Journal of Molecular Biology

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  • Editorial Board
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7









    Categories: Journal Articles
  • Contents List
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7









    Categories: Journal Articles
  • Core Structures of Ubiquitin Dictate Its Dynamics and Function
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Shuya Fukai







    Categories: Journal Articles
  • Transcription Factor Seeks DNA—Cognate Site Preferred
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Joel Mackay







    Categories: Journal Articles
  • The Ins and Outs of Viral RNA Polymerase Translocation
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): David D. Boehr







    Categories: Journal Articles
  • Alanine Scan of Core Positions in Ubiquitin Reveals Links between Dynamics, Stability, and Function
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Shirley Y. Lee , Lester Pullen , Daniel J. Virgil , Carlos A. Castañeda , Dulith Abeykoon , Daniel N.A. Bolon , David Fushman

    Mutations at solvent-inaccessible core positions in proteins can impact function through many biophysical mechanisms including alterations to thermodynamic stability and protein dynamics. As these properties of proteins are difficult to investigate, the impacts of core mutations on protein function are poorly understood for most systems. Here, we determined the effects of alanine mutations at all 15 core positions in ubiquitin on function in yeast. The majority (13 of 15) of alanine substitutions supported yeast growth as the sole ubiquitin. Both the two null mutants (I30A and L43A) were less stable to temperature-induced unfolding in vitro than wild type (WT) but were well folded at physiological temperatures. Heteronuclear NMR studies indicated that the L43A mutation reduces temperature stability while retaining a ground-state structure similar to WT. This structure enables L43A to bind to common ubiquitin receptors in vitro. Many of the core alanine ubiquitin mutants, including one of the null variants (I30A), exhibited an increased accumulation of high-molecular-weight species, suggesting that these mutants caused a defect in the processing of ubiquitin-substrate conjugates. In contrast, L43A exhibited a unique accumulation pattern with reduced levels of high-molecular-weight species and undetectable levels of free ubiquitin. When conjugation to other proteins was blocked, L43A ubiquitin accumulated as free ubiquitin in yeast. Based on these findings, we speculate that ubiquitin's stability to unfolding may be required for efficient recycling during proteasome-mediated substrate degradation.
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    Categories: Journal Articles
  • Steric Mechanism of Auto-Inhibitory Regulation of Specific and Non-Specific DNA Binding by the ETS Transcriptional Repressor ETV6
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Soumya De , Anson C.K. Chan , H. Jerome Coyne III , Niraja Bhachech , Ulrike Hermsdorf , Mark Okon , Michael E.P. Murphy , Barbara J. Graves , Lawrence P. McIntosh

    DNA binding by the ETS transcriptional repressor ETV6 (or TEL) is auto-inhibited ~50-fold due to an α-helix that sterically blocks its ETS domain binding interface. Using NMR spectroscopy, we demonstrate that this marginally stable helix is unfolded, and not displaced to a non-inhibitory position, when ETV6 is bound to DNA containing a consensus 5′GGAA3′ recognition site. Although significantly lower in affinity, binding to non-specific DNA is auto-inhibited ~5-fold and is also accompanied by helix unfolding. Based on NMR chemical shift perturbations, both specific and non-specific DNA are bound via the same canonical ETS domain interface. However, spectral perturbations are smaller for the non-specific complex, suggesting weaker and less well-defined interactions than in the specific complex. In parallel, the crystal structure of ETV6 bound to a specific DNA duplex was determined. The structure of this complex reveals that a non-conserved histidine residue in the ETS domain recognition helix helps establish the specificity of ETV6 for DNA-binding sites containing 5′GGAA3′ versus 5′GGAT3′. These studies provide a unified steric mechanism for attenuating ETV6 binding to both specific and non-specific DNA and expand the repertoire of characterized auto-inhibitory strategies utilized to regulate ETS factors.
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    Categories: Journal Articles
  • Distinct Conformations of a Putative Translocation Element in Poliovirus Polymerase
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Aaron J. Sholders , Olve B. Peersen

