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Items: 49

1.

Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations.

Makepeace KAT, Brodie NI, Popov KI, Gudavicius G, Nelson CJ, Petrotchenko EV, Dokholyan NV, Borchers CH.

J Proteomics. 2020 Jan 16;211:103544. doi: 10.1016/j.jprot.2019.103544. Epub 2019 Nov 1.

2.

Insight into the Structure of the "Unstructured" Tau Protein.

Popov KI, Makepeace KAT, Petrotchenko EV, Dokholyan NV, Borchers CH.

Structure. 2019 Nov 5;27(11):1710-1715.e4. doi: 10.1016/j.str.2019.09.003. Epub 2019 Oct 15.

PMID:
31628033
3.

MeCP2-E1 isoform is a dynamically expressed, weakly DNA-bound protein with different protein and DNA interactions compared to MeCP2-E2.

Martínez de Paz A, Khajavi L, Martin H, Claveria-Gimeno R, Tom Dieck S, Cheema MS, Sanchez-Mut JV, Moksa MM, Carles A, Brodie NI, Sheikh TI, Freeman ME, Petrotchenko EV, Borchers CH, Schuman EM, Zytnicki M, Velazquez-Campoy A, Abian O, Hirst M, Esteller M, Vincent JB, Malnou CE, Ausió J.

Epigenetics Chromatin. 2019 Oct 10;12(1):63. doi: 10.1186/s13072-019-0298-1.

4.

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.

Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A.

Anal Chem. 2019 Jun 4;91(11):6953-6961. doi: 10.1021/acs.analchem.9b00658. Epub 2019 May 22.

5.

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations.

Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH.

PLoS Comput Biol. 2019 Mar 27;15(3):e1006859. doi: 10.1371/journal.pcbi.1006859. eCollection 2019 Mar.

6.

Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation.

Brodie NI, Huguet R, Zhang T, Viner R, Zabrouskov V, Pan J, Petrotchenko EV, Borchers CH.

Anal Chem. 2018 Mar 6;90(5):3079-3082. doi: 10.1021/acs.analchem.7b03655. Epub 2018 Feb 1.

PMID:
29336549
7.

The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module.

Dilworth D, Upadhyay SK, Bonnafous P, Edoo AB, Bourbigot S, Pesek-Jardim F, Gudavicius G, Serpa JJ, Petrotchenko EV, Borchers CH, Nelson CJ, Mackereth CD.

Nucleic Acids Res. 2017 Nov 16;45(20):11989-12004. doi: 10.1093/nar/gkx852.

8.

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.

Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH.

Sci Adv. 2017 Jul 7;3(7):e1700479. doi: 10.1126/sciadv.1700479. eCollection 2017 Jul.

9.

The novel isotopically coded short-range photo-reactive crosslinker 2,4,6-triazido-1,3,5-triazine (TATA) for studying protein structures.

Brodie NI, Petrotchenko EV, Borchers CH.

J Proteomics. 2016 Oct 21;149:69-76. doi: 10.1016/j.jprot.2016.02.024. Epub 2016 Feb 28.

PMID:
26931439
10.

Expression and purification of the full murine NPM2 and study of its interaction with protamines and histones.

Ellard K, Serpa JJ, Petrotchenko EV, Borchers CH, Ausió J.

Biochem Biophys Rep. 2016 Apr 8;6:165-171. doi: 10.1016/j.bbrep.2016.04.002. eCollection 2016 Jul.

11.

Protein unfolding as a switch from self-recognition to high-affinity client binding.

Groitl B, Horowitz S, Makepeace KAT, Petrotchenko EV, Borchers CH, Reichmann D, Bardwell JCA, Jakob U.

Nat Commun. 2016 Jan 20;7:10357. doi: 10.1038/ncomms10357.

12.

HDX match software for the data analysis of top-down ECD-FTMS hydrogen/deuterium exchange experiments.

Petrotchenko EV, Borchers CH.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1895-8. doi: 10.1007/s13361-015-1213-z. Epub 2015 Jul 11.

PMID:
26162650
13.

Comprehensive identification of disulfide bonds using non-specific proteinase K digestion and CID-cleavable crosslinking analysis methodology for Orbitrap LC/ESI-MS/MS data.

Makepeace KA, Serpa JJ, Petrotchenko EV, Borchers CH.

Methods. 2015 Nov 1;89:74-8. doi: 10.1016/j.ymeth.2015.02.021. Epub 2015 Mar 6.

PMID:
25752848
14.

Structure of EspB from the ESX-1 type VII secretion system and insights into its export mechanism.

Solomonson M, Setiaputra D, Makepeace KAT, Lameignere E, Petrotchenko EV, Conrady DG, Bergeron JR, Vuckovic M, DiMaio F, Borchers CH, Yip CK, Strynadka NCJ.

Structure. 2015 Mar 3;23(3):571-583. doi: 10.1016/j.str.2015.01.002. Epub 2015 Feb 12.

15.

Architecture of the RNA polymerase II-Mediator core initiation complex.

Plaschka C, Larivière L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P.

Nature. 2015 Feb 19;518(7539):376-80. doi: 10.1038/nature14229. Epub 2015 Feb 4.

PMID:
25652824
16.

DXMSMS Match Program for Automated Analysis of LC-MS/MS Data Obtained Using Isotopically Coded CID-Cleavable Cross-Linking Reagents.

Petrotchenko EV, Makepeace KA, Borchers CH.

Curr Protoc Bioinformatics. 2014 Dec 12;48:8.18.1-19. doi: 10.1002/0471250953.bi0818s48.

PMID:
25501944
17.

Isotopically-coded short-range hetero-bifunctional photo-reactive crosslinkers for studying protein structure.

Brodie NI, Makepeace KA, Petrotchenko EV, Borchers CH.

J Proteomics. 2015 Apr 6;118:12-20. doi: 10.1016/j.jprot.2014.08.012. Epub 2014 Sep 2.

PMID:
25192908
18.

Modern mass spectrometry-based structural proