Journal of Molecular Biology

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  • Hierarchical Description and Extensive Classification of Protein Structural Changes by Motion Tree
    [Jan 2014]

    Publication date: 6 February 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 3

    Author(s): Ryotaro Koike , Motonori Ota , Akinori Kidera

    The structures of the same protein, determined under different conditions, provide clues toward understanding the role of structural changes in the protein's function. Structural changes are usually identified as rigid-body motions, which are defined using a particular threshold of rigidity, such as domain motions. However, each protein actually undergoes motions with various size and magnitude ranges. In this study, to describe protein structural changes more comprehensively, we propose a method based on hierarchical clustering. This method enables the illustration of a wide range of protein motions in a single tree diagram, named the “Motion Tree”. We applied the method to 432 proteins exhibiting large structural changes and classified their Motion Trees in terms of the characteristic indices of the trees. This classification of the Motion Trees revealed clear relationships to their protein functions. Especially, complex structural changes are significantly correlated with multi-step protein functions.
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  • Visualizing Side Chains of Invisible Protein Conformers by Solution NMR
    [Jan 2014]

    Publication date: 6 February 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 3

    Author(s): Guillaume Bouvignies , Pramodh Vallurupalli , Lewis E. Kay

    Sparsely populated and transiently formed protein conformers can play key roles in many biochemical processes. Understanding the structure function paradigm requires, therefore, an atomic-resolution description of these rare states. However, they are difficult to study because they cannot be observed using standard biophysical techniques. In the past decade, NMR methods have been developed for structural studies of these elusive conformers, focusing primarily on backbone 1H, 15N and 13C nuclei. Here we extend the methodology to include side chains by developing a 13C-based chemical exchange saturation transfer experiment for the assignment of side-chain aliphatic 13C chemical shifts in uniformly 13C labeled proteins. A pair of applications is provided, involving the folding of β-sheet Fyn SH3 and α-helical FF domains. Over 96% and 89% of the side-chain 13C chemical shifts for excited states corresponding to the unfolded conformation of the Fyn SH3 domain and a folding intermediate of the FF domain, respectively, have been obtained, providing insight into side-chain packing and dynamics.
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  • Corrigendum to “Identification of New Human Cadherin Genes Using a Combination of Protein Motif Search and Gene Finding Methods” [J. Mol. Biol. 337 (2004) 307–317]
    [Jan 2014]

    Publication date: 6 February 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 3

    Author(s): Julia C. Hoeng , Nikolai V. Ivanov , Paul Hodor , Menghang Xia , Nan Wei , Richard Blevins , David Gerhold , Mark Borodovsky , Yuan Liu







    Categories: Journal Articles
  • Editorial Board
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2









    Categories: Journal Articles
  • Contents List
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2









    Categories: Journal Articles
  • The Molecular V Brake
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Alastair G. Stewart







    Categories: Journal Articles
  • Positional Effects of AAN Motifs in rpoS Regulation by sRNAs and Hfq
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Yi Peng , Toby J. Soper , Sarah A. Woodson

    The Escherichia coli stationary phase transcription factor RpoS is translated in response to small noncoding RNAs (sRNAs), which base pair with the rpoS mRNA leader. The bacterial Sm-like protein Hfq anneals sRNAs with their mRNA targets by simultaneously binding the mRNA and sRNA. Intriguingly, Hfq is recruited to the rpoS leader via AAN motifs far upstream of the sRNA. SHAPE (selective 2′-hydroxyl acylation and primer extension) chemical footprinting showed that the rpoS leader is divided into a far upstream domain, an Hfq binding domain, and a downstream inhibitory stem–loop containing the sRNA and ribosome binding sites. To investigate how Hfq promotes sRNA–mRNA base pairing from a distance, we deleted the natural AAN Hfq binding site, and we inserted artificial AAN binding sites at various positions in the rpoS leader. All the relocated AAN motifs restored tight Hfq binding in vitro, but only insertion at the natural position restored Hfq-dependent sRNA annealing in vitro and sRNA regulation of rpoS translation in vivo. Furthermore, U-rich motifs in the downstream inhibitory domain stabilized the rpoS mRNA–Hfq complex and contributed to regulation of rpoS expression. We propose that the natural Hfq binding domain is optimal for positive regulation because it recruits Hfq to the mRNA and allows it to act on incoming sRNAs without opening the inhibitory stem–loop when sRNA is absent.
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  • Subunit Positioning and Stator Filament Stiffness in Regulation and Power Transmission in the V1 Motor of the Manduca sexta V-ATPase
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Stephen P. Muench , Sjors H.W. Scheres , Markus Huss , Clair Phillips , Olga Vitavska , Helmut Wieczorek , John Trinick , Michael A. Harrison

