Publications
151 results found
Lu D, Fillet S, Meng C, et al., 2010, Crystal structure of TtgV in complex with its DNA operator reveals a general model for cooperative DNA binding of tetrameric gene regulators, GENES & DEVELOPMENT, Vol: 24, Pages: 2556-2565, ISSN: 0890-9369
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- Citations: 29
Ghosh T, Bose D, Zhang X, 2010, Mechanisms for activating bacterial RNA polymerase, FEMS MICROBIOLOGY REVIEWS, Vol: 34, Pages: 611-627, ISSN: 0168-6445
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- Citations: 59
Bush M, Ghosh T, Tucker N, et al., 2010, Nitric oxide-responsive interdomain regulation targets the σ54-interaction surface in the enhancer binding protein NorR, MOLECULAR MICROBIOLOGY, Vol: 77, Pages: 1278-1288, ISSN: 0950-382X
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- Citations: 18
Sweeney TR, Cisnetto V, Bose D, et al., 2010, Foot-and-Mouth Disease Virus 2C Is a Hexameric AAA plus Protein with a Coordinated ATP Hydrolysis Mechanism, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 285, Pages: 24347-24359
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- Citations: 50
Daniels C, Daddaoua A, Lu D, et al., 2010, Domain Cross-talk during Effector Binding to the Multidrug Binding TTGR Regulator, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 285, Pages: 21372-21381
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- Citations: 22
Tucker NP, Ghosh T, Bush M, et al., 2010, Essential roles of three enhancer sites in Σ<SUP>54</SUP>-dependent transcription by the nitric oxide sensing regulatory protein NorR, NUCLEIC ACIDS RESEARCH, Vol: 38, Pages: 1182-1194, ISSN: 0305-1048
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- Citations: 34
Nan B, Liu X, Zhou Y, et al., 2010, From signal perception to signal transduction: ligand-induced dimeric switch of DctB sensory domain in solution, MOLECULAR MICROBIOLOGY, Vol: 75, Pages: 1484-1494, ISSN: 0950-382X
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- Citations: 18
Ewens CA, Kloppsteck P, Foerster A, et al., 2010, Structural and functional implications of phosphorylation and acetylation in the regulation of the AAA+ protein p97, BIOCHEMISTRY AND CELL BIOLOGY-BIOCHIMIE ET BIOLOGIE CELLULAIRE, Vol: 88, Pages: 41-48, ISSN: 0829-8211
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- Citations: 30
Carmen Herrera M, Krell T, Zhang X, et al., 2009, PhhR Binds to Target Sequences at Different Distances with Respect to RNA Polymerase in Order to Activate Transcription, JOURNAL OF MOLECULAR BIOLOGY, Vol: 394, Pages: 576-586, ISSN: 0022-2836
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- Citations: 14
Burrows PC, Schumacher J, Amartey S, et al., 2009, Functional roles of the pre-sensor I insertion sequence in an AAA plus bacterial enhancer binding protein, Molecular Microbiology, Vol: 73, Pages: 519-533, ISSN: 0950-382X
Molecular machines belonging to the AAA+ superfamily of ATPases use NTP hydrolysis to remodel their versatile substrates. The presence of an insertion sequence defines the major phylogenetic pre‐sensor I insertion (pre‐SIi) AAA+ superclade. In the bacterial σ54‐dependent enhancer binding protein phage shock protein F (PspF) the pre‐SIi loop adopts different conformations depending on the nucleotide‐bound state. Single amino acid substitutions within the dynamic pre‐SIi loop of PspF drastically change the ATP hydrolysis parameters, indicating a structural link to the distant hydrolysis site. We used a site‐specific protein–DNA proximity assay to measure the contribution of the pre‐SIi loop in σ54‐dependent transcription and demonstrate that the pre‐SIi loop is a major structural feature mediating nucleotide state‐dependent differential engagement with Eσ54. We suggest that much, if not all, of the action of the pre‐SIi loop is mediated through the L1 loop and relies on a conserved molecular switch, identified in a crystal structure of one pre‐SIi variant and in accordance with the high covariance between some pre‐SIi residues and distinct residues outside the pre‐SIi sequence.
Xu Y, Liu M, Simpson PJ, et al., 2009, Automated Assignment in Selectively Methyl-Labeled Proteins, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 131, Pages: 9480-+, ISSN: 0002-7863
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- Citations: 27
Huo Y-X, Zhang Y-T, Xiao Y, et al., 2009, IHF-binding sites inhibit DNA loop formation and transcription initiation, NUCLEIC ACIDS RESEARCH, Vol: 37, Pages: 3878-3886, ISSN: 0305-1048
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- Citations: 22
Burrows PC, Joly N, Cannon WV, et al., 2009, Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting, JOURNAL OF MOLECULAR BIOLOGY, Vol: 387, Pages: 306-319, ISSN: 0022-2836
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- Citations: 12
Fillet S, Velez M, Lu D, et al., 2009, TtgV Represses Two Different Promoters by Recognizing Different Sequences, JOURNAL OF BACTERIOLOGY, Vol: 191, Pages: 1901-1909, ISSN: 0021-9193
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- Citations: 15
Lu D, Wörmann ME, Zhang X, et al., 2009, Structure-based mechanism of lipoteichoic acid synthesis by Staphylococcus aureus LtaS.
