Xiaodong Zhang's Publications
2012 (4)
84 — original research
Niwa H, Ewens CA, Tsang C, Yeung HO, Zhang X, Freemont PS
"The role of the N-domain in the ATPase activity of the mammalian AAA ATPase p97/VCP"
J Biol Chem 278:8561-70 (2012) – [Pubmed]
83 — original research
Bebeacua C, Förster A, McKeown C, Meyer HH, Zhang X, Freemont PS
"Distinct conformations of the protein complex p97-Ufd1-Npl4 revealed by electron cryomicroscopy"
Proc Natl Acad Sci USA 109:1098-103 (2012) – [Pubmed]
82 — review article
Joly N, Zhang N, Buck M, Zhang X
"Coupling AAA protein function to regulated gene expression"
Biochim Biophys Acta 1823:108-16 (2012) – [Pubmed]
81 — review article
Kloppsteck P, Ewens CA, Förster A, Zhang X, Freemont PS
"Regulation of p97 in the Ubiquitin-Proteasome System by the UBX protein-family"
Biochim Biophys Acta 1823:125-9 (2012) – [Pubmed]
2011 (4)
80 — original research
Bush M, Ghosh T, Tucker N, Zhang X, Dixon R
"Transcriptional regulation by the dedicated nitric oxide sensor, NorR: a route towards NO detoxification"
Biochem Soc Trans 39:289-93 (2011) – [Pubmed]
79 — original research
Jovanovic M, Burrows PC, Bose D, Cámara B, Wiesler S, Zhang X, Wigneshweraraj S, Weinzierl RO, Buck M
"Activity map of the Escherichia coli RNA polymerase bridge helix"
J Biol Chem 286:14469-79 (2011) – [Pubmed]
78 — original research
Fillet S, Krell T, Morel B, Lu D, Zhang X, Ramos JL
"Intramolecular signal transmission in a tetrameric repressor of the IclR family"
Proc Natl Acad Sci USA 108:15372-7 (2011) – [Pubmed]
77 — original research
Klein BJ, Bose D, Baker KJ, Yusoff ZM, Zhang X, Murakami KS
"RNA polymerase and transcription elongation factor Spt4/5 complex structure"
Proc Natl Acad Sci USA 108:546-50 (2011) – [Pubmed]
2010 (7)
76 — original research
Sweeney TR, Cisnetto V, Bose D, Bailey M, Wilson JR, Zhang X, Belsham GJ, Curry S
"Foot-and-mouth disease virus 2C is a hexameric AAA+ protein with a coordinated ATP hydrolysis mechanism"
J Biol Chem 285:24347-59 (2010) – [Pubmed]
75 — original research
Lu D, Fillet S, Meng C, Alguel Y, Kloppsteck P, Bergeron J, Krell T, Gallegos MT, Ramos J, Zhang X
"Crystal structure of TtgV in complex with its DNA operator reveals a general model for cooperative DNA binding of tetrameric gene regulators"
Genes Dev 24:2556-65 (2010) – [Pubmed]
74 — original research
Alguel Y, Lu D, Quade N, Sauter S, Zhang X
"Crystal structure of MexZ, a key repressor responsible for antibiotic resistance in Pseudomonas aeruginosa"
J Struct Biol 172:305-10 (2010) – [Pubmed]
73 — original research
Bush M, Ghosh T, Tucker N, Zhang X, Dixon R
"Nitric oxide-responsive interdomain regulation targets the σ54-interaction surface in the enhancer binding protein NorR"
Mol Microbiol 77:1278-88 (2010) – [Pubmed]
72 — review article
Ghosh T, Bose D, Zhang X
"Mechanisms for activating bacterial RNA polymerase"
FEMS Microbiol Rev 34:611-27 (2010) – [Pubmed]
71 — review article
Ewens CA, Kloppsteck P, Förster A, Zhang X, Freemont PS
"Structural and functional implications of phosphorylation and acetylation in the regulation of the AAA+ protein p97"
Biochem Cell Biol 88:41-8 (2010) – [Pubmed]
70 — original research