    The vacuolar H+-ATPase (V-ATPase) is an ATP-driven proton pump essential to the function of eukaryotic cells. Its cytoplasmic V1 domain is an ATPase, normally coupled to membrane-bound proton pump Vo via a rotary mechanism. How these asymmetric motors are coupled remains poorly understood. Low energy status can trigger release of V1 from the membrane and curtail ATP hydrolysis. To investigate the molecular basis for these processes, we have carried out cryo-electron microscopy three-dimensional reconstruction of deactivated V1 from Manduca sexta. In the resulting model, three peripheral stalks that are parts of the mechanical stator of the V-ATPase are clearly resolved as unsupported filaments in the same conformations as in the holoenzyme. They are likely therefore to have inherent stiffness consistent with a role as flexible rods in buffering elastic power transmission between the domains of the V-ATPase. Inactivated V1 adopted a homogeneous resting state with one open active site adjacent to the stator filament normally linked to the H subunit. Although present at 1:1 stoichiometry with V1, both recombinant subunit C reconstituted with V1 and its endogenous subunit H were poorly resolved in three-dimensional reconstructions, suggesting structural heterogeneity in the region at the base of V1 that could indicate positional variability. If the position of H can vary, existing mechanistic models of deactivation in which it binds to and locks the axle of the V-ATPase rotary motor would need to be re-evaluated.
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  • An Iron–Sulfur Cluster in the Polymerase Domain of Yeast DNA Polymerase ε
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Rinku Jain , Eva S. Vanamee , Boris G. Dzikovski , Angeliki Buku , Robert E. Johnson , Louise Prakash , Satya Prakash , Aneel K. Aggarwal

    DNA polymerase ε (Polε) is a multi-subunit polymerase that contributes to genomic stability via its roles in leading strand replication and the repair of damaged DNA. Polε from Saccharomyces cerevisiae is composed of four subunits—Pol2, Dpb2, Dpb3, and Dpb4. Here, we report the presence of a [Fe-S] cluster directly within the active polymerase domain of Pol2 (residues 1–1187). We show that binding of the [Fe-S] cluster is mediated by cysteines in an insertion (Pol2ins) that is conserved in Pol2 orthologs but is absent in the polymerase domains of Polα, Polδ, and Polζ. We also show that the [Fe-S] cluster is required for Pol2 polymerase activity but not for its exonuclease activity. Collectively, our work suggests that Polε is perhaps more sensitive than other DNA polymerases to changes in oxidative stress in eukaryotic cells.
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  • Structural Analysis and Optimization of the Covalent Association between SpyCatcher and a Peptide Tag
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Long Li , Jacob O. Fierer , Tom A. Rapoport , Mark Howarth

    Peptide tagging is a key strategy for observing and isolating proteins. However, the interactions of proteins with peptides are nearly all rapidly reversible. Proteins tagged with the peptide SpyTag form an irreversible covalent bond to the SpyCatcher protein via a spontaneous isopeptide linkage, thereby offering a genetically encoded way to create peptide interactions that resist force and harsh conditions. Here, we determined the crystal structure of the reconstituted covalent complex of SpyTag and SpyCatcher at 2.1Å resolution. The structure showed the expected reformation of the β-sandwich domain seen in the parental streptococcal adhesin, but flanking sequences at both N- and C-termini of SpyCatcher were disordered. In addition, only 10 out of 13 amino acids of the SpyTag peptide were observed to interact with SpyCatcher, pointing to specific contacts important for rapid split protein reconstitution. Based on these structural insights, we expressed a range of SpyCatcher variants and identified a minimized SpyCatcher, 32 residues shorter, that maintained rapid reaction with SpyTag. Together, these results give insight into split protein β-strand complementation and enhance a distinct approach to ultrastable molecular interaction.
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  • Cross-talk between Diverse Serine Integrases
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Shweta Singh , Kate Rockenbach , Rebekah M. Dedrick , Andrew P. VanDemark , Graham F. Hatfull