    The mechanism whereby RNA is translocated by the single subunit viral RNA-dependent RNA polymerases is not yet understood. These enzymes lack homologs of the “O-helix” structures and associated fingers domain movements thought to be responsible for translocation in many DNA-templated polymerases. The structures of multiple picornavirus polymerase elongation complexes suggest that these enzymes use a different molecular mechanism where translocation is not strongly coupled to the opening of the active site following catalysis. Here we present the 2.0- to 2.6-Å-resolution crystal structures and biochemical data for 12 poliovirus polymerase mutants that together show how proper enzyme functions and translocation activity requires conformational flexibility of a loop sequence in the palm domain B-motif. Within the loop, the Ser288-Gly289-Cys290 sequence is shown to play a major role in the catalytic cycle based on RNA binding, processive elongation activity, and single nucleotide incorporation assays. The structures show that Ser288 forms a key hydrogen bond with Asp238, the backbone flexibility of Gly289 is required for translocation competency, and Cys290 modulates the overall elongation activity of the enzyme. Some conformations of the loop represent likely intermediates on the way to forming the catalytically competent closed active site, while others are consistent with a role in promoting translocation of the nascent base pair out of the active site. The loop structure and key residues surrounding it are highly conserved, suggesting that the structural dynamics we observe in poliovirus 3Dpol are a common feature of viral RNA-dependent RNA polymerases.
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    Categories: Journal Articles
  • Crystal Structure of the F27G AIM2 PYD Mutant and Similarities of Its Self-Association to DED/DED Interactions
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Alvin Lu , Venkataraman Kabaleeswaran , Tianmin Fu , Venkat Giri Magupalli , Hao Wu

    Absent in melanoma 2 (AIM2) is a cytoplasmic double-stranded DNA sensor involved in innate immunity. It uses its C-terminal HIN domain for recognizing double-stranded DNA and its N-terminal pyrin domain (PYD) for eliciting downstream effects through recruitment and activation of apoptosis-associated Speck-like protein containing CARD (ASC). ASC in turn recruits caspase-1 and/or caspase-11 to form the AIM2 inflammasome. The activated caspases process proinflammatory cytokines IL-1β and IL-18 and induce the inflammatory form of cell death pyroptosis. Here we show that AIM PYD (AIM2PYD) self-oligomerizes. We notice significant sequence homology of AIM2PYD with the hydrophobic patches of death effector domain (DED)-containing proteins and confirm that mutations on these residues disrupt AIM2PYD self-association. The crystal structure at 1.82Å resolution of such a mutant, F27G of AIM2PYD, shows the canonical six-helix (H1–H6) bundle fold in the death domain superfamily. In contrast to the wild-type AIM2PYD structure crystallized in fusion with the large maltose-binding protein tag, the H2–H3 region of the AIM2PYD F27G is well defined with low B-factors. Structural analysis shows that the conserved hydrophobic patches engage in a type I interaction that has been observed in DED/DED and other death domain superfamily interactions. While previous mutagenesis studies of PYDs point to the involvement of charged interactions, our results reveal the importance of hydrophobic interactions in the same interfaces. These centrally localized hydrophobic residues within fairly charged patches may form the hot spots in AIM2PYD self-association and may represent a common mode of PYD/PYD interactions in general.
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    Categories: Journal Articles
  • Identification of Novel Alternative Splicing Events in the Huntingtin Gene and Assessment of the Functional Consequences Using Structural Protein Homology Modelling
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Alis C. Hughes , Matthew Mort , Lyn Elliston , Rhian M. Thomas , Simon P. Brooks , Stephen B. Dunnett , Lesley Jones