Tucker NP, Ghosh T, Bush M, Zhang X, Dixon R
"Essential roles of three enhancer sites in σ54-dependent transcription by the nitric oxide sensing regulatory protein NorR"
Nucleic Acids Res 38:1182 (2010) – [Pubmed]
2009 (5)
69 — original research
Burrows PC, Schumacher J, Amartey S, Ghosh T, Burgis TA, Zhang X, Nixon BT, Buck M
"Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein"
Mol Microbiol 73:519-33 (2009) – [Pubmed]
68 — original research
Huo YX, Zhang YT, Xiao Y, Zhang X, Buck M, Kolb A, Wang YP
"IHF-binding sites inhibit DNA loop formation and transcription initiation"
Nucleic Acids Res 37:3878-86 (2009) – [Pubmed]
67 — original research
Xu Y, Liu M, Simpson PJ, Isaacson R, Cota E, Marchant J, Yang D, Zhang X, Freemont P, Matthews S
"Automated assignment in selectively methyl-labeled proteins"
J Am Chem Soc 131:9480-1 (2009) – [Pubmed]
66 — original research
Burrows PC, Joly N, Cannon WV, Cámara BP, Rappas M, Zhang X, Dawes K, Nixon BT, Wigneshweraraj SR, Buck M
"Coupling sigma factor conformation to RNA polymerase reorganisation for DNA melting"
J Mol Biol 387:306-19 (2009) – [Pubmed]
65 — original research
Lu D, Wörmann ME, Zhang X, Schneewind O, Gründling A, Freemont PS
"Structure-based mechanism of lipoteichoic acid synthesis by Staphylococcus aureus LtaS"
Proc Natl Acad Sci USA 106:1584-9 (2009) – [Pubmed]
2008 (9)
64 — original research
Bose D, Pape T, Burrows PC, Rappas M, Wigneshweraraj SR, Buck M, Zhang X
"Organisation of an activator-bound RNA polymerase holoenzyme"
Molecular Cell 32:337-346 (2008) – [Pubmed]
63 — original research
Zhang X, Wigley DB
"The glutamate switch provides a link between ATPase activity and ligand binding in AAA+ proteins"
Nat Struct Mol Biol 15:1223-7 (2008) – [Pubmed]
62 — original research
Briggs LC, Baldwin GS, Miyata N, Kondo H, Zhang X, Freemont PS
"Analysis of nucleotide binding to P97 reveals the properties of a tandem AAA hexameric ATPase"
J Biol Chem 283:13745-52 (2008) – [Pubmed]
61 — review article
Wigneshweraraj S, Bose D, Burrows PC, Joly N, Schumacher J, Rappas M, Pape T, Zhang X, Stockley P, Severinov K, Buck M
"Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor"
Mol Microbiol 68:538-46 (2008) – [Pubmed]
60 — review article
Bose D, Joly N, Pape T, Rappas M, Schumacher J, Buck M, Zhang X
"Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins"
Biochem Soc Trans 36:83-8 (2008) – [Pubmed]
59 — review article
Burrows PC, Wigneshweraraj S, Bose D, Joly N, Schumacher J, Rappas M, Pape T, Stockley PG, Zhang X, Buck M
"Visualizing the organization and reorganization of transcription complexes for gene expression"
Biochem Soc Trans 36:776-9 (2008) – [Pubmed]
58 — review article
Yeung HO, Kloppsteck P, Niwa H, Isaacson RL, Matthews S, Zhang X, Freemont PS
"Insights into adaptor binding to the AAA protein p97"
Biochem Soc Trans 36:62-7 (2008) – [Pubmed]
57 — original research
Joly N, Rappas M, Buck M, Zhang X
"Trapping of a transcription complex using a new nucleotide analogue: AMP aluminium fluoride"
J Mol Biol 375:1206-11 (2008) – [Pubmed]
56 — original research
Schumacher J, Joly N, Claeys-Bouuaert IL, Aziz SA, Rappas M, Zhang X, Buck M