    Phage-encoded serine integrases are large serine recombinases that mediate integrative and excisive site-specific recombination of temperate phage genomes. They are well suited for use in heterologous systems and for synthetic genetic circuits as the attP and attB attachment sites are small (<50bp), there are no host factor or DNA supercoiling requirements, and they are strongly directional, doing only excisive recombination in the presence of a recombination directionality factor. Combining different recombinases that function independently and without cross-talk to construct complex synthetic circuits is desirable, and several different serine integrases are available. However, we show here that these functions are not reliably predictable, and we describe a pair of serine integrases encoded by mycobacteriophages Bxz2 and Peaches with unusual and unpredictable specificities. The integrases share only 59% amino acid sequence identity and the attP sites have fewer than 50% shared bases, but they use the same attB site and there is non-reciprocal cross-talk between the two systems. The DNA binding specificities do not result from differences in specific DNA contacts but from the constraints imposed by the configuration of the component half-sites within each of the attachment site DNAs.
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  • Novel Interaction of Ornithine Decarboxylase with Sepiapterin Reductase Regulates Neuroblastoma Cell Proliferation
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Ingo Lange , Dirk Geerts , David J. Feith , Gabor Mocz , Jan Koster , André S. Bachmann

    Ornithine decarboxylase (ODC) is the sentinel enzyme in polyamine biosynthesis. Both ODC and polyamines regulate cell division, proliferation, and apoptosis. Sepiapterin reductase (SPR) catalyzes the last step in the biosynthesis of tetrahydrobiopterin (BH4), an essential cofactor of nitric oxide synthase, and has been implicated in neurological diseases but not yet in cancer. In this study, we present compelling evidence that native ODC and SPR physically interact, and we defined the individual amino acid residues involved in both enzymes using in silico protein–protein docking simulations. The resulting heterocomplex is a surprisingly compact structure, featuring two energetically and structurally equivalent binding modes both in monomer and in dimer conformations. The novel interaction between ODC and SPR proteins was confirmed under physiological conditions by co-immunoprecipitation and co-localization in neuroblastoma (NB) cells. Importantly, we showed that siRNA (small interfering RNA)-mediated knockdown of SPR expression significantly reduced endogenous ODC enzyme activity in NB cells, thus demonstrating the biological relevance of the ODC–SPR interaction. Finally, in a cohort of 88 human NB tumors, we found that high SPR mRNA expression correlated significantly with poor survival prognosis using a Kaplan–Meier analysis (log-rank test, P =5×10−4), suggesting an oncogenic role for SPR in NB tumorigenesis. In conclusion, we showed that ODC binds SPR and thus propose a new concept in which two well-characterized biochemical pathways converge via the interaction of two enzymes. We identified SPR as a novel regulator of ODC enzyme activity and, based on clinical evidence, present a model in which SPR drives ODC-mediated malignant progression in NB.
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  • Kinetic Control in Protein Folding for Light Chain Amyloidosis and the Differential Effects of Somatic Mutations
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Luis.M. Blancas-Mejía , Alexander Tischer , James R. Thompson , Jonathan Tai , Lin Wang , Matthew Auton , Marina Ramirez-Alvarado

    Light chain amyloidosis is a devastating disease where immunoglobulin light chains form amyloid fibrils, resulting in organ dysfunction and death. Previous studies have shown a direct correlation between the protein thermodynamic stability and the propensity for amyloid formation for some proteins involved in light chain amyloidosis. Here we investigate the effect of somatic mutations on protein stability and in vitro fibril formation of single and double restorative mutants of the protein AL-103 compared to the wild-type germline control protein. A scan rate dependence and hysteresis in the thermal unfolding and refolding was observed for all proteins. This indicates that the unfolding/refolding reaction is kinetically determined with different kinetic constants for unfolding and refolding even though the process remains experimentally reversible. Our structural analysis of AL-103 and AL-103 delP95aIns suggests a kinetic coupling of the unfolding/refolding process with cis–trans prolyl isomerization. Our data reveal that the deletion of proline 95a (AL-103 delP95aIns), which removes the trans–cis di-proline motif present in the patient protein AL-103, results in a dramatic increment in the thermodynamic stability and a significant delay in fibril formation kinetics with respect to AL-103. Fibril formation is pH dependent; all proteins form fibrils at pH2; reactions become slower and more stochastic as the pH increases up to pH7. Based on these results, we propose that, in addition to thermodynamic stability, kinetic stability (possibly influenced by the presence of cis proline 95a) plays a major role in the AL-103 amyloid fibril formation process.
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  • Spontaneous Aggregation of the Insulin-Derived Steric Zipper Peptide VEALYL Results in Different Aggregation Forms with Common Features
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Dirk Matthes , Venita Daebel , Karsten Meyenberg , Dietmar Riedel , Gudrun Heim , Ulf Diederichsen , Adam Lange , Bert L. de Groot