    Huntington's disease (HD) is an inherited progressive neurodegenerative disorder caused by a pathological CAG trinucleotide repeat expansion in the large multi-exon gene, huntingtin (HTT). Although multiple pathogenic mechanisms have been proposed for HD, there is increasing interest in the RNA processing of the HTT gene. In mammals, most multi-exon genes are alternatively spliced; however, few alternative transcripts have been described for HTT. Given the numerous protein bands detected in mouse and human brain tissue by Western blotting using anti-huntingtin antibodies, we examined whether alternative splicing of HTT may account for some of these fragments. Using RT-PCR in mouse brain, we detected two novel splice variants of Htt that lacked the 111-bp exon 29 (Htt∆ex29) or retained a 57-bp portion of intron 28 (Htt+57in28) via use of a cryptic splice site. The alternative transcripts were present in wild-type and homozygous Hdh(Q150/Q150) mouse brain at all ages and in all brain regions and peripheral tissues studied. Differential splicing of Htt∆ex29 was found in the cerebellum of Hdh(Q150/Q150) mice with a significant reduction in transcript levels in mutant animals. In human brain, we detected similar splice variants lacking exons 28 and 29. The ability of alternatively spliced transcripts to encode different protein isoforms with individual functions in the cell, combined with the known role of splicing in disease, renders these novel transcripts of interest in the context of HD pathogenesis.
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    Categories: Journal Articles
  • Galectin-3 Interactions with Glycosphingolipids
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Patrick M. Collins , Khuchtumur Bum-Erdene , Xing Yu , Helen Blanchard

    Galectins have essential roles in pathological states including cancer, inflammation, angiogenesis and microbial infections. Endogenous receptors include members of the lacto- and neolacto-series glycosphingolipids present on mammalian cells and contain the tetrasaccharides lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT) that form their core structural components and also ganglio-series glycosphingolipids. We present crystallographic structures of the carbohydrate recognition domain of human galectin-3, both wild type and a mutant (K176L) that influenced ligand affinity, in complex with LNT, LNnT and acetamido ganglioside a-GM3 (α2,3-sialyllactose). Key structural features revealed include galectin-3's demonstration of a binding mode towards gangliosides distinct from that to the lacto/neolacto-glycosphingolipids, with its capacity for recognising the core β-galactoside region being challenged when the core oligosaccharide epitope of ganglio-series glycosphingolipids (GM3) is embedded within particular higher-molecular-weight glycans. The lacto- and neolacto- glycosphingolipids revealed different orientations of their terminal galactose in the galectin-3-bound LNT and LNnT structures that has significant ramifications for the capacity of galectin-3 to interact with higher-order lacto/neolacto-series glycosphingolipids such as ABH blood group antigens and the HNK-1 antigen that is common on leukocytes. LNnT also presents an important model for poly-N-acetyllactosamine-containing glycans and provides insight into galectin-3's accommodation of extended oligosaccharides such as the poly-N-acetyllactosamine-modified N- and O-glycans that, via galectin-3 interaction, facilitate progression of lung and bladder cancers, respectively. These findings provide the first atomic detail of galectin-3's interactions with the core structures of mammalian glycosphingolipids, providing information important in understanding the capacity of galectin-3 to engage with receptors identified as facilitators of major disease.
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    Categories: Journal Articles
  • Structural Characterization of the Glycoprotein GP2 Core Domain from the CAS Virus, a Novel Arenavirus-Like Species
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Jayne F. Koellhoffer , Zhou Dai , Vladimir N. Malashkevich , Mark D. Stenglein , Yanyun Liu , Rafael Toro , Joseph S. Harrison , Kartik Chandran , Joseph L. DeRisi , Steven C. Almo , Jonathan R. Lai

    Fusion of the viral and host cell membranes is a necessary first step for infection by enveloped viruses and is mediated by the envelope glycoprotein. The transmembrane subunits from the structurally defined “class I” glycoproteins adopt an α-helical “trimer-of-hairpins” conformation during the fusion pathway. Here, we present our studies on the envelope glycoprotein transmembrane subunit, GP2, of the CAS virus (CASV). CASV was recently identified from annulated tree boas (Corallus annulatus) with inclusion body disease and is implicated in the disease etiology. We have generated and characterized two protein constructs consisting of the predicted CASV GP2 core domain. The crystal structure of the CASV GP2 post-fusion conformation indicates a trimeric α-helical bundle that is highly similar to those of Ebola virus and Marburg virus GP2 despite CASV genome homology to arenaviruses. Denaturation studies demonstrate that the stability of CASV GP2 is pH dependent with higher stability at lower pH; we propose that this behavior is due to a network of interactions among acidic residues that would destabilize the α-helical bundle under conditions where the side chains are deprotonated. The pH-dependent stability of the post-fusion structure has been observed in Ebola virus and Marburg virus GP2, as well as other viruses that enter via the endosome. Infection experiments with CASV and the related Golden Gate virus support a mechanism of entry that requires endosomal acidification. Our results suggest that, despite being primarily arenavirus like, the transmembrane subunit of CASV is extremely similar to the filoviruses.
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    Categories: Journal Articles
  • Structural and Functional Analysis of Fucose-Processing Enzymes from Streptococcus pneumoniae
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Melanie A. Higgins , Michael D. Suits , Candace Marsters , Alisdair B. Boraston

