123. Minor C, Takayesu A, Ha S-M, Salwinski L, Sawaya MR, Pellegrini M and Clubb RT. A genomic analysis reveals the diversity of cellulosome displaying bacteria. (submitted)
122. Goring AK, Hale S, Dasika P, Chen Y, Clubb RT and Loo JA The exoproteome and surfaceome of toxigenic Corynebacterium diphtheriae 1737 and its response to iron-restriction and growth on human hemoglobin. (submitted)
121. Mahoney BJ, Lyman LR, Ford J, Jordan Ford, Soule J, Goring AK, Collazo M, Cascio D, Ton-That H, Schmitt MP, and Clubb RT. Molecular basis of hemoglobin capture by Corynebacterium diphtheriae (submitted)
120. Takayesu A, Mahoney BJ, Goring AK, Tobie Jessup, T, Ogorzalek-Loo RR, Loo JA and Clubb RT. Insight into the autoproteolysis mechanism of the RsgI9 anti-σ factor from Clostridium thermocellum. Proteins 2024 (doi: 10.1002/prot.26690)
119. Cheung N, Song M, Sue CK and Clubb RT. Quantifying the kinetics of pilus-specific sortase-catalyzed crosslinking using high-performance liquid chromatography. Methods in Molecular Biology 2024 2727; 135-143.
118. Mahoney BJ, Goring AK, Wang Y, Dasika P, Zhou A, Grossbard E, Cascio D, Loo JA and Clubb RT. Development and atomic structure of a new fluorescence-based sensor to probe heme transfer in bacterial pathogens. Journal of Inorganic Biochemistry 2023 249; 112369
117. Sue CK, Cheung N, Mahoney BJ, McConnell SA, Scully JM, Fu JY, Chang C, Ton-That H, Loo JA and Clubb RT. The basal and major pilins in the Corynebacterium diphtheriae SpaA pilus adopt similar structures that competitively react with the pilin polymerase. Biopolymers (in press)
116. Macdonald R, Mahoney BJ, Soule J, Goring A, Ford J, Loo JA, Cascio D and Clubb RT. The Shr receptor from Streptococcus pyogenes uses a 'cap and release' mechanism to acquire heme-iron from human hemoglobin. Proceedings of the National Academy of Sciences (USA) 120(5) 2023; e2211939120
115. Clayton J, Ellis-Guardiola K, Mahoney B, Soule J, Liu W, Clubb RT and Wereszczynski J. Directed inter-domain motions enable the IsdH Staphylococcus aureus receptor to rapidly extract heme from human hemoglobin. Journal of Molecular Biology 2022 434 2022; 167623.
114. Mahoney BJ, Takayesu A, Zhou A, Cascio D and Clubb RT. The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism of biomass sensing. Proteins 90 2022; 1457-1467.
113. Martinez OE, Mahoney BJ, Goring AK, Yi SW, Tran DP, Cascio D, Phillips ML, Muthana MM, Chen X, Jung ME, Loo JA and Clubb RT. Insight into the molecular basis of substrate recognition by the wall teichoic acid glycosyltransferase TagA. Journal of Biological Chemistry 298 2022; 101464.
112. Ellis-Guardiola K, Soule J and Clubb RT. Methods to extract heme prosthetic groups from hemoproteins. Bio-protocols 11 2021; e4156
111. McConnell SA, McAllister RA, Amer BR, Mahoney B, Sue CK, Chang C, Ton-That H. and Clubb RT. Sortase-assembled pili in Corynebacterium diphtheriae are built using a latch mechanism. Proceedings of the National Academy of Sciences (USA) 118 2021; e2019649118
110. Ellis-Guardiola K, Mahoney B and Clubb RT. NEAr Transporter (NEAT) domains: novel surface displayed heme chaperones that enable Gram-positive bacteria to capture heme-iron from hemoglobin. Frontiers in Microbiology 11 2021; 607679
109. Sue CK, McConnell SA, Ellis-Guardiola K, Muroski JM, McAllister RA, Yu J, Alvarez AI, Chang C, Ogorzalek Loo RR, Loo JA, Ton-That H. and Clubb RT. Kinetics and optimization of the lysine-isopeptide bond forming activity of the pilus-specific sortase from Corynebacterium diphtheriae. Bioconjugation Chemistry 31 2020; 1624-1634.
