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Items: 1 to 50 of 65

1.

Substrate Profile of the Phosphotriesterase Homology Protein from Escherichia coli.

Nemmara VV, Xiang DF, Fedorov AA, Fedorov EV, Bonanno JB, Almo SC, Raushel FM.

Biochemistry. 2018 Oct 30;57(43):6219-6227. doi: 10.1021/acs.biochem.8b00935. Epub 2018 Oct 16.

PMID:
30277746
2.

Functional assignment of multiple catabolic pathways for D-apiose.

Carter MS, Zhang X, Huang H, Bouvier JT, Francisco BS, Vetting MW, Al-Obaidi N, Bonanno JB, Ghosh A, Zallot RG, Andersen HM, Almo SC, Gerlt JA.

Nat Chem Biol. 2018 Jul;14(7):696-705. doi: 10.1038/s41589-018-0067-7. Epub 2018 Jun 4.

3.

Comparison of Alicyclobacillus acidocaldarius o-Succinylbenzoate Synthase to Its Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Relatives.

Odokonyero D, McMillan AW, Ramagopal UA, Toro R, Truong DP, Zhu M, Lopez MS, Somiari B, Herman M, Aziz A, Bonanno JB, Hull KG, Burley SK, Romo D, Almo SC, Glasner ME.

Biochemistry. 2018 Jul 3;57(26):3676-3689. doi: 10.1021/acs.biochem.8b00088. Epub 2018 May 30.

PMID:
29767960
4.

Anti-CTLA-4 therapy requires an Fc domain for efficacy.

Ingram JR, Blomberg OS, Rashidian M, Ali L, Garforth S, Fedorov E, Fedorov AA, Bonanno JB, Le Gall C, Crowley S, Espinosa C, Biary T, Keliher EJ, Weissleder R, Almo SC, Dougan SK, Ploegh HL, Dougan M.

Proc Natl Acad Sci U S A. 2018 Apr 10;115(15):3912-3917. doi: 10.1073/pnas.1801524115. Epub 2018 Mar 26.

5.

X-ray and EPR Characterization of the Auxiliary Fe-S Clusters in the Radical SAM Enzyme PqqE.

Barr I, Stich TA, Gizzi AS, Grove TL, Bonanno JB, Latham JA, Chung T, Wilmot CM, Britt RD, Almo SC, Klinman JP.

Biochemistry. 2018 Feb 27;57(8):1306-1315. doi: 10.1021/acs.biochem.7b01097. Epub 2018 Feb 6.

6.

Mechanism and Structure of γ-Resorcylate Decarboxylase.

Sheng X, Patskovsky Y, Vladimirova A, Bonanno JB, Almo SC, Himo F, Raushel FM.

Biochemistry. 2018 Jun 5;57(22):3167-3175. doi: 10.1021/acs.biochem.7b01213. Epub 2018 Jan 19.

7.

Structures of the L27 Domain of Disc Large Homologue 1 Protein Illustrate a Self-Assembly Module.

Ghosh A, Ramagopal UA, Bonanno JB, Brenowitz M, Almo SC.

Biochemistry. 2018 Feb 27;57(8):1293-1305. doi: 10.1021/acs.biochem.7b01074. Epub 2018 Feb 7.

8.

Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1.

Lewis-Ballester A, Pham KN, Batabyal D, Karkashon S, Bonanno JB, Poulos TL, Yeh SR.

Nat Commun. 2017 Nov 22;8(1):1693. doi: 10.1038/s41467-017-01725-8.

9.

Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides.

Grove TL, Himes PM, Hwang S, Yumerefendi H, Bonanno JB, Kuhlman B, Almo SC, Bowers AA.

J Am Chem Soc. 2017 Aug 30;139(34):11734-11744. doi: 10.1021/jacs.7b01283. Epub 2017 Aug 21.

10.

Structural basis for cancer immunotherapy by the first-in-class checkpoint inhibitor ipilimumab.

Ramagopal UA, Liu W, Garrett-Thomson SC, Bonanno JB, Yan Q, Srinivasan M, Wong SC, Bell A, Mankikar S, Rangan VS, Deshpande S, Korman AJ, Almo SC.

Proc Natl Acad Sci U S A. 2017 May 23;114(21):E4223-E4232. doi: 10.1073/pnas.1617941114. Epub 2017 May 8.

11.

