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Items: 1 to 50 of 118

1.

Tools for 3D Interactome Visualization.

Keller A, Chavez JD, Eng JK, Thornton Z, Bruce JE.

J Proteome Res. 2019 Feb 1;18(2):753-758. doi: 10.1021/acs.jproteome.8b00703. Epub 2018 Dec 18.

PMID:
30520642
2.

Elusive Conformational Dynamics of PPARĪ³ Inactivation Tied Down by Chemical Cross-Linking.

Mohr JP, Bruce JE.

Structure. 2018 Nov 6;26(11):1425-1427. doi: 10.1016/j.str.2018.10.015.

PMID:
30403991
3.

Chemical cross-linking with mass spectrometry: a tool for systems structural biology.

Chavez JD, Bruce JE.

Curr Opin Chem Biol. 2019 Feb;48:8-18. doi: 10.1016/j.cbpa.2018.08.006. Epub 2018 Aug 30. Review.

PMID:
30172868
4.

Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks.

Keller A, Chavez JD, Bruce JE.

Bioinformatics. 2019 Mar 1;35(5):895-897. doi: 10.1093/bioinformatics/bty720.

PMID:
30137231
5.

Parallel detection in a single ICR cell: Spectral averaging and improved S/N without increased acquisition time.

Park SG, Anderson GA, Bruce JE.

Int J Mass Spectrom. 2018 Apr;427:29-34. doi: 10.1016/j.ijms.2017.08.020. Epub 2017 Sep 8.

PMID:
29731686
6.

Characterization of Harmonic Signal Acquisition with Parallel Dipole and Multipole Detectors.

Park SG, Anderson GA, Bruce JE.

J Am Soc Mass Spectrom. 2018 Jul;29(7):1394-1402. doi: 10.1007/s13361-018-1954-6. Epub 2018 Apr 24.

PMID:
29691781
7.

Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification.

Mohr JP, Perumalla P, Chavez JD, Eng JK, Bruce JE.

Anal Chem. 2018 May 15;90(10):6028-6034. doi: 10.1021/acs.analchem.7b04991. Epub 2018 Apr 27.

PMID:
29676898
8.

Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.

Vreven T, Schweppe DK, Chavez JD, Weisbrod CR, Shibata S, Zheng C, Bruce JE, Weng Z.

J Mol Biol. 2018 Jun 8;430(12):1814-1828. doi: 10.1016/j.jmb.2018.04.010. Epub 2018 Apr 14.

PMID:
29665372
9.

Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue.

Chavez JD, Lee CF, Caudal A, Keller A, Tian R, Bruce JE.

Cell Syst. 2018 Jan 24;6(1):136-141.e5. doi: 10.1016/j.cels.2017.10.017. Epub 2017 Nov 29.

10.

Intrinsic disorder within AKAP79 fine-tunes anchored phosphatase activity toward substrates and drug sensitivity.

Nygren PJ, Mehta S, Schweppe DK, Langeberg LK, Whiting JL, Weisbrod CR, Bruce JE, Zhang J, Veesler D, Scott JD.

Elife. 2017 Oct 2;6. pii: e30872. doi: 10.7554/eLife.30872.

11.

Ageing and hypoxia cause protein aggregation in mitochondria.

Kaufman DM, Wu X, Scott BA, Itani OA, Van Gilst MR, Bruce JE, Crowder CM.

Cell Death Differ. 2017 Oct;24(10):1730-1738. doi: 10.1038/cdd.2017.101. Epub 2017 Jun 23.

12.

Insights in luteovirid structural biology guided by chemical cross-linking and high resolution mass spectrometry.

Alexander MM, Mohr JP, DeBlasio SL, Chavez JD, Ziegler-Graff V, Brault V, Bruce JE, Heck MC.

Virus Res. 2017 Sep 15;241:42-52. doi: 10.1016/j.virusres.2017.05.005. Epub 2017 May 11.

PMID:
28502641
13.

Restoring Cystic Fibrosis Transmembrane Conductance Regulator Function Reduces Airway Bacteria and Inflammation in People with Cystic Fibrosis and Chronic Lung Infections.