108. Gosschalk JE, Wu C, Sue CK, Kattke MD, Yi SW, Damoiseaux R, Jung ME, Ton-That H and Clubb RT. A cell-based screen in Actinomyces oris to identify sortase inhibitors. Scientific Reports 10 2020; 8520
107. McConnell S, Cannon K, Morgan C, McAllister R, Amer B, Clubb RT and Yeates T. Designed protein cages as scaffolds for building multi-enzyme materials. ACS Synthetic Biology 9 2020; 381-391
106. Ellis-Guardiola K, Clayton J, Pham C, Mahoney B, Wereszczynski J and Clubb RT. The Staphylococcus aureus IsdH receptor forms a dynamic complex with human hemoglobin and triggers heme release via two distinct hot spots. Journal of Molecular Biology 432 2019; 1064-1082.
105. Chang C, Wu C, Osipiuk J, Siegel SD, Zhu S, Liu X, Joachimiak A, Clubb RT, Das A and Ton-That H. Cell-to-cell interaction requires optimal positioning of a pilus tip adhesin modulated by gram-positive transpeptidase enzymes. Proceedings of the National Academy of Sciences (USA) 116 2019; 18041-18049
104. Tsui HS, Pham NVB, Amer BR, Bradley MC, Gosschalk JE, Gallagher-Jones M, Ibarra H, Clubb RT, Blaby-Haas CE, Clarke CF. Human COQ10A and COQ10B are distinct START domain proteins required for coenzyme Q function. J Lipid Res. 2019 May 2. pii: jlr.M093534.
103. Macdonald R, Mahoney BJ, Ellis-Guardiola K, Maresso M and Clubb RT. NMR Experiments Redefine the Hemoglobin Binding Properties of Bacterial NEAr-iron Transporter (NEAT) Domains. Protein Science. 28 2019; 1513-1523
102. Kattke MD, Gosschalk JE, Martinez OE, Cascio D, Sawaya MR, Phillips M, Kumar G, Gale RT, Brown ED and Clubb RT. Structure and mechanism of TagA, a novel membrane-associated glycosyltransferase that produces wall teichoic acids in pathogenic bacteria. PLoS Pathog. 15 2019; e1007723
101. Siegel SD, Amer BR, Wu C, Sawaya MR, Gosschalk JE, Clubb RT and Ton-That H. A phosphotransferase LCP enzyme mediates glycosylation of a Gram-positive cell wall anchored protein. mBio. 10 2019; e01580-18
100. Macdonald R, Cascio D, Collazo MJ, Phillips M and Clubb RT. The Streptococcus pyogenes Shr protein captures human hemoglobin using two structurally unique binding domains. Journal of Biological Chemistry 293 2018; 18365-18377
99. McConnell SA, Amer BR, Muroski J, Fu J, Loo RO, Loo JA, Osipiuk J, Ton-That J and Clubb RT. Protein labeling via a specific lysine-isopeptide bond using the pilin polymerizing sortase from Corynebacterium diphtheria. Journal of the American Chemical Society 2018; 140: 8420-8423
98. Chang C, Amer BR, Osipiuk J, McConnell SA, Huang I-H, Hsieh V, Fu J, Nguyen HH, Muroski J, Flores E, Loo RO, Loo JA, Putkey JA, Joachimiak A, Das A, Clubb RT and Ton-That H. In vitro reconstitution of sortase-catalyzed pilus polymerization reveals structural elements involved in pilin crosslinking. Proceedings of the National Academy of Sciences (USA) 115 2018; E5477-E5486
97. Huang GL, Gosschalk JE, Kim YS and Clubb RT. Stabilizing displayed proteins on vegetative Bacillus subtilis cells. Appl Microbiol Biotechnol. 2018. doi:10.1007/s00253-018-9062-x.
96. Sjodt M, Macdonald R, Marshall JD, et al. Energetics Underlying Hemin Extraction from Human Hemoglobin by Staphylococcus aureus. J Biol Chem. 2018. doi:10.1074/jbc.RA117.000803.
95. Jacobitz AW, Kattke MD, Wereszczynski J, Clubb RT. Sortase Transpeptidases: Structural Biology and Catalytic Mechanism. Adv Protein Chem Struct Biol. 2017;109. doi:10.1016/bs.apcsb.2017.04.008.
94. Sjodt M, Clubb RT. Nitroxide Labeling of Proteins and the Determination of Paramagnetic Relaxation Derived Distance Restraints for NMR Studies. Bio-protocol. 2017;7(7):e2207. doi:10.21769/BioProtoc.2207.