Stilbene epoxidation and detoxification in a Photorhabdus luminescens-nematode symbiosis.

Park HB, Sampathkumar P, Perez CE, Lee JH, Tran J, Bonanno JB, Hallem EA, Almo SC, Crawford JM.

J Biol Chem. 2017 Apr 21;292(16):6680-6694. doi: 10.1074/jbc.M116.762542. Epub 2017 Feb 28.

12.

Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex.

Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J.

Structure. 2017 Mar 7;25(3):434-445. doi: 10.1016/j.str.2017.01.006. Epub 2017 Feb 2.

13.

Crystal Structure of the Complex of Human FasL and Its Decoy Receptor DcR3.

Liu W, Ramagopal U, Cheng H, Bonanno JB, Toro R, Bhosle R, Zhan C, Almo SC.

Structure. 2016 Nov 1;24(11):2016-2023. doi: 10.1016/j.str.2016.09.009.

14.

Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase.

Vladimirova A, Patskovsky Y, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Hillerich B, Seidel RD, Richards NG, Almo SC, Raushel FM.

J Am Chem Soc. 2016 Jan 27;138(3):826-36. doi: 10.1021/jacs.5b08251. Epub 2016 Jan 12.

15.

Increased Heterologous Protein Expression in Drosophila S2 Cells for Massive Production of Immune Ligands/Receptors and Structural Analysis of Human HVEM.

Liu W, Vigdorovich V, Zhan C, Patskovsky Y, Bonanno JB, Nathenson SG, Almo SC.

Mol Biotechnol. 2015 Oct;57(10):914-22. doi: 10.1007/s12033-015-9881-2.

PMID:
26202493
16.

Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification.

Kim J, Xiao H, Koh J, Wang Y, Bonanno JB, Thomas K, Babbitt PC, Brown S, Lee YS, Almo SC.

Nucleic Acids Res. 2015 May 19;43(9):4602-13. doi: 10.1093/nar/gkv206. Epub 2015 Apr 8.

17.

Histone H2A and H4 N-terminal tails are positioned by the MEP50 WD repeat protein for efficient methylation by the PRMT5 arginine methyltransferase.

Burgos ES, Wilczek C, Onikubo T, Bonanno JB, Jansong J, Reimer U, Shechter D.

J Biol Chem. 2015 Apr 10;290(15):9674-89. doi: 10.1074/jbc.M115.636894. Epub 2015 Feb 24.

18.

Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.

Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss TM, Shi Y, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Chait BT, Almo SC, Rout MP, Sali A.

Mol Cell Proteomics. 2014 Nov;13(11):2911-26. doi: 10.1074/mcp.M114.040915. Epub 2014 Aug 19.

19.

Mechanistic basis for functional promiscuity in the TNF and TNF receptor superfamilies: structure of the LIGHT:DcR3 assembly.

Liu W, Zhan C, Cheng H, Kumar PR, Bonanno JB, Nathenson SG, Almo SC.

Structure. 2014 Sep 2;22(9):1252-1262. doi: 10.1016/j.str.2014.06.013. Epub 2014 Jul 31.

20.

Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.

Odokonyero D, Sakai A, Patskovsky Y, Malashkevich VN, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Agarwal R, Wang C, Ozerova ND, Yew WS, Sauder JM, Swaminathan S, Burley SK, Almo SC, Glasner ME.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8535-40. doi: 10.1073/pnas.1318703111. Epub 2014 May 28.

21.

Structural context of disease-associated mutations and putative mechanism of autoinhibition revealed by X-ray crystallographic analysis of the EZH2-SET domain.

Antonysamy S, Condon B, Druzina Z, Bonanno JB, Gheyi T, Zhang F, MacEwan I, Zhang A, Ashok S, Rodgers L, Russell M, Gately Luz J.

PLoS One. 2013 Dec 19;8(12):e84147. doi: 10.1371/journal.pone.0084147. eCollection 2013.

22.

Divergent evolution of ligand binding in the o-succinylbenzoate synthase family.

Odokonyero D, Ragumani S, Lopez MS, Bonanno JB, Ozerova ND, Woodard DR, Machala BW, Swaminathan S, Burley SK, Almo SC, Glasner ME.

Biochemistry. 2013 Oct 22;52(42):7512-21. doi: 10.1021/bi401176d. Epub 2013 Oct 9.

23.

Discovery of new enzymes and metabolic pathways by using structure and genome context.

Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt PC, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP.

Nature. 2013 Oct 31;502(7473):698-702. doi: 10.1038/nature12576. Epub 2013 Sep 22.

24.

Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function.

Kim J, Xiao H, Bonanno JB, Kalyanaraman C, Brown S, Tang X, Al-Obaidi NF, Patskovsky Y, Babbitt PC, Jacobson MP, Lee YS, Almo SC.

Nature. 2013 Jun 6;498(7452):123-6. doi: 10.1038/nature12180. Epub 2013 May 15.

25.

Crystal structure of human Karyopherin β2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2.

Soniat M, Sampathkumar P, Collett G, Gizzi AS, Banu RN, Bhosle RC, Chamala S, Chowdhury S, Fiser A, Glenn AS, Hammonds J, Hillerich B, Khafizov K, Love JD, Matikainen B, Seidel RD, Toro R, Rajesh Kumar P, Bonanno JB, Chook YM, Almo SC.

J Struct Funct Genomics. 2013 Jun;14(2):31-5. doi: 10.1007/s10969-013-9150-1. Epub 2013 Mar 28.

26.

Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.

Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL, Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z, Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, Burley SK, Sali A, Rout MP, Almo SC.

Structure. 2013 Apr 2;21(4):560-71. doi: 10.1016/j.str.2013.02.005. Epub 2013 Mar 14.

27.

Structure of the arginine methyltransferase PRMT5-MEP50 reveals a mechanism for substrate specificity.

Ho MC, Wilczek C, Bonanno JB, Xing L, Seznec J, Matsui T, Carter LG, Onikubo T, Kumar PR, Chan MK, Brenowitz M, Cheng RH, Reimer U, Almo SC, Shechter D.

PLoS One. 2013;8(2):e57008. doi: 10.1371/journal.pone.0057008. Epub 2013 Feb 25. Erratum in: PLoS One. 2013;8(8). doi:10.1371/annotation/e6b5348e-9052-4a3b-8f06-90d01dc88fc2.

28.

1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum.

Warlick BP, Evans BS, Erb TJ, Ramagopal UA, Sriram J, Imker HJ, Sauder JM, Bonanno JB, Burley SK, Tabita FR, Almo SC, Sweedler JS, Gerlt JA.

Biochemistry. 2012 Oct 23;51(42):8324-6. doi: 10.1021/bi301215g. Epub 2012 Oct 8.

29.

Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases.

Garside EL, Schellenberg MJ, Gesner EM, Bonanno JB, Sauder JM, Burley SK, Almo SC, Mehta G, MacMillan AM.

RNA. 2012 Nov;18(11):2020-8. doi: 10.1261/rna.033100.112. Epub 2012 Sep 24.

30.

Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex.

Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Burley SK.

Proteins. 2011 May;79(5):1672-7. doi: 10.1002/prot.22973. Epub 2011 Mar 1. No abstract available.

31.

Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR.

Wisedchaisri G, Dranow DM, Lie TJ, Bonanno JB, Patskovsky Y, Ozyurt SA, Sauder JM, Almo SC, Wasserman SR, Burley SK, Leigh JA, Gonen T.

Structure. 2010 Nov 10;18(11):1512-21. doi: 10.1016/j.str.2010.08.014.

32.

Structural bases of PAS domain-regulated kinase (PASK) activation in the absence of activation loop phosphorylation.

Kikani CK, Antonysamy SA, Bonanno JB, Romero R, Zhang FF, Russell M, Gheyi T, Iizuka M, Emtage S, Sauder JM, Turk BE, Burley SK, Rutter J.

J Biol Chem. 2010 Dec 24;285(52):41034-43. doi: 10.1074/jbc.M110.157594. Epub 2010 Oct 13.

33.

Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution.

Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, Burley SK.

Proteins. 2010 Nov 1;78(14):3056-62. doi: 10.1002/prot.22829. No abstract available.

34.

Pnictogen-hydride activation by (silox)3Ta (silox = (t)Bu3SiO); attempts to circumvent the constraints of orbital symmetry in N2 activation.

Hulley EB, Bonanno JB, Wolczanski PT, Cundari TR, Lobkovsky EB.

Inorg Chem. 2010 Sep 20;49(18):8524-44. doi: 10.1021/ic101147x.

PMID:
20722448
35.