    Fucose metabolism pathways are present in many bacterial species and typically contain the central fucose-processing enzymes fucose isomerase (FcsI), fuculose kinase (FcsK), and fuculose-1-phosphate aldolase (FcsA). Fucose initially undergoes isomerization by FcsI producing fuculose, which is then phosphorylated by FcsK. FcsA cleaves the fuculose-1-phosphate product into lactaldehyde and dihydroxyacetone phosphate, which can be incorporated into central metabolism allowing the bacterium to use fucose as an energy source. Streptococcus pneumoniae has fucose-processing operons containing homologs of FcsI, FcsK, and FcsA; however, this bacterium appears unable to utilize fucose as an energy source. To investigate this contradiction, we performed biochemical and structural studies of the S. pneumoniae fucose-processing enzymes SpFcsI, SpFcsK, and SpFcsA. These enzymes are demonstrated to act in a sequential manner to ultimately produce dihydroxyacetone phosphate and have structural features entirely consistent with their observed biochemical activities. Analogous to the regulation of the Escherichia coli fucose utilization operon, fuculose-1-phosphate appears to act as an inducing molecule for activation of the S. pneumoniae fucose operon. Despite our evidence that S. pneumoniae appears to have the appropriate regulatory and biochemical machinery for fucose metabolism, we confirmed the inability of the S. pneumoniae TIGR4 strain to grow on fucose or on the H-disaccharide, which is the probable substrate of the transporter for the pathway. On the basis of these observations, we postulate that the S. pneumoniae fucose-processing pathway has a non-metabolic role in the interaction of this bacterium with its human host.
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    Categories: Journal Articles
  • The Solution Structure of the Regulatory Domain of Tyrosine Hydroxylase
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Shengnan Zhang , Tao Huang , Udayar Ilangovan , Andrew P. Hinck , Paul F. Fitzpatrick

    Tyrosine hydroxylase (TyrH) catalyzes the hydroxylation of tyrosine to form 3,4-dihydroxyphenylalanine in the biosynthesis of the catecholamine neurotransmitters. The activity of the enzyme is regulated by phosphorylation of serine residues in a regulatory domain and by binding of catecholamines to the active site. Available structures of TyrH lack the regulatory domain, limiting the understanding of the effect of regulation on structure. We report the use of NMR spectroscopy to analyze the solution structure of the isolated regulatory domain of rat TyrH. The protein is composed of a largely unstructured N-terminal region (residues 1–71) and a well-folded C-terminal portion (residues 72–159). The structure of a truncated version of the regulatory domain containing residues 65–159 has been determined and establishes that it is an ACT domain. The isolated domain is a homodimer in solution, with the structure of each monomer very similar to that of the core of the regulatory domain of phenylalanine hydroxylase. Two TyrH regulatory domain monomers form an ACT domain dimer composed of a sheet of eight strands with four α-helices on one side of the sheet. Backbone dynamic analyses were carried out to characterize the conformational flexibility of TyrH65–159. The results provide molecular details critical for understanding the regulatory mechanism of TyrH.
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    Categories: Journal Articles
  • The N-Terminal Amphipathic Helices Determine Regulatory and Effector Functions of Phage Shock Protein A (PspA) in Escherichia coli
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Goran Jovanovic , Parul Mehta , Christopher McDonald , Anthony C. Davidson , Povilas Uzdavinys , Liming Ying , Martin Buck