93. Chan AH, Yi SW, Weiner EM, et al. NMR structure-based optimization of Staphylococcus aureus sortase A pyridazinone inhibitors. Chem Biol Drug Des. 2017;90(3):327-344. doi:10.1111/cbdd.12962.
92. Kattke MD, Chan AH, Duong A, et al. Crystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting Signal. Ton-That H, ed. PLoS ONE. 2016;11(12):e0167763. doi:10.1371/journal.pone.0167763.
91. Jacobitz AW, Naziga EB, Yi SW, et al. The “Lid” in the Streptococcus Pneumoniae SrtC1 Sortase Adopts a Rigid Structure that Regulates Substrate Access to the Active Site. The journal of physical chemistry B. 2016;120(33):8302-8312. doi:10.1021/acs.jpcb.6b01930.
90. Amer BR, Macdonald R, Jacobitz AW, Liauw B, Clubb RT. Rapid Addition of Unlabeled Silent Solubility Tags to Proteins Using a New Substrate-Fused Sortase Reagent. Journal of biomolecular NMR. 2016;64(3):197-205. doi:10.1007/s10858-016-0019-z.
89. Tekeste S, Wilkinson T, Weiner E, Miller J, Le Grice S, Clubb RT and Chow S. Interaction between reverse transcriptase and integrase is required for reverse transcription during HIV-1 replication. J Virol. 2015 Dec 1;89(23):12058-69.
88. Chan A, Yi SW, Terwilliger AL, Maresso AW, Jung ME and Clubb RT. Structure of the Bacillus anthracis sortase A enzyme bound to its sorting signal: a flexible amino-terminal appendage modulates substrate access. J Biol Chem. 2015 Oct 16;290(42):25461-74.
87. Zilbermintz L, Leonardi W, Jeong S-Y, Sjodt M, McComb R, Ho CC, Retterer C, Gharaibeh D, Zamani R, Soloveva V, Bavari S, Levitin A, West J, Bradley KA, Clubb RT, Cohen SN, Gupta V and Martchenko. Identification of agents effective against multiple toxins and viruses by host-oriented cell targeting. Sci Rep. 2015 Aug 27;5:13476.
86. Macdonald R, Sarkar D, Amer B and Clubb RT. Structure of the PhoP DNA binding-domain from Mycobacterium tuberculosis. J Biomol NMR. 2015 Sep;63(1):111-7.
85. Zhang J, Malmirchegini GR, Clubb RT and Loo JA. Native top-down mass spectrometry for the structural characterization of human hemoglobin. Eur J Mass Spectrom (Chichester, Eng). 2015;21(3):221-31.
84. Claire F, Dickson CF, Jacques D, Clubb RT, Guss JM and Gell DA. The structure of haemoglobin bound to the haemoglobin-receptor, IsdH, from Staphylococcus aureus shows disruption of the native alpha-globin haem pocket. Acta Crystallogr D Biol Crystallogr. 2015 Jun;71(Pt 6):1295-306.
83. Sjodt M, Macdonald R, Spirig T, Chan AH, Dickson CF, Fabian M, Olson JS, Gell DA and Clubb RT. The PRE-derived NMR model of the 38.8-kDa tri-domain IsdH protein from Staphylococcus aureus suggests that it adaptively recognizes human hemoglobin. J Mol Biol. 2015 Feb 14. [Epub ahead of print]
82. Malmirchegini GR, Sjodt M, Shnitkind S, Sawaya MR, Rosinski J, Newton SM, Klebba PE, Clubb RT. Novel mechanism of hemin capture by Hbp2, the hemoglobin-binding hemophore from Listeria monocytogenes. J Biol Chem. 2014 Dec 12;289(50):34886-99
81. Amer BR, Clubb RT. A Sweet New Role for LCP enzymes in Protein Glycosylation. Mol Microbiol. 2014 Dec;94(6):1197-200
80. Twu O, Dessí D, Vu A, Mercer F, Stevens GC, de Miguel N, Rappelli P, Cocco AR, Clubb RT, Fiori PL, Johnson PJ. Trichomonas vaginalis homolog of macrophage migration inhibitory factor induces prostate cell growth, invasiveness, and inflammatory responses. Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8179-84.