Hisert KB, Heltshe SL, Pope C, Jorth P, Wu X, Edwards RM, Radey M, Accurso FJ, Wolter DJ, Cooke G, Adam RJ, Carter S, Grogan B, Launspach JL, Donnelly SC, Gallagher CG, Bruce JE, Stoltz DA, Welsh MJ, Hoffman LR, McKone EF, Singh PK.

Am J Respir Crit Care Med. 2017 Jun 15;195(12):1617-1628. doi: 10.1164/rccm.201609-1954OC.

14.

Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers.

Zhong X, Navare AT, Chavez JD, Eng JK, Schweppe DK, Bruce JE.

J Proteome Res. 2017 Feb 3;16(2):720-727. doi: 10.1021/acs.jproteome.6b00752. Epub 2016 Nov 30.

15.

Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry.

Schweppe DK, Chavez JD, Lee CF, Caudal A, Kruse SE, Stuppard R, Marcinek DJ, Shadel GS, Tian R, Bruce JE.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1732-1737. doi: 10.1073/pnas.1617220114. Epub 2017 Jan 27.

16.

Parallel Spectral Acquisition with Orthogonal ICR Cells.

Park SG, Anderson GA, Bruce JE.

J Am Soc Mass Spectrom. 2017 Mar;28(3):515-524. doi: 10.1007/s13361-016-1573-z. Epub 2017 Jan 5.

17.

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.

Chavez JD, Eng JK, Schweppe DK, Cilia M, Rivera K, Zhong X, Wu X, Allen T, Khurgel M, Kumar A, Lampropoulos A, Larsson M, Maity S, Morozov Y, Pathmasiri W, Perez-Neut M, Pineyro-Ruiz C, Polina E, Post S, Rider M, Tokmina-Roszyk D, Tyson K, Vieira Parrine Sant'Ana D, Bruce JE.

PLoS One. 2016 Dec 20;11(12):e0167547. doi: 10.1371/journal.pone.0167547. eCollection 2016.

18.

In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075.

Wu X, Chavez JD, Schweppe DK, Zheng C, Weisbrod CR, Eng JK, Murali A, Lee SA, Ramage E, Gallagher LA, Kulasekara HD, Edrozo ME, Kamischke CN, Brittnacher MJ, Miller SI, Singh PK, Manoil C, Bruce JE.

Nat Commun. 2016 Nov 11;7:13414. doi: 10.1038/ncomms13414.

19.

Normalization of NAD+ Redox Balance as a Therapy for Heart Failure.

Lee CF, Chavez JD, Garcia-Menendez L, Choi Y, Roe ND, Chiao YA, Edgar JS, Goo YA, Goodlett DR, Bruce JE, Tian R.

Circulation. 2016 Sep 20;134(12):883-94. doi: 10.1161/CIRCULATIONAHA.116.022495. Epub 2016 Aug 3.

20.

InĀ Vivo Conformational Dynamics of Hsp90 and Its Interactors.

Chavez JD, Schweppe DK, Eng JK, Bruce JE.

Cell Chem Biol. 2016 Jun 23;23(6):716-26. doi: 10.1016/j.chembiol.2016.05.012.

21.

XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data.

Schweppe DK, Zheng C, Chavez JD, Navare AT, Wu X, Eng JK, Bruce JE.

Bioinformatics. 2016 Sep 1;32(17):2716-8. doi: 10.1093/bioinformatics/btw232. Epub 2016 Apr 29.

22.

Spectral Library Searching To Identify Cross-Linked Peptides.

Schweppe DK, Chavez JD, Navare AT, Wu X, Ruiz B, Eng JK, Lam H, Bruce JE.

J Proteome Res. 2016 May 6;15(5):1725-31. doi: 10.1021/acs.jproteome.6b00014. Epub 2016 Apr 28.

23.

Parallel Spectral Acquisition with an Ion Cyclotron Resonance Cell Array.

Park SG, Anderson GA, Navare AT, Bruce JE.

Anal Chem. 2016 Jan 19;88(2):1162-8. doi: 10.1021/acs.analchem.5b02987. Epub 2015 Dec 24.

24.

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology.

DeBlasio SL, Chavez JD, Alexander MM, Ramsey J, Eng JK, Mahoney J, Gray SM, Bruce JE, Cilia M.

J Virol. 2015 Dec 9;90(4):1973-87. doi: 10.1128/JVI.01706-15. Print 2016 Feb 15.

25.

Host-Microbe Protein Interactions during Bacterial Infection.