"Mechanism of homotropic control to coordinate hydrolysis in a hexameric AAA+ ring ATPase"
J Mol Biol 381:1-12 (2008) – [Pubmed]
2007 (7)
55 — original research
Alguel Y, Meng C, Terán W, Krell T, Ramos JL, Gallegos MT, Zhang X
"Crystal structures of multidrug binding protein TtgR in complex with antibiotics and plant antimicrobials"
J Mol Biol 369:829-40 (2007) – [Pubmed]
54 — original research
Pye V, Beuron F, Keetch C, McKeown C, Robinson CV, Zhang X, Freemont P
"Structural insights into the p97-Ufd1-Npl4 complex"
Proc Natl Acad Sci USA 104:467-72 (2007) – [Pubmed]
53 — review article
Rappas M, Bose D, Zhang X
"Bacterial enhancer-binding proteins: Unlocking σ54-dependent gene transcription"
Curr Opin Struct Biol 17:110-6 (2007) – [Pubmed]
52 — original research
Joly N, Rappas M, Wigneshweraraj SR, Zhang X, Buck M
"Coupling nucleotide hydrolysis to transcription activation performance in a bacterial enhancer binding protein"
Mol Microbiol 66:583-95 (2007) – [Pubmed]
51 — original research
Schumacher J, Joly N, Rappas M, Bradley D, Wigneshweraraj SR, Zhang X, Buck M
"Sensor I threonine of the AAA+ ATPase transcriptional activator PspF is involved in coupling nucleotide triphosphate hydrolysis to the restructuring of σ 54-RNA polymerase"
J Biol Chem 282:9825-33 (2007) – [Pubmed]
50 — original research
Isaacson R, Simpson P, Liu M, Cota E, Zhang X, Freemont P, Matthews S
"A new labeling method for methyl transverse relaxation-optimized spectroscopy NMR spectra of alanine residues"
J Am Chem Soc 129:15428-9 (2007) – [Pubmed]
49 — original research
Isaacson RL, Pye VE, Simpson P, Meyer HH, Zhang X, Freemont PS, Matthews S
"Detailed structural insights into the p97-Npl4-Ufd1 interface"
J Biol Chem 282:21361-9 (2007) – [Pubmed]
2006 (9)
48 — book chapter
Briggs LC, Dreveny I, Pye VE, Beuron F, Mckeown C, Zhang X, Freemont PS
"p97 and Ubiquitin : A complex story"
in Protein Degradation, Vol. 3: Cell Biology of the Ubiquitin-Proteasome System (edited by Ciechanover A, Rechsteiner M, Mayer RJ), Verlag Chemie (2006)
47 — original research
Beuron F, Dreveny I, Yuan X, Pye VE, Mckeown C, Briggs LC, Cliff MJ, Kaneko Y, Wallis R, Isaacson EL, Ladbury JE, Matthews SJ, Kondo H, Zhang X, Freemont PS
"Conformational changes in the AAA ATPase p97-p47 adaptor complex"
EMBO J 25:1967-76 (2006) – [Pubmed]
46 — original research
Rappas M, Schumacher J, Niwa H, Buck M, Zhang X
"Structural basis of nucleotide-driven conformational changes in the AAA+ domain of transcriptional activator PspF"
J Mol Biol 357:481-92 (2006) – [Pubmed]
45 — original research
Buck M, Bose D, Burrows P, Cannon W, Joly N, Pape T, Rappas M, Schumacher J, Wigneshweraraj S, Zhang X
"A second paradigm for gene activation in bacteria"
Biochem Soc Trans 34:1067-71 (2006) – [Pubmed]
44 — original research
Uchiyama K, Totsukawa G, Puhka M, Kaneko Y, Jokitalo E, Dreveny I, Beuron F, Zhang X, Freemont P, Kondo H
"p37 is a p97 adaptor required for Golgi and ER biogenesis in interphase and at the end of mitosis"
Dev Cell 11:755-7 (2006) – [Pubmed]
43 — review article
Pye VE, Dreveny I, Briggs LC, Sands C, Beuron F, Zhang X, Freemont PS
"Going through the motions: The ATPase cycle of p97"
J Struct Biol 156:12-28 (2006) – [Pubmed]