79. Jacobitz AW, Wereszczynski J, Yi SW, Amer BR, Huang GL, Nguyen AV, Sawaya MR, Jung ME, McCammon JA, Clubb RT. Structural and computational studies of the Staphylococcus aureus Sortase B-substrate complex reveal a substrate-stabilized oxyanion hole. J Biol Chem. 2014 Feb 11. [Epub ahead of print]
78. Dickson CF, Krishna Kumar K, Jacques DA, Malmirchegini GR, Spirig T, Mackay JP, Clubb RT, Guss JM, Gell DA. Structure of the Hemoglobin-IsdH Complex Reveals the Molecular Basis of Iron Capture by Staphylococcus aureus. J Biol Chem. 2014 Jan 14. [Epub ahead of print]
77. Huang GL, Anderson TD, Clubb RT. Engineering microbial surfaces to degrade lignocellulosic biomass. Bioengineered. 2013 Dec 18;5(3). [Epub ahead of print] Review.
76. Ran Y, Malmirchegini GR, Clubb RT, Lei B. Axial ligand replacement mechanism in heme transfer from streptococcal heme-binding protein Shp to HtsA of the HtsABC transporter. Biochemistry 52(37) 2013; 6537-47. doi: 10.1021/bi400965u. [Epub ahead of print].
75. Chan AH, Wereszczynski J, Amer BR, Yi SW, Jung ME, McCammon JA, Clubb RT. Discovery of Staphylococcus aureus Sortase A Inhibitors Using Virtual Screening and the Relaxed Complex Scheme. Chem Biol Drug Des. 2013 May 23. doi: 10.1111/cbdd.12167. [Epub ahead of print] .
74. Spirig T, Malmirchegini GR, Zhang J, Robson SA, Sjodt M, Liu M, Krishna Kumar K, Dickson CF, Gell DA, Lei B, Loo JA, Clubb RT. Staphylococcus aureus uses a novel multidomain receptor to break apart human hemoglobin and steal its heme. J Biol Chem. 288(2) 2013; 1065-78.
73. Kappel K, Wereszczynski J, Clubb RT, McCammon JA. The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations., Protein Sci. 21 2012; 1858-71.
72. Robson, S. A., Jacobitz, A. W., Phillips, M. L. & Clubb, R. T. Solution Structure of the Sortase Required for Efficient Production of Infectious Bacillus anthracis Spores. Biochemistry 51 2012; 7953–7963.
71. Sam MD and Clubb RT. Preparation and optimization of protein-DNA complexes that are suitable for detailed NMR studies. Methods in Molecular Biology 831 2012; 219-32.
70. Spirig T and Clubb RT. Backbone 1H, 13C and 15N resonance assignments of the 39 kDa staphylococcal hemoglobin receptor IsdH. Biomolecular NMR Assignments 6(2), 2012; 169-172.
69. Spirig T, Weiner EM, and Clubb RT. Sortase enzymes in Gram-positive bacteria. Molecular Microbiology 82 2011; 1044-59.
68. Kumar KK, Jacques DA, Pishchany G,Caradoc-Davies T, Spirig T, Malmirchegini GR, Langley DB, Dickson CF, Mackay JP, Clubb RT, Skaar EP, Guss MJ, and Gell DA. The structural basis for hemoglobin capture by the Staphylococcus aureus cell-surface protein, IsdH. Journal of Biological Chemistry 44 2011; 38439-47
67. Villareal VA, Spirig T, Robson SA, Liu M, Lei B, and Clubb RT. Transient Weak Protein-Protein Complexes Transfer Heme Across the Cell Wall of Staphylococcus aureus. Journal of the American Chemical Society 133 2011; 14176-9.
66. Januszyk K, Fleissner MR, Atchabahian L, Shieh F-K, Martin SL, Guo F, Hubbell WL, and Clubb RT. Site-directed spin labeling electron paramagnetic resonance study of the ORF1 protein from a mouse L1 retrotransposon. Protein Science 20 2011; 1231-43.
65. Ramey JD, Villareal VA, Ng C, Ward SC, Xiong JP, Clubb RT, Bradley KA. Anthrax toxin receptor 1/tumor endothelial marker 8: mutation of conserved inserted domain residues overrides cytosolic control of protective antigen binding. Biochemistry. 2010 Aug 31;49(34):7403-10.PMID: 20690680 [PubMed - in process] Related citations.
64. Robson SA, Peterson R, Bouchard LS, Villareal VA and Clubb RT. A heteronuclear zero quantum coherence Nz-exchange experiment that resolves resonance overlap and its application to measure the rates of heme binding to the IsdC protein. J Am Chem Soc. 2010 Jul 21;132(28):9522-3. PMID: 20578738 [PubMed - in process]
63. Senturia R, Faller M, Yin S, Loo JA, Cascio D, Sawaya MR, Hwang D, Clubb RT and Guo F. Structure of the dimerization domain of DiGeorge Critical Region 8. Protein Science 19 2010; p134-65.