Schweppe DK, Harding C, Chavez JD, Wu X, Ramage E, Singh PK, Manoil C, Bruce JE.

Chem Biol. 2015 Nov 19;22(11):1521-1530. doi: 10.1016/j.chembiol.2015.09.015. Epub 2015 Nov 5.

26.

XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.

Schweppe DK, Chavez JD, Bruce JE.

Bioinformatics. 2016 Jan 15;32(2):306-8. doi: 10.1093/bioinformatics/btv519. Epub 2015 Sep 26.

27.

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs.

Jorth P, Staudinger BJ, Wu X, Hisert KB, Hayden H, Garudathri J, Harding CL, Radey MC, Rezayat A, Bautista G, Berrington WR, Goddard AF, Zheng C, Angermeyer A, Brittnacher MJ, Kitzman J, Shendure J, Fligner CL, Mittler J, Aitken ML, Manoil C, Bruce JE, Yahr TL, Singh PK.

Cell Host Microbe. 2015 Sep 9;18(3):307-19. doi: 10.1016/j.chom.2015.07.006. Epub 2015 Aug 20.

28.

Quantitative interactome analysis reveals a chemoresistant edgotype.

Chavez JD, Schweppe DK, Eng JK, Zheng C, Taipale A, Zhang Y, Takara K, Bruce JE.

Nat Commun. 2015 Aug 3;6:7928. doi: 10.1038/ncomms8928.

29.

Dynamic Proteome Response of Pseudomonas aeruginosa to Tobramycin Antibiotic Treatment.

Wu X, Held K, Zheng C, Staudinger BJ, Chavez JD, Weisbrod CR, Eng JK, Singh PK, Manoil C, Bruce JE.

Mol Cell Proteomics. 2015 Aug;14(8):2126-37. doi: 10.1074/mcp.M115.050161. Epub 2015 May 27.

30.

Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry.

Navare AT, Chavez JD, Zheng C, Weisbrod CR, Eng JK, Siehnel R, Singh PK, Manoil C, Bruce JE.

Structure. 2015 Apr 7;23(4):762-73. doi: 10.1016/j.str.2015.01.022. Epub 2015 Mar 19.

31.

Analysis of the Campylobacter jejuni genome by SMRT DNA sequencing identifies restriction-modification motifs.

O'Loughlin JL, Eucker TP, Chavez JD, Samuelson DR, Neal-McKinney J, Gourley CR, Bruce JE, Konkel ME.

PLoS One. 2015 Feb 19;10(2):e0118533. doi: 10.1371/journal.pone.0118533. eCollection 2015.

32.

Role of the tumor suppressor IQGAP2 in metabolic homeostasis: Possible link between diabetes and cancer.

Vaitheesvaran B, Hartil K, Navare A, Zheng, OBroin P, Golden A, Guha, Lee W, Kurland IJ, Bruce JE.

Metabolomics. 2014 Oct 1;10(5):920-937.

33.

Evidence for lysine acetylation in the coat protein of a polerovirus.

Cilia M, Johnson R, Sweeney M, DeBlasio SL, Bruce JE, MacCoss MJ, Gray SM.

J Gen Virol. 2014 Oct;95(Pt 10):2321-7. doi: 10.1099/vir.0.066514-0. Epub 2014 Jun 17.

34.

Solid-phase N-terminal peptide enrichment study by optimizing trypsin proteolysis on homoarginine-modified proteins by mass spectrometry.

Chowdhury SM, Munske GR, Yang J, Zhukova D, Nguyen H, Bruce JE.

Rapid Commun Mass Spectrom. 2014 Mar 30;28(6):635-44. doi: 10.1002/rcm.6820.

35.

Performance evaluation of a dual linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer for proteomics research.

Weisbrod CR, Hoopmann MR, Senko MW, Bruce JE.

J Proteomics. 2013 Aug 2;88:109-19. doi: 10.1016/j.jprot.2013.04.009. Epub 2013 Apr 13.

36.

In vivo protein interaction network identified with a novel real-time cross-linked peptide identification strategy.

Weisbrod CR, Chavez JD, Eng JK, Yang L, Zheng C, Bruce JE.

J Proteome Res. 2013 Apr 5;12(4):1569-79. doi: 10.1021/pr3011638. Epub 2013 Feb 28.