Bose D, Pape T, Burrows PC, et al., 2008, Organization of an Activator-Bound RNA Polymerase Holoenzyme, MOLECULAR CELL, Vol: 32, Pages: 337-346, ISSN: 1097-2765
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- Citations: 59
Zhang X, Wigley DB, 2008, The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA plus proteins, Nature Structural and Molecular Biology, Vol: 15, Pages: 1223-1227, ISSN: 1545-9985
AAA+ proteins carry out diverse functions in cells. In most cases, their ATPase activity is tightly regulated by protein partners and target ligands, but the mechanism for this control has remained unclear. We have identified a conserved link between the ligand binding and ATPase sites in AAA+ proteins. This link, which we call the 'glutamate switch', regulates ATPase activity directly in response to the binding of target ligands by controlling the orientation of the conserved glutamate residue in the DExx motif, switching it between active and inactive conformations. The reasons for this level of control of the ATPase activity are discussed in the context of the biological processes catalyzed by AAA+ proteins.
Schumacher J, Joly N, Claeys-Bouuaert IL, et al., 2008, Mechanism of homotropic control to coordinate hydrolysis in a hexameric AAA plus ring ATPase, JOURNAL OF MOLECULAR BIOLOGY, Vol: 381, Pages: 1-12, ISSN: 0022-2836
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- Citations: 9
Burrows PC, Wigneshweraraj S, Bose D, et al., 2008, Visualizing the organization and reorganization of transcription complexes for gene expression, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 36, Pages: 776-779, ISSN: 0300-5127
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- Citations: 4
Briggs LC, Baldwin GS, Miyata N, et al., 2008, Analysis of nucleotide binding to p97 reveals the properties of a tandem AAA hexameric ATPase, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 283, Pages: 13745-13752
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- Citations: 64
Wigneshweraraj S, Bose D, Burrows PC, et al., 2008, <i>Modus operandi</i> of the bacterial RNA polymerase containing the σ<SUP>54</SUP> promoter-specificity factor, MOLECULAR MICROBIOLOGY, Vol: 68, Pages: 538-546, ISSN: 0950-382X
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- Citations: 101
Joly N, Rappas M, Buck M, et al., 2008, Trapping of a transcription complex using a new nucleotide analogue: AMP aluminium fluoride, JOURNAL OF MOLECULAR BIOLOGY, Vol: 375, Pages: 1206-1211, ISSN: 0022-2836
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- Citations: 14
Bose D, Joly N, Pape T, et al., 2008, Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 36, Pages: 83-88, ISSN: 0300-5127
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- Citations: 20
Yeung HO, Kloppsteck P, Niwa H, et al., 2008, Insights into adaptor binding to the AAA protein p97, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 36, Pages: 62-67, ISSN: 0300-5127
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- Citations: 107
Wigneshweraraj S, Burrows P, Bose D, et al., 2008, THE MECHANISTIC BASIS OF <i>nif</i> GENE ACTIVATION, Joint Conference of the 15th International Congress on Nitrogen Fixation/12 International Conference of the African-Association-for-Biological-Nitrogen-Fixation, Publisher: SPRINGER, Pages: 339-+, ISSN: 0924-1949
Isaacson RL, Simpson PJ, Liu M, et al., 2007, A new labeling method for methyl transverse relaxation-optimized spectroscopy NMR spectra of alanine residues, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 129, Pages: 15428-+, ISSN: 0002-7863
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- Citations: 89
Briggs LC, Dreveny I, Pye VE, et al., 2007, p97 and Ubiquitin: A Complex Story, Protein Degradation, Pages: 149-193, ISBN: 9783527318780
p97 is an abundant, hexameric AAA ATPase, constituting 1% of the cytosol. It carries out diverse cellular roles, and is increasingly linked to ubiquitin in these processes. Ubiquitin modification determines the fate of many cellular proteins. Conjugation with a single ubiquitin molecule is a signal associated with altered protein trafficking whereas conjugation of a chain of ubiquitin can target a substrate protein to the proteasome for degradation, a function of the ubiquitin- proteasome system (UPS). Recent advances have established p97 (also known as VCP in mammals and Cdc48 in yeast) as a key part of the UPS, best characterized in the ERAD pathway. The UPS is a nonlysosomal proteolytic system, in which a candidate protein (short-lived or misfolded) is identified, modified with a ubiquitin chain, escorted to the proteasome and then unfolded, deubiquitinated and subjected to proteolysis. This involves recognition of the substrate protein and the actions of a succession of proteins on it. p97 is of particular importance as it is able to interact with many different proteins in this series of events. Current evidence points to a role for p97 in the identification and possible subsequent partial unfolding or disassembly of a given protein or protein complex. In the UPS, for example, this could be the disassembly of ubiquitinated proteins from unmodified proteins, prior to capture by the following interacting protein. It appears that this functionality possibly extends to other cellular processes that p97 participates in, such as post-mitotic membrane fusion. In this chapter we will give an overview of these p97 interacting proteins and detail how p97 targets ubiquitin-modified proteins in cellular processes such as ERAD. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA.
Briggs LC, Dreveny I, Pye VE, et al., 2007, p97 and Ubiquitin: A Complex Story, Protein Degradation: Cell Biology of the Ubiquitin-Proteasome System, Pages: 149-193, ISBN: 9783527314355
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- Citations: 1
Joly N, Rappas M, Wigneshweraraj SR, et al., 2007, Coupling nucleotide hydrolysis to transcription activation performance in a bacterial enhancer binding protein, MOLECULAR MICROBIOLOGY, Vol: 66, Pages: 583-595, ISSN: 0950-382X
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- Citations: 31
Isaacson RL, Pye VE, Simpson P, et al., 2007, Detailed structural insights into the p97-Npl4-Ufd1 interface, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 282, Pages: 21361-21369
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- Citations: 55
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