42 — review article
Schumacher J, Joly N, Rappas M, Zhang X, Buck M
"Structures and organisation of AAA+ enhancer binding proteins in transcriptional activation"
J Struct Biol 156:190-9 (2006) – [Pubmed]
41 — original research
Suno R, Niwa H, Tsuchiya D, Zhang X, Yoshida M, Morikawa K
"Structure of the whole cytosolic region of ATP-dependent protease FtsH"
Mol Cell 22:575-85 (2006) – [Pubmed]
40 — original research
Huo Y, Tian Z, Rappas M, Wen J, Chen Y, You C, Zhang X, Buck M, Wang Y, Kolb A
"Protein-induced DNA bending clarifies the architectural organization of the σ54-dependent glnAp2 promoter"
Mol Microbiol 59:168-80 (2006) – [Pubmed]
2005 (5)
39 — original research
Rappas M, Schumacher J, Beuron F, Niwa H, Bordes P, Wigneshweraraj S, Keetch CA, Robinson CV, Buck M, Zhang X
"Structural insights into the activity of enhancer-binding protein"
Science 307:1972-5 (2005) – [Pubmed]
38 — review article
Wigneshweraraj SR, Burrows PC, Bordes P, Schumacher J, Rappas M, Finn RD, Cannon WV, Zhang X, Buck M
"The second paradigm for activation of transcription"
Prog Nucleic Acid Res Mol Biol 79:339-69 (2005) – [Pubmed]
37 — original research
Wang Q, Song C, Irizarry L, Dai R, Zhang X, Li C
"Multifunctional roles of the conserved Arg residues in the second region of homology of p97/valosin-containing protein"
J Biol Chem 280:40515-23 (2005) – [Pubmed]
36 — review article
Ramos JR, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R
"The TetR family of transcriptional repressors"
Microbiol Mol Biol Rev 69:326-56 (2005) – [Pubmed]
35 — original research
Guazzaroni ME, Krell T, Felipe A, Ruiz R, Meng C, Zhang X, Gallegos MT, Ramos JL
"The multidrug efflux regulator TtgV recognizes a wide range of structurally different effectors in solution and complexed with target DNA: Evidence from isothermal titration calorimetry"
J Biol Chem 280:20887-93 (2005) – [Pubmed]
2004 (9)
34 — review article
Rappas M, Niwa H, Zhang X
"Mechanisms of ATPases – a multi-disciplinary approach"
Curr Protein Pept Sci 5:89-105 (2004) – [Pubmed]
33 — original research
Dreveny I, Kondo H, Uchiyama K, Shaw A, Zhang X, Freemont PS
"Structural Basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47"
EMBO J 23:1030-9 (2004) – [Pubmed]
32 — original research
Yuan X, Simpson P, McKeown C, Kondo H, Uchiyama K, Wallis R, Dreveny I, Keetch C, Zhang X, Robinson C, Freemont P, Matthews S
"Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97"
EMBO J 23:1463-73 (2004) – [Pubmed]
31 — review article
Dreveny I, Pye VE, Beuron F, Briggs LC, Isaacson RL, Matthews SJ, McKeown C, Yuan X, Zhang X, Freemont PS
"p97 and close encounters of every kind: A brief review"
Biochem Soc Trans 32:715-20 (2004) – [Pubmed]
30 — original research
Schumacher J, Zhang X, Jones S, Bordes P, Buck M
"ATP-dependent transcriptional activation by bacterial PspF AAA+ protein"
J Mol Biol 338:863-75 (2004) – [Pubmed]
29 — original research
Yuan X, Simpson P, Kondo H, McKeown C, Dreveny I, Zhang X, Freemont PS, Matthews S
"Complete backbone resonance assignments of p47: The 41kDa adaptor protein of the AAA ATPase p97"
J Biomol NMR 28:309-10 (2004) – [Pubmed]
28 — original research