Periplasmic domains of Pseudomonas aeruginosa PilN and PilO form a stable heterodimeric complex.

Sampaleanu LM, Bonanno JB, Ayers M, Koo J, Tammam S, Burley SK, Almo SC, Burrows LL, Howell PL.

J Mol Biol. 2009 Nov 20;394(1):143-59. doi: 10.1016/j.jmb.2009.09.037.

PMID:
19857646
36.

Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin.

Leiman PG, Basler M, Ramagopal UA, Bonanno JB, Sauder JM, Pukatzki S, Burley SK, Almo SC, Mekalanos JJ.

Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4154-9. doi: 10.1073/pnas.0813360106. Epub 2009 Feb 27.

37.

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.

Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A.

J Struct Funct Genomics. 2009 Apr;10(2):107-25. doi: 10.1007/s10969-008-9056-5. Epub 2009 Feb 14.

38.

Protein production and purification.

Structural Genomics Consortium; China Structural Genomics Consortium; Northeast Structural Genomics Consortium, Gräslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schütz A, Heinemann U, Yokoyama S, Büssow K, Gunsalus KC.

Nat Methods. 2008 Feb;5(2):135-46. doi: 10.1038/nmeth.f.202. Review. Erratum in: Nat Methods. 2008 Apr;5(4):369. Hallberg, B Martin [added].

39.

Structural genomics of protein phosphatases.

Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR, Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y, Alvarado J, Ramagopal UA, Faber-Barata J, Chance MR, Sali A, Fiser A, Zhang ZY, Lawrence DS, Burley SK.

J Struct Funct Genomics. 2007 Sep;8(2-3):121-40. Epub 2007 Dec 5. Review.

40.

Evidence for strong tantalum-to-boron dative interactions in (silox)3Ta(BH3) and (silox)3Ta(eta2-B,Cl-BCl2Ph) (silox = tBu3SiO)1.

Bonanno JB, Henry TP, Wolczanski PT, Pierpont AW, Cundari TR.

Inorg Chem. 2007 Feb 19;46(4):1222-32. Epub 2007 Jan 24.

PMID:
17249656
41.

Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit.

Rao KN, Bonanno JB, Burley SK, Swaminathan S.

Proteins. 2006 Nov 1;65(2):514-8. No abstract available.

PMID:
16909422
43.

Crystal structure of trehalose-6-phosphate phosphatase-related protein: biochemical and biological implications.

Rao KN, Kumaran D, Seetharaman J, Bonanno JB, Burley SK, Swaminathan S.

Protein Sci. 2006 Jul;15(7):1735-44.

44.

Mechanism of action of a flavin-containing monooxygenase.

Eswaramoorthy S, Bonanno JB, Burley SK, Swaminathan S.

Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9832-7. Epub 2006 Jun 15. Erratum in: Proc Natl Acad Sci U S A. 2007 Sep 4;104(36):14543.

45.

Structure determination of an FMN reductase from Pseudomonas aeruginosa PA01 using sulfur anomalous signal.

Agarwal R, Bonanno JB, Burley SK, Swaminathan S.

Acta Crystallogr D Biol Crystallogr. 2006 Apr;62(Pt 4):383-91. Epub 2006 Mar 18.

46.

Crystal structures of two putative phosphoheptose isomerases.

Seetharaman J, Rajashankar KR, Solorzano V, Kniewel R, Lima CD, Bonanno JB, Burley SK, Swaminathan S.

Proteins. 2006 Jun 1;63(4):1092-6. No abstract available.

47.

Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis.

Seetharaman J, Kumaran D, Bonanno JB, Burley SK, Swaminathan S.

Proteins. 2006 Jun 1;63(4):1087-91. No abstract available.

48.

New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative.

Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, Burley SK.

J Struct Funct Genomics. 2005;6(2-3):225-32.

PMID:
16211523
49.

High-throughput limited proteolysis/mass spectrometry for protein domain elucidation.

Gao X, Bain K, Bonanno JB, Buchanan M, Henderson D, Lorimer D, Marsh C, Reynes JA, Sauder JM, Schwinn K, Thai C, Burley SK.

J Struct Funct Genomics. 2005;6(2-3):129-34.

PMID:
16211509
50.

X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing.

Sickmier EA, Brekasis D, Paranawithana S, Bonanno JB, Paget MS, Burley SK, Kielkopf CL.

Structure. 2005 Jan;13(1):43-54.

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