    The phage shock protein (Psp) systems found in bacteria, archaea and higher plants respond to extracytoplasmic stresses that damage the cytoplasmic membrane and enable cells to repair their membranes. The conserved membrane-associated effector protein PspA has four α-helical domains (HD1–HD4) and helps to repair the membrane as a high-order oligomer. In enterobacteria, under non-stress conditions, PspA as a low-order assembly directly inhibits its cognate transcription activator PspF. Here we show that N-terminal amphipathic helices ahA and ahB in PspA HD1 are functional determinants involved in negative gene control and stress signal perception and its transduction via interactions with the PspBC membrane stress sensors and the inner membrane (IM). The amphipathic helices enable PspA to switch from a low-order gene regulator into an IM-bound high-order effector complex under membrane stress. Conserved residue proline 25 is involved in sequential use of the amphipathic helices and ahA–IM interaction. Single molecule imaging of eGFP-PspA and its amphipathic helices variants in live Escherichia coli cells show distinct spatial and temporal organisations of PspA corresponding to its negative control and effector functions. These findings inform studies on the role of the Psp system in persister cell formation and cell envelope protection in bacterial pathogens and provide a basis for exploring the specialised roles of PspA homologues such as YjfJ, LiaH and Vipp1.
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    Categories: Journal Articles
  • The 1.8-Å Crystal Structure of the N-Terminal Domain of an Archaeal MCM as a Right-Handed Filament
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Yang Fu , Ian M. Slaymaker , Junfeng Wang , Ganggang Wang , Xiaojiang S. Chen

    Mini-chromosome maintenance (MCM) proteins are the replicative helicase necessary for DNA replication in both eukarya and archaea. Most of archaea only have one MCM gene. Here, we report a 1.8-Å crystal structure of the N-terminal MCM from the archaeon Thermoplasma acidophilum (tapMCM). In the structure, the MCM N-terminus forms a right-handed filament that contains six subunits in each turn, with a diameter of 25Å of the central channel opening. The inner surface is highly positively charged, indicating DNA binding. This filament structure with six subunits per turn may also suggests a potential role for an open-ring structure for hexameric MCM and dynamic conformational changes in initiation and elongation stages of DNA replication.
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    Categories: Journal Articles
  • Structure and Dynamics of DNA Duplexes Containing a Cluster of Mutagenic 8-Oxoguanine and Abasic Site Lesions
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Jan Zálešák , Morgane Lourdin , Lumίr Krejčί , Jean-François Constant , Muriel Jourdan

    Clustered DNA damage sites are caused by ionizing radiation. They are much more difficult to repair than are isolated single lesions, and their biological outcomes in terms of mutagenesis and repair inhibition are strongly dependent on the type, relative position and orientation of the lesions present in the cluster. To determine whether these effects on repair mechanism could be due to local structural properties within DNA, we used 1H NMR spectroscopy and restrained molecular dynamics simulation to elucidate the structures of three DNA duplexes containing bistranded clusters of lesions. Each DNA sequence contained an abasic site in the middle of one strand and differed by the relative position of the 8-oxoguanine, staggered on either the 3′ or the 5′ side of the complementary strand. Their repair by base excision repair protein Fpg was either complete or inhibited. All the studied damaged DNA duplexes adopt an overall B-form conformation and the damaged residues remain intrahelical. No striking deformations of the DNA chain have been observed as a result of close proximity of the lesions. These results rule out the possibility that differential recognition of clustered DNA lesions by the Fpg protein could be due to changes in the DNA's structural features induced by those lesions and provide new insight into the Fpg recognition process.
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    Categories: Journal Articles
  • The NreA Protein Functions as a Nitrate Receptor in the Staphylococcal Nitrate Regulation System
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Volker Niemann , Mareike Koch-Singenstreu , Ancilla Neu , Stephanie Nilkens , Friedrich Götz , Gottfried Unden , Thilo Stehle

