp, B E , Poumbourios, P
    Proceedings of the National Academy of Sciences of the United States of America v.96 no.8 ,pp. 4319 - 4324 , 1999 , 0027-8424 ,

    초록

    Retroviral entry into cells depends on envelope glycoproteins, whereby receptor binding to the surface-exposed subunit triggers membrane fusion by the transmembrane protein (TM) subunit. We determined the crystal structure at 2.5-A resolution of the ectodomain of gp21, the TM from human T cell leukemia virus type 1. The gp21 fragment was crystallized as a maltose-binding protein chimera, and the maltose-binding protein domain was used to solve the initial phases by the method of molecular replacement. The structure of gp21 comprises an N-terminal trimeric coiled coil, an adjacent disulfide-bonded loop that stabilizes a chain reversal, and a C-terminal sequence structurally distinct from HIV type 1/simian immunodeficiency virus gp41 that packs against the coil in an extended antiparallel fashion. Comparison of the gp21 structure with the structures of other retroviral TMs contrasts the conserved nature of the coiled coil-forming region and adjacent disulfide-bonded loop with the variable nature of the C-terminal ectodomain segment. The structure points to these features having evolved to enable the dual roles of retroviral TMs: conserved fusion function and an ability to anchor diverse surface-exposed subunit structures to the virion envelope and infected cell surface. The structure of gp21 implies that the N-terminal fusion peptide is in close proximity to the C-terminal transmembrane domain and likely represents a postfusion conformation.

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  8. [해외논문]   Selective killing of transformed cells by cyclin/cyclin-dependent kinase 2 antagonists.  

    Chen, Y N , Sharma, S K , Ramsey, T M , Jiang, L , Martin, M S , Baker, K , Adams, P D , Bair, K W , Kaelin, W G
    Proceedings of the National Academy of Sciences of the United States of America v.96 no.8 ,pp. 4325 - 4329 , 1999 , 0027-8424 ,

    초록

    Recent studies identified a short peptide motif that serves as a docking site for cyclin/cyclin-dependent kinase (cdk) 2 complexes. Peptides containing this motif block the phosphorylation of substrates by cyclin A/cdk2 or cyclin E/cdk2. Here we report that cell membrane-permeable forms of such peptides preferentially induced transformed cells to undergo apoptosis relative to nontransformed cells. Deregulation of E2F family transcription factors is a common event during transformation and was sufficient to sensitize cells to the cyclin/cdk2 inhibitory peptides. These results suggest that deregulation of E2F and inhibition of cdk2 are synthetically lethal and provide a rationale for the development of cdk2 antagonists as antineoplastic agents.

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  9. [해외논문]   RXP 407, a phosphinic peptide, is a potent inhibitor of angiotensin I converting enzyme able to differentiate between its two active sites.  

    Dive, V , Cotton, J , Yiotakis, A , Michaud, A , Vassiliou, S , Jiracek, J , Vazeux, G , Chauvet, M T , Cuniasse, P , Corvol, P
    Proceedings of the National Academy of Sciences of the United States of America v.96 no.8 ,pp. 4330 - 4335 , 1999 , 0027-8424 ,

    초록

    The human somatic angiotensin converting enzyme (ACE) contains two homologous domains, each bearing a zinc-dependent active site. All of the synthetic inhibitors of this enzyme used in clinical applications interact with these two active sites to a similar extent. Recently, several lines of evidence have suggested that the N-terminal active site of ACE might be involved in specific hydrolysis of some important physiological substrates, like Acetyl-Seryl-Aspartyl-Lysyl-Proline, a negative regulator of hematopoietic stem cell differentiation and proliferation. These findings have stimulated studies aimed at identifying new ACE inhibitors able to block only one of the two active sites of this enzyme. By screening phosphinic peptide libraries, we discovered a phosphinic peptide Ac-Asp-(L)Phepsi(PO2-CH2)(L)Ala-Ala-NH2, called RXP 407, which is able to differentiate the two ACE active sites, with a dissociation constant three orders of magnitude lower for the N-domain of the enzyme. The usefulness of a combinatorial chemistry approach to develop new lead structures is underscored by the unusual chemical structure of RXP 407, as compared with classical ACE inhibitors. As a highly potent and selective inhibitor of the N-terminal active site of wild ACE (Ki = 12 nM), RXP 407, which is metabolically stable in vivo, may lead to a new generation of ACE inhibitors able to block in vivo only a subset of the different functions regulated by ACE.

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  10. [해외논문]   BglG, the transcriptional antiterminator of the bgl system, interacts with the beta' subunit of the Escherichia coli RNA polymerase.  

    Nussbaum-Shochat, A , Amster-Choder, O
    Proceedings of the National Academy of Sciences of the United States of America v.96 no.8 ,pp. 4336 - 4341 , 1999 , 0027-8424 ,

    초록

    The Escherichia coli BglG protein antiterminates transcription at two terminator sites within the bgl operon in response to the presence of beta-glucosides in the growth medium. BglG was previously shown to be an RNA-binding protein that recognizes a specific sequence located just upstream of each of the terminators and partially overlapping with them. We show here that BglG also binds to the E. coli RNA polymerase, both in vivo and in vitro. By using several techniques, we identified the beta' subunit of RNA polymerase as the target for BglG binding. The region that contains the binding site for BglG was mapped to the N-terminal region of beta'. The beta' subunit, produced in excess, prevented BglG activity as a transcriptional antiterminator. Possible roles of the interaction between BglG and the polymerase beta' subunit are discussed.

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