37.

XLink-DB: database and software tools for storing and visualizing protein interaction topology data.

Zheng C, Weisbrod CR, Chavez JD, Eng JK, Sharma V, Wu X, Bruce JE.

J Proteome Res. 2013 Apr 5;12(4):1989-95. doi: 10.1021/pr301162j. Epub 2013 Mar 5.

38.

Protein interactions, post-translational modifications and topologies in human cells.

Chavez JD, Weisbrod CR, Zheng C, Eng JK, Bruce JE.

Mol Cell Proteomics. 2013 May;12(5):1451-67. doi: 10.1074/mcp.M112.024497. Epub 2013 Jan 25.

39.

In vivo protein complex topologies: sights through a cross-linking lens.

Bruce JE.

Proteomics. 2012 May;12(10):1565-75. doi: 10.1002/pmic.201100516. Review.

40.

Peripheral effects of FAAH deficiency on fuel and energy homeostasis: role of dysregulated lysine acetylation.

Vaitheesvaran B, Yang L, Hartil K, Glaser S, Yazulla S, Bruce JE, Kurland IJ.

PLoS One. 2012;7(3):e33717. doi: 10.1371/journal.pone.0033717. Epub 2012 Mar 19.

41.

Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions.

Chavez JD, Cilia M, Weisbrod CR, Ju HJ, Eng JK, Gray SM, Bruce JE.

J Proteome Res. 2012 May 4;11(5):2968-81. doi: 10.1021/pr300041t. Epub 2012 Mar 30.

42.

Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification.

Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE.

J Proteome Res. 2012 Mar 2;11(3):1621-32. doi: 10.1021/pr2008175. Epub 2012 Feb 21.

43.

In vivo application of photocleavable protein interaction reporter technology.

Yang L, Zheng C, Weisbrod CR, Tang X, Munske GR, Hoopmann MR, Eng JK, Bruce JE.

J Proteome Res. 2012 Feb 3;11(2):1027-41. doi: 10.1021/pr200775j. Epub 2012 Jan 9.

44.

AKAP2 anchors PKA with aquaporin-0 to support ocular lens transparency.

Gold MG, Reichow SL, O'Neill SE, Weisbrod CR, Langeberg LK, Bruce JE, Gonen T, Scott JD.

EMBO Mol Med. 2012 Jan;4(1):15-26. doi: 10.1002/emmm.201100184. Epub 2011 Nov 16.

45.

SILACtor: software to enable dynamic SILAC studies.

Hoopmann MR, Chavez JD, Bruce JE.

Anal Chem. 2011 Nov 15;83(22):8403-10. doi: 10.1021/ac2017053. Epub 2011 Oct 27.

46.

The fasted/fed mouse metabolic acetylome: N6-acetylation differences suggest acetylation coordinates organ-specific fuel switching.

Yang L, Vaitheesvaran B, Hartil K, Robinson AJ, Hoopmann MR, Eng JK, Kurland IJ, Bruce JE.

J Proteome Res. 2011 Sep 2;10(9):4134-49. doi: 10.1021/pr200313x. Epub 2011 Aug 16.

47.

Cross-linking measurements of in vivo protein complex topologies.

Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE.

Mol Cell Proteomics. 2011 Oct;10(10):M110.006841. doi: 10.1074/mcp.M110.006841. Epub 2011 Jun 22.

48.

Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells.

Chavez JD, Hoopmann MR, Weisbrod CR, Takara K, Bruce JE.

PLoS One. 2011;6(5):e19892. doi: 10.1371/journal.pone.0019892. Epub 2011 May 26.

49.

Architecture and dynamics of an A-kinase anchoring protein 79 (AKAP79) signaling complex.

Gold MG, Stengel F, Nygren PJ, Weisbrod CR, Bruce JE, Robinson CV, Barford D, Scott JD.

Proc Natl Acad Sci U S A. 2011 Apr 19;108(16):6426-31. doi: 10.1073/pnas.1014400108. Epub 2011 Apr 4.

50.

Quantification of protein-protein interactions with chemical cross-linking and mass spectrometry.

Chavez JD, Liu NL, Bruce JE.

J Proteome Res. 2011 Apr 1;10(4):1528-37. doi: 10.1021/pr100898e. Epub 2011 Feb 18.

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