    Recently, several short peptides have been shown to self-assemble into amyloid fibrils with generic cross-β spines, so-called steric zippers, suggesting common underlying structural features and aggregation mechanisms. Understanding these mechanisms is a prerequisite for designing fibril-binding compounds and inhibitors of fibril formation. The hexapeptide VEALYL, corresponding to the residues B12-17 of full-length insulin, has been identified as one of these short segments. Here, we analyzed the structures of multiple, morphologically different (fibrillar, microcrystal-like, oligomeric) [13C,15N]VEALYL samples by solid-state nuclear magnetic resonance complemented with results from molecular dynamics simulations. By performing NHHC/CHHC experiments, we could determine that the β-strands within a given sheet of the amyloid-like fibrils formed by the insulin hexapeptide VEALYL are stacked in an antiparallel manner, whereas the sheet-to-sheet packing arrangement was found to be parallel. Experimentally observed secondary chemical shifts for all aggregate forms, as well as ∅ and ψ backbone torsion angles calculated with TALOS, are indicative of β-strand conformation, consistent with the published crystal structure (PDB ID: 2OMQ). Thus, we could demonstrate that the structural features of all the observed VEALYL aggregates are in agreement with the previously observed homosteric zipper spine packing in the crystalline state, suggesting that several distinct aggregate morphologies share the same molecular architecture.
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  • Visualizing Compaction of Polysomes in Bacteria
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Nicolas Cougot , Anne-Elisabeth Molza , Jérémy Delesques , Emmanuel Giudice , Annie Cavalier , Jean-Paul Rolland , Gwennola Ermel , Carlos Blanco , Daniel Thomas , Reynald Gillet

    During protein synthesis, many translating ribosomes are bound together with an mRNA molecule to form polysomes (or polyribosomes). While the spatial organization of bacterial polysomes has been well studied in vitro, little is known about how they cluster when cellular conditions are highly constrained. To better understand this, we used electron tomography, template matching, and three-dimensional modeling to analyze the supramolecular network of ribosomes after induction of translational pauses. In Escherichia coli, we overexpressed an mRNA carrying a polyproline motif known to induce pausing during translation. When working with a strain lacking transfer-messenger RNA, the principle actor in the “trans-translation” rescuing system, the cells survived the hijacking of the translation machinery but this resulted in a sharp modification of the ribosomal network. The results of our experiments demonstrate that single ribosomes are replaced with large amounts of compacted polysomes. These polysomes are highly organized, principally forming hairpins and dimers of hairpins that stack together. We propose that these spatial arrangements help maintain translation efficiency when the rescue systems are absent or overwhelmed.
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  • Cooperative KaiA–KaiB–KaiC Interactions Affect KaiB/SasA Competition in the Circadian Clock of Cyanobacteria
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Roger Tseng , Yong-Gang Chang , Ian Bravo , Robert Latham , Abdullah Chaudhary , Nai-Wei Kuo , Andy LiWang

    The circadian oscillator of cyanobacteria is composed of only three proteins, KaiA, KaiB, and KaiC. Together, they generate an autonomous ~24-h biochemical rhythm of phosphorylation of KaiC. KaiA stimulates KaiC phosphorylation by binding to the so-called A-loops of KaiC, whereas KaiB sequesters KaiA in a KaiABC complex far away from the A-loops, thereby inducing KaiC dephosphorylation. The switch from KaiC phosphorylation to dephosphorylation is initiated by the formation of the KaiB–KaiC complex, which occurs upon phosphorylation of the S431 residues of KaiC. We show here that formation of the KaiB–KaiC complex is promoted by KaiA, suggesting cooperativity in the initiation of the dephosphorylation complex. In the KaiA–KaiB interaction, one monomeric subunit of KaiB likely binds to one face of a KaiA dimer, leaving the other face unoccupied. We also show that the A-loops of KaiC exist in a dynamic equilibrium between KaiA-accessible exposed and KaiA-inaccessible buried positions. Phosphorylation at the S431 residues of KaiC shift the A-loops toward the buried position, thereby weakening the KaiA–KaiC interaction, which is expected to be an additional mechanism promoting formation of the KaiABC complex. We also show that KaiB and the clock-output protein SasA compete for overlapping binding sites, which include the B-loops on the CI ring of KaiC. KaiA strongly shifts the competition in KaiB's favor. Thus, in addition to stimulating KaiC phosphorylation, it is likely that KaiA plays roles in switching KaiC from phosphorylation to dephosphorylation, as well as regulating clock output.
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    Categories: Journal Articles
  • Crystal Structures of CusC Review Conformational Changes Accompanying Folding and Transmembrane Channel Formation
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Hsiang-Ting Lei , Jani Reddy Bolla , Nicholas R. Bishop , Chih-Chia Su , Edward W. Yu