62. Weiner EM, Robson SA, Marohn M and Clubb RT. The sortase A enzyme that attaches proteins to the cell wall of B. anthracis contains an unusual active site architecture. Journal of Biological Chemistry. J Biol Chem. 2010 Jul 23;285(30):23433-43. Epub 2010 May 19.
61. Suree N, Yi SW, Thieu W, Marohn M, Damoiseaux R, Chan A, Jung ME and Clubb RT. Discovery and structure activity relationship analysis of Staphylococcus aureus sortase A inhibitors. Bioorganic & Medicinal Chemistry 17 2009; p7174-85. NIHMSID: NIHMS208860.
60. Fadeev EA, Sam MD, Clubb RT. NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove. J Mol Biol. 2009 May 15;388(4):682-90. Epub 2009 Mar 24.
59. Suree N, Liew CK, Villareal VA, Thieu W, Fadeev EA, Clemens JJ, Jung ME, Clubb RT. The structure Of the staphylococcus aureus sortase-substrate complex reveals how the universally conserved Lpxtg sorting signal is recognized. J Biol Chem. 2009 Jul 10. [Epub ahead of print]. PMID: 19592495 [PubMed - as supplied by publisher]
58. Wilkinson TA, Januszyk K, Phillips ML, Tekeste SS, Zhang M, Miller JT, Le Grice SF, Clubb RT. and Chow SA. Identifying and characterizing a functional HIV-1 reverse transcriptase-binding site on integrase. J Biol Chem. 284 2009; 7931-9
57. Pilpa RM, Robson SA, Villareal VA, Wong ML, Phillips M, Clubb RT. Functionally distinct NEAT (NEAr transporter) domains within the staphylococcus aureus IsdH/HarA protein extract heme from methemoglobin. J Biol Chem. 2009 Jan 9;284(2):1166-76. Epub 2008 Nov 3
56. Villareal VA, Pilpa RM, Robson SA, Fadeev EA, and Clubb RT. The IsdC Protein from Staphylococcus aureus Uses a Flexible Binding Pocket to Capture Heme. J Biol Chem. 2008 Nov 14;283(46):31591-600. Epub 2008 Aug
55. Clubb RT and Yeates T.O. How some pili pull. Science 318 (2007); 1558-9
54. Januszyk K, Li PW, Villareal V, Branciforte D, Wu H, Xie Y, Feigon J, Loo JA, Martin SL, and Clubb RT. Identification and solution structure of a highly conserved C-terminal domain within ORF1p required for retrotransposition of long interspersed nuclear element-1. Journal of Biological Chemistry 282 (2007); 24893-904
53. Suree N, Jung ME, and Clubb RT. Recent advances towards new anti-infective agents that inhibit cell surface protein anchoring in Staphylococcus aureus and other gram-positive pathogens. Mini-Reviews in Medicinal Chemistry 7 (2007); 991-1000
52. Papagiannis CV, Sam MD, Abbani M, Yoo D, Cascio D, Clubb RT and Johnson R. Fis targets the assembly of the Xis nucleoprotein filament to promote excisive recombination by phage lambda. Journal of Molecular Biology 367 (2007); 328-43
51. Abbani M, Papagiannis CV, Sam MD, Cascio D, Johnson R and Clubb RT. Structure of the cooperative Excisionase (Xis)-DNA complex reveals a micronucleoprotein filament that regulates phage lambda intasome assembly. Proceedings of the National Academy of Sciences (USA) 104 (2007); 2109-14
50. Sam MD, Abbani M, Cascio D, Johnson R and Clubb RT. Crystallization, dehydration and preliminary X-ray analysis of the Excisionase (Xis) proteins cooperatively bound to DNA. Acta Crystallographica Section F 62 (2006); 825-8
49. Pilpa R, Fadeev, EA, Villareal V, Wong ML, Phillips M and Clubb RT. Solution structure of the NEAT (NEAr Transporter) domain from IsdH/HarA: the human hemoglobin receptor in Staphylococcus aureus. Journal of Molecular Biology 360 (2006); 435-4
48. Naik MT, Suree N, Ilangovan U, Liew, CK, Theiu W, Campbell DO, Clemens JJ, Jung ME and Clubb RT. "Staphylococcus aureus Sortase A transpeptidase. Calcium promotes sorting signal binding by altering the mobility and structure of an active site loop" J Biol Chem. (2006) Jan 20;281(3):1817-26.