Guazzaroni ME, Terán W, Zhang X, Gallegos MT, Ramos JL
"TtgV bound to a complex operator site represses transcription of the promoter for the multidrug and solvent extrusion TtgGHI pump"
J Bacteriol 186:2921-7 (2004) – [Pubmed]
27 — original research
Smith GR, Contreras-Moreira B, Zhang X, Bates PA
"A link between sequence conservation and domain motion within the AAA+ family"
J Struct Biol 146:189-204 (2004) – [Pubmed]
26 — original research
Bordes P, Wigneshweraraj SR, Zhang X, Buck M
"σ54-dependent transcription activator phage shock protein F of Escherichia coli: A fragmentation approach to identify sequences that contribute to self-association"
Biochem J 378:735-44 (2004) – [Pubmed]
2003 (4)
25 — original research
Beuron F, Flynn TC, Ma J, Kondo H, Zhang X, Freemont PS
"Motions and negative cooperativity between p97 domains revealed by cryo-electron microscopy and quantised elastic deformational model"
J Mol Biol 327:619-29 (2003) – [Pubmed]
24 — original research
Huyton T, Pye VE, Briggs LC, Flynn TC, Beuron F, Kondo H, Ma J, Zhang X, Freemont PS
"The crystal structure of murine p97/VCP at 3.6Å"
J Struct Biol 144:337-48 (2003) – [Pubmed]
23 — original research
Uchiyama K, Jokitalo E, Lindman M, Jackman M, Kano F, Murata M, Zhang X, Kondo H
"The localization and phosphorylation of p47 are important for Golgi disassembly-assembly during the cell cycle"
J Cell Biol 161:1067-79 (2003) – [Pubmed]
22 — original research
Bordes P, Wigneshweraraj SR, Schumacher J, Zhang X, Chaney M, Buck M
"The ATP hydrolyzing transcription activator phage shock protein F of Escherichia coli: Identifying a surface that binds σ 54"
Proc Natl Acad Sci USA 100:2278-83 (2003) – [Pubmed]
2002 (3)
21 — original research
Uchiyama K, Jokitalo E, Kano F, Murata M, Zhang X, Canas B, Newman R, Rabouille C, Pappin D, Freemont P, Kondo H
"VCIP135, a novel essential factor for p97/p47-mediated membrane fusion, is required for Golgi and ER assembly in vivo"
J Cell Biol 159:855-66 (2002) – [Pubmed]
20 — review article
Zhang X, Chaney M, Wigneshweraraj SR, Schumacher J, Bordes P, Cannon W, Buck M
"Mechanochemical ATPases and transcriptional activation"
Mol Microbiol 45:895-903 (2002) – [Pubmed]
19 — review article
Zhang X, Beuron F, Freemont PS
"Machinery of protein folding and unfolding"
Curr Opin Struct Biol 12:231-8 (2002) – [Pubmed]
2001 (2)
18 — original research
Yuan X, Shaw A, Zhang X, Kondo H, Lally J, Freemont PS, Matthews S
"Solution structure and interaction surface of the C-terminal domain from p47: A major p97-cofactor involved in SNARE disassembly"
J Mol Biol 311:255-63 (2001) – [Pubmed]
17 — original research
Dulic A, Bates P, Zhang X, Freemont PS, Lindahl T, Barnes D
"BRCT domain interactions in the heterodimeric DNA repair protein XRCC1-DNA ligase III"
Biochemistry 40:5906-13 (2001) – [Pubmed]
2000 (2)
16 — original research
Zhang X, Shaw A, Bates P, Newman R, Gowen B, Orlova E, Gorman M, Kondo H, Dokurno P, Lally J, Leonard G, Meyer H, van Heel M, Freemont PS
"Structure of the AAA ATPase p97"
Molecular Cell 6:1473-84 (2000) – [Pubmed]
15 — review article
Huyton T, Bates PA, Zhang X, Sternberg MJ, Freemont PS
"The BRCA1 C-terminal domain: Structure and function"