    Gram-negative bacteria, such as Escherichia coli, frequently utilize tripartite efflux complexes in the RND (resistance–nodulation–cell division) family to expel diverse toxic compounds from the cell. These complexes span both the inner and outer membranes of the bacterium via an α-helical, inner membrane transporter; a periplasmic membrane fusion protein; and a β-barrel, outer membrane channel. One such efflux system, CusCBA, is responsible for extruding biocidal Cu(I) and Ag(I) ions. To remove these toxic ions, the CusC outer membrane channel must form a β-barrel structural domain, which creates a pore and spans the entire outer membrane. We here report the crystal structures of wild-type CusC, as well as two CusC mutants, suggesting that the first N-terminal cysteine residue plays an important role in protein–membrane interactions and is critical for the insertion of this channel protein into the outer membrane. These structures provide insight into the mechanisms on CusC folding and transmembrane channel formation. It is found that the interactions between CusC and membrane may be crucial for controlling the opening and closing of this β-barrel, outer membrane channel.
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  • The Structure of Xis Reveals the Basis for Filament Formation and Insight into DNA Bending within a Mycobacteriophage Intasome
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Shweta Singh , Joseph G. Plaks , Nicholas J. Homa , Christopher G. Amrich , Annie Héroux , Graham F. Hatfull , Andrew P. VanDemark

    The recombination directionality factor, Xis, is a DNA bending protein that determines the outcome of integrase-mediated site-specific recombination by redesign of higher-order protein–DNA architectures. Although the attachment site DNA of mycobacteriophage Pukovnik is likely to contain four sites for Xis binding, Xis crystals contain five subunits in the asymmetric unit, four of which align into a Xis filament and a fifth that is generated by an unusual domain swap. Extensive intersubunit contacts stabilize a bent filament-like arrangement with Xis monomers aligned head to tail. The structure implies a DNA bend of ~120°, which is in agreement with DNA bending measured in vitro. Formation of attR-containing intasomes requires only Int and Xis, distinguishing Pukovnik from lambda. Therefore, we conclude that, in Pukovnik, Xis-induced DNA bending is sufficient to promote intramolecular Int-mediated bridges during intasome formation.
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  • Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Yilin Meng , Benoît Roux

    Molecular dynamics umbrella sampling simulations are used to compare the relative stability of the active conformation of the catalytic domain of c-Src kinase while the tyrosine 416 in the activation loop (A-loop) is either unphosphorylated or phosphorylated. When the A-loop is unphosphorylated, there is considerable flexibility of the kinase. While the active conformation of the kinase is not forbidden and can be visited transiently, it is not the predominant state. This is consistent with the view that c-Src displays some catalytic activity even when the A-loop is unphosphorylated. In contrast, phosphorylation of the A-loop contributes to stabilize several structural features that are critical for catalysis, such as the hydrophobic regulatory spine, the HRD motif, and the electrostatic switch. In summary, the free-energy landscape calculations demonstrate that phosphorylation of tyrosine 416 in the A-loop essentially “locks” the kinase into its catalytically competent conformation.
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    Categories: Journal Articles
  • Binding of MgtR, a Salmonella Transmembrane Regulatory Peptide, to MgtC, a Mycobacterium tuberculosis Virulence Factor: A Structural Study
    [Jan 2014]

    Publication date: 23 January 2014
    Source:Journal of Molecular Biology, Volume 426, Issue 2

    Author(s): Frantz L. Jean-Francois , Jian Dai , Lu Yu , Alissa Myrick , Eric Rubin , Piotr G. Fajer , Likai Song , Huan-Xiang Zhou , Timothy A. Cross

    MgtR, a highly hydrophobic peptide expressed in Salmonella enterica serovar Typhimurium, inhibits growth in macrophages through binding to the membrane protein MgtC that has been identified as essential for replication in macrophages. While the Mycobacterium tuberculosis MgtC is highly homologous to its S. Typhi analogue, there does not appear to be an Mtb homologue for MgtR, raising significant pharmacological interest in this system. Here, solid-state NMR and EPR spectroscopy in lipid bilayer preparations were used to demonstrate the formation of a heterodimer between S. Typhi MgtR and the transmembrane helix 4 of Mtb MgtC. Based on the experimental restraints, a structural model of this heterodimer was developed using computational techniques. The result is that MgtR appears to be ideally situated in the membrane to influence the functionality of MgtC.
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    Categories: Journal Articles