    Staphylococci are able to use nitrate as an alternative electron acceptor during anaerobic respiration. The regulation of energy metabolism is dependent on the presence of oxygen and nitrate. Under anaerobic conditions, staphylococci employ the nitrate regulatory element (Nre) for transcriptional activation of genes involved in reduction and transport of nitrate and nitrite. Of the three proteins that constitute the Nre system, NreB has been characterized as an oxygen sensor kinase and NreC has been characterized as its cognate response regulator. Here, we present structural and functional data that establish NreA as a new type of nitrate receptor. The structure of NreA with bound nitrate was solved at 2.35Å resolution, revealing a GAF domain fold. Isothermal titration calorimetry experiments showed that NreA binds nitrate with low micromolar affinity (K D =22μM). Two crystal forms for NreA were obtained, with either bound nitrate or iodide. While the binding site is hydrophobic, two helix dipoles and polar interactions contribute to specific binding of the ions. The expression of nitrate reductase (NarGHI) was examined using a narG-lip (lipase) reporter gene assay in vivo. Expression was regulated by the presence of NreA and nitrate. Structure-guided mutations of NreA reduced its nitrate binding affinity and also affected the gene expression, thus providing support for the function of NreA as a nitrate receptor.
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    Categories: Journal Articles
  • Evidence Against the “Y–T Coupling” Mechanism of Activation in the Response Regulator NtrC
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Janice Villali , Francesco Pontiggia , Michael W. Clarkson , Michael F. Hagan , Dorothee Kern

    The dominant theory on the mechanism of response regulators activation in two-component bacterial signaling systems is the “Y–T coupling” mechanism, wherein the χ1 rotameric state of a highly conserved aromatic residue correlates with the activation of the protein via structural rearrangements coupled to a conserved tyrosine. In this paper, we present evidence that, in the receiver domain of the response regulator nitrogen regulatory protein C (NtrCR), the interconversion of this tyrosine (Y101) between its rotameric states is actually faster than the rate of inactive/active conversion and is not correlated to the activation process. Data gathered from NMR relaxation dispersion experiments show that a subset of residues surrounding the conserved tyrosine sense a process that is occurring at a faster rate than the inactive/active conformational transition. We show that this process is related to χ1 rotamer exchange of Y101 and that mutation of this aromatic residue to a leucine eliminated this second faster process without affecting activation. Computational simulations of NtrCR in its active conformation further demonstrate that the rotameric state of Y101 is uncorrelated with the global conformational transition during activation. Moreover, the tyrosine does not appear to be involved in the stabilization of the active form upon phosphorylation and is not essential in propagating the signal downstream for ATPase activity of the central domain. Our data provide experimental evidence against the generally accepted “Y–T coupling” mechanism of activation in NtrCR.
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    Categories: Journal Articles
  • Prokaryotic Ancestry of Eukaryotic Protein Networks Mediating Innate Immunity and Apoptosis
    [Apr 2014]

    Publication date: 3 April 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 7

    Author(s): Stanislaw Dunin-Horkawicz , Klaus O. Kopec , Andrei N. Lupas

    Protein domains characteristic of eukaryotic innate immunity and apoptosis have many prokaryotic counterparts of unknown function. By reconstructing interactomes computationally, we found that bacterial proteins containing these domains are part of a network that also includes other domains not hitherto associated with immunity. This network is connected to the network of prokaryotic signal transduction proteins, such as histidine kinases and chemoreceptors. The network varies considerably in domain composition and degree of paralogy, even between strains of the same species, and its repetitive domains are often amplified recently, with individual repeats sharing up to 100% sequence identity. Both phenomena are evidence of considerable evolutionary pressure and thus compatible with a role in the “arms race” between host and pathogen. In order to investigate the relationship of this network to its eukaryotic counterparts, we performed a cluster analysis of organisms based on a census of its constituent domains across all fully sequenced genomes. We obtained a large central cluster of mainly unicellular organisms, from which multicellular organisms radiate out in two main directions. One is taken by multicellular bacteria, primarily cyanobacteria and actinomycetes, and plants form an extension of this direction, connected via the basal, unicellular cyanobacteria. The second main direction is taken by animals and fungi, which form separate branches with a common root in the α-proteobacteria of the central cluster. This analysis supports the notion that the innate immunity networks of eukaryotes originated from their endosymbionts and that increases in the complexity of these networks accompanied the emergence of multicellularity.
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    Categories: Journal Articles