Mutat Res 460:319-32 (2000) – [Pubmed]
1999 (1)
14 — original research
Zhang X, Rosenthal PB, Formanowski F, Fitz W, Wong CH, Meier-Ewert H, Skehel JJ, Wiley DC
"X-ray crystallographic determination of the structure of the influenza C virus haemagglutinin-esterase-fusion glycoprotein"
Acta Crystallogr D Biol Crystallogr 55:945-61 (1999) – [Pubmed]
1998 (2)
13 — original research
Rosenthal PB, Zhang X, Formanowski F, Fitz W, Wong CH, Meier-Ewert H, Skehel JJ, Wiley DC
"Structure of the haemagglutinin-esterase-fusion glycoprotein of influenza C virus"
Nature 396:92-6 (1998) – [Pubmed]
12 — original research
Zhang X, Moréra S, Bates PA, Whitehead PC, Coffer AI, Hainbucher K, Nash RA, Sternberg MJ, Lindahl T, Freemont PS
"Structure of an XRCC1 BRCT domain: A new protein-protein interaction module"
EMBO J 17:6404-11 (1998) – [Pubmed]
1997 (1)
11 — original research
Buckley CJ, Khaleque N, Bellamy SJ, Robins M, Zhang X
"Mapping the organic and inorganic components of tissue using NEXAFS"
J Phys IV 7:83-90 (1997)
1996 (2)
10 — review article
Jacobsen C, Chapman HN, Fu J, Kalinovsky A, Kirz J, Maser J, Osanna A, Spector S, Tennant D, Wang S, Wirick S, Zhang X
"Biological microscopy and soft x-ray optics at Stony Brook"
J Electron Spectrosc 80:337-341 (1996)
9 — original research
Zhang X, Balhorn R, Mazrimas J, Kirz J
"Mapping and measuring DNA to protein ratios in mammalian sperm head by XANES imaging"
J Struct Biol 116:335-44 (1996) – [Pubmed]
1995 (1)
8 — original research
Zhang X, Jacobsen C, Lindaas S, Williams S
"Exposure strategies for polymethyl methacrylate from in situ x-ray absorption near edge structure spectroscopy"
J Vac Sci Technol B 13:1477 (1995)
1994 (1)
7 — review article
Zhang X, Ade H, Jacobsen C, Kirz J, Lindaas S, Williams S, Wirick S
"Micro-Xanes – Chemical contrast in the scanning-transmission x-ray microscope"
Nucl Instrum Meth A 347:431-5 (1994)
1993 (3)
6 — original research
Williams S, Zhang X, Jacobsen C, Kirz J, Lindaas S, Van't Hof J, Lamm JJ
"Measurements of wet metaphase chromosomes in the scanning transmission x-ray microscope"
J Microsc 170:155-65 (1993)
5 — review article
Jacobsen C, Lindaas S, Williams S, Zhang X
"Scanning luminescence x-ray microscopy: Imaging fluorescence dyes at suboptical resolution"
J Microsc 172:121-29 (1993)
4 — original research
Kirz J, Ade H, Anderson E, Buckley C, Chapman H, Howells M, Jacobsen C, Ko Ch, Lindaas S, Sayre D, Williams S, Wirick S, Zhang X
"New results in soft-x-ray microscopy"
Nucl Instrum Meth B 87:92-7 (1993)
1992 (2)
3 — original research
Ade H, Zhang X, Cameron S, Costello C, Kirz J, Williams S
"Chemical contrast in x-ray microscopy and spatially resolved XANES spectroscopy of organic specimens"
Science 258:972-5 (1992) – [Pubmed]
2 — review article
Kirz J, Ade H, Jacobsen C, Ko Ch, Lindaas S, McNulty I, Sayre D, Williams S, Zhang X, Howells M
"Soft-x-ray microscopy with coherent x-rays"
Rev Sci Instrum 63:557-63 (1992)
1991 (1)
1 — original research
Jacobsen C, Williams S, Anderson E, Browne MT, Buckley CJ, Kern D, Kirz J, Rivers M, and Zhang X
"Diffraction-limited imaging in a scanning transmission x-ray microscope"
Optics Communications 86:351-361 (1991)