47. Pilpa and Clubb RT. "NMR resonance assignments of the NEAT (NEAr Transporter) domain from the Staphylococcus aureus IsdH protein." J Biomol NMR. (2005) Oct;33(2):137.
46. Jung ME, Clemens JJ, Suree N, Liew CK, Pilpa R, Campbell DO and Clubb RT. "Synthesis of (2R,3S) 3-amino-4-mercapto-2-butanol, a threonine analogue for covalent inhibition of sortases." Bioorg Med Chem Lett. (2005):5076-9.
45. Iwahara J, Peterson R and Clubb RT. "Compensating increases in protein backbone flexibility occur when the Dead ringer AT-rich Interaction Domain (ARID) site-specifically binds DNA: a NMR nitrogen-15 relaxation study." Protein Science 14 (2005); 1140-50
44. Abbani, M, Iwahara M and Clubb RT. "The structure of the excisionase (Xis) protein from conjugative transposon Tn916 provides insights into the regulation of heterobivalent tyrosine recombinases." Journal of Molecular Biology 347 (2005); 11-25.
43. Liew CK, Smith BT, Pilpa R, Suree N, Ilangovan U, Connolly KM, Jung ME and, Clubb RT. "Localization and mutagenesis of the sorting signal binding site on sortase A from staphylococcus aureus." FEBS Letters 571 (2004); 221-26
42. Comfort D, Clubb RT. "A comparative genome analysis identifies distinct sorting pathways in gram-positive bacteria" Infect Immun. May;72(5)(2004); 2710-22
41. Sam MD, Cascio D, Johnson RC, Clubb RT. "Crystal structure of the excisionase-DNA complex from bacteriophage lambda" J Mol Biol. Apr 23;338(2) (2004); 229-40.
40. Sam MD, Cascio D, Johnson R, Clubb RT. "Crystallization and preliminary X-ray crystallographic analysis of the excisionase-DNA complex from bacteriophage lambda" Acta Crystallogr D Biol Crystallogr. Jul;59(Pt 7) (2003);1238-40.
39. Connolly KM, Smith BT, Pilpa R, Ilangovan U, Jung ME, and Clubb RT. "Sortase from S. aureus does not contain a thiolateimidazolium ion pair in its active site." Journal of Biological Chemistry Sep 5;278(36) (2003); 34061-5.
38. Warren D, Sam MD, Manley K, Sarkar D, Lee SY, Abbani M, Wojciak JM, Clubb RT, and Landy A. "Identification of the lambda integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation." Proceedings of the National Academy of Sciences (USA) 100 (2003); 8176-8181.
37. Sam MD, Cascio D, Johnson R, and Clubb RT. "Crystallization and preliminary X-ray crystallographic analysis of the excisionase-DNA complex from bacteriophage lambda." Acta Crystallographic D59 (2003) 1238-1240.
36. Milev S, Gorfe A, Karshikoff A, Clubb RT, Bosshard HR, and Jelesarov I. "Energetics of sequence-specific protein-DNA association: Conformational stability of the DNA binding domain of integrase Tn916 and its cognate DNA duplex." Biochemistry 42 (2003) 3492-3502.
35. Milev S, Gorfe A, Karshikoff A, Clubb RT, Bosshard HR, and Jelesarov I. "Energetics of sequence-specific protein-DNA ssociation: Binding of integrase Tn916 to its target DNA." Biochemistry 42 (2003) 3481-3491.
34. Sam MD, Papagiannis C, Connolly KM, Corselli L, Iwahara J, Lee J, Phillips M, Wojciak JM, Johnson R, and Clubb RT. "Regulation of directionality in bacteriophage lambda site-specific recombination: structure of the Xis protein." Journal of Molecular Biology 324 (2002) 791-805.
33. Connolly, K.M., Iwahara, M. and Clubb, R.T. "Xis protein binding to the left arm stimulates the excision of conjugative transposon Tn916". Journal of Bacteriology 184 (2002); 2088-2099.
32. Wojciak, J.M., Sarkar, D, Landy, A. and Clubb, R.T. "Arm-site binding by the lambda integrase protein: solution structure and functional characterization of its amino-terminal domain." Proceedings of the National Academy of Sciences (USA), 99 (2002); 3434-3439.
31. Iwahara, J., Iwahara, M., Daughdrill, G.W., Ford, J and Clubb, R.T. "The structure of the Dead ringer-DNA complex reveals how AT-Rich Interaction Domains (ARIDs) recognize DNA." The EMBO Journal, 21 (2002); 1197-1209.
30. Iwahara, J., Wojciak, J. and Clubb, R.T. "An efficient NMR experiment to analyze sugar-puckering in unlabeled DNA: Application to the 26 kilodalton Dead ringer-DNA complex." Journal of Magnetic Resonance, 153 (2001); 262-266.
29. Wojciak, J.M., Iwahara, J. and Clubb, R.T. "The Mu repressor-DNA complex contains an immobilized ' wing', within the minor groove." Nature Structural Biology 8:1 (2001); 84-90.
28. Ilangovan, U., Iwahara, J., Ton-That, H., Schneewind, O. and Clubb, R.T. "Assignment of the 1H, 13C and 15N Signals of Sortase." Journal of Biomolecular NMR 19:14 (2001); 379-380.
27. Iwahara, J. Wojciak, J.M., and Clubb, R.T. "Improved NMR spectra of a protein-DNA complex through rational mutagenesis and the application of a sensitivity optimized isotope-filtered NOESY experiment." Journal of Biomolecular NMR 19:3 (2001); 231-241.
26. Ilangovan, U., Ton-That, H., Iwahara, J., Schneewind, O. and Clubb, R.T. "Structure of sortase, the transpeptidase that anchors proteins to the cell wall of Staphylococcus aureus." Proceedings of the National Academy of Sciences (USA), 98 (2001); 6056-6061.
25. Wojciak, J.M., Clubb, R.T. "Finding the function buried in SAND." Nature Structural Biology 8.7 (2001); 568-570.
24. Ilangovan,U.,Ton-That,U., Iwahara, J., Schneewind,O., Clubb, R.T. "Assignment of the 1H, 13C, and 15N signals of sortase." J Biomol NMR; In press (2001)
23. Connolly, K.M., Illangovan, U., J.M. Wojciak, M. Iwahara, Clubb, R.T. "Major Groove Recognition by Three-Stranded Beta-Sheets: Affinity Determinants and Conserved Structural Features."J. Mol. Biol.; 300.4(2000):841-856
22. Illangovan, U., Wojciak, J.M., Connolly, K.M., Clubb, R.T. "NMR structure and functional studies of the Mu repressor DNA-binding domain." Biochemistry 38.26 (1999) :8367-8376.
21. Iwahara, J., Clubb, R.T. "Solution Structure of the DNA-Binding Domain from Dead Ringer, a Sequence Specific AT-Rich Interaction Domain (ARID)." EMBO J. 18(1999): 6084-6094
20. Iwahara, J.,Clubb, R.T. "1H, 13C, and 15N resonance assignments of the AT-rich interaction domain from the Dead Ringer protein." J Biomol NMR 15(1)(1999): 85-86
19. Wojciak, J.M., Connolly, K.M., Clubb, R.T. "NMR structure of the Tn916 integrase-DNA complex." Nature Structural Biology 6:4(1999): 366-73
18. Connolly, K.M., Wojciak, J.M., Clubb, R.T. "Resonance assignments of the Tn916 integrase DNA-binding domain and the integrase:DNA complex." J Biomol NMR 14(1)(1999): 95-6
17. Connolly, K.M., Wojciak, J.M., Clubb, R.T. "Site-specific DNA binding using a variation of the double stranded RNA binding motif." Nature Structural Biology 5(7)(1998): 546-50
16. Clubb, R.T., Schumacher,S., Mizuuchi, K., Gronenborn, A.M., Glore, G.M. "Solution structure of the I gamma subdomain of the Mu end DNA-binding domain of phage Mu transposase." J Mol Biol 273:1 (1997): 19-25
15. S. Schumacher, Clubb, R.T., M. Cai, Mizuuchi, K., Glore, G.M., Gronenborn, A.M. "Solution structure of the Mu end DNA-binding ibeta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains." [In Process Citation] EMBO J 16(24) (1997): 7532-41
14. Clubb, R.T., Mizuuchi, M., Huth, J.R., Omichinski, J.G., Savilahti, H., Mizuuchi, K., Glore, G.M., Gronenborn, A.M. "The wing of the enhancer-binding domain of Mu phage transposase is flexible and is essential for efficient transposition." PNAS 93(3)(1996): 1146-50
13. Clubb, R.T., Omichinski, J.G., Sakaguchi, K., Appella, E., Gronenborn, A.M., Glore, G.M. "Backbone dynamics of the oligomerization domain of p53 determined from 15N NMR relaxation measurements." Protein Science 4.5 (1995): 855-862
12. Ernst, J.A., Clubb, R.T., Zhou, H.X., Gronenborn, A.M., Glore, G.M.. "Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR [see comments] Science 267(5205)(1995): 1813-7
11. Glore, G.M., J. Ernst, R. Clubb, Omichinski, J.G., Kennedy, W.M., Sakaguchi, K., Appella, E., Gronenborn, A.M. "Refined solution structure of the oligomerization domain of the tumour suppressor p53." [see comments] Nature Structural Biology 2:4 (1995): 321-33
10. Clubb, R.T., Omichinski, J.G., Savilahti, H., Mizuuchi, K., Gronenborn, A.M., Glore, G.M. "A novel class of winged helix-turn-helix protein: the DNA-binding domain of Mu transposase." Structure 2(11)(1994): 1041-8
9. Clubb, R.T., Omichinski, J.G., Glore, G.M., Gronenborn, A.M. "Mapping the binding surface of interleukin-8 complexes with an N- terminal fragment of the type 1 human interleukin-8 receptor." FEBS Lett 338(1)(1994): 93-7
8. Fejzo, J., Etzhorn, F.A., Clubb, R.T., Shi, Y., Walsh, C.T., Wagner, G. "The mutant Escherichia coli F112W cyclophilin binds cyclosporin A in nearly identical conformation as human cyclophilin." Biochemistry 33(19)(1994): 5711-20
7. Clubb, R.T., Ferguson, S.B., Walsh, C.T., Wagner, G. "Three-dimensional solution structure of Escherichia coli periplasmic cyclophilin." Biochemistry 33(10)(1994): 2761-72
6. Clubb, R.T., Thanabal, V., Fejzo, J., Ferguson, S.B., Zydowsky, L., Baker, C.H., Walsh, C.T., Wagner, G. "Secondary structure and backbone resonance assignments of the periplasmic cyclophilin type peptidyl-prolyl isomerase from Escherichia coli." Biochemistry 32(25)(1993): 6391-401
5. Clubb, R.T., Thanabal, V., Wagner, G. "A constant-time 3-dimensional triple-resonance pulse scheme to correlate intraresidue H-1(N), N-15, and C-13(') chemical shifts in N-15-C-13-labeled proteins." J Magn Reson 97(1)(1992): 213-217
4. Clubb, R.T., Thanabal, V., Wagner, G. "A new 3D HN(CA)HA experiment for obtaining fingerprint HN-Halpha peaks in 15N- and 13C-labeled proteins." J Biomol NMR 2(2)(1992): 203-10
3. Clubb, R.T. and Wagner, G. "A triple-resonance pulse scheme for selectively correlating amide 1HN and 15N nuclei with the 1H alpha proton of the preceding residue."J Biomol NMR 2(4)(1992): 389-94
2. Wagner, G., Thanabal, V., Stockman, B.J., Peng, J.W., Nirmala, N.R., Hyberts, S.G., Goldberg, M.S., Detlefsen, D.J., Clubb, R.T., Adler, M. "NMR studies of structure and dynamics of isotope enriched proteins." Biopolymers 32(4)(1992): 381-90
1. Clubb, R.T., Thanabal, V., Osborne, C., Wagner, G. "1H and 15N resonance assignments of oxidized flavodoxin from Anacystis nidulans with 3D NMR." Biochemistry 30(31)(1991): 7718-30
Book Chapters
Connolly, KM., and Clubb, RT. (2005) in Structural biology of bacterial pathogenesis (Waksman, G., Caparon, M., and Hultgren, C., eds), pp. 101-127, ASM Press, Washington DC
Patents
1. U.S. Patent 10,766,923. METHODS AND COMPOSITIONS TO INCREASE THE RATE OF LIGATION REACTIONS CATALYZED BY A SORTASE. September 8, 2020. Inventors: Robert T. Clubb and Brendan Amer
2. U.S. Patent Number 11,634,699.REAGENT TO LABEL PROTEINS VIA LYSINE ISOPEPTIDE BONDS, April 25, 2023. Inventors: Robert T. Clubb, Brendan Rayhan Amer, Janine Y. Fu, Scott McConnell and Hung Ton-That
3. U.S. Provisional Patent. UCLA Case 2020-762-2. MAKING AND USES OF COVALENTLY_LINKED BACTERIAL PILI, Filed: April 8, 2021. Inventors: Hung Ton-That, Chungyu Chang, Nicholas A. Ramirez and Robert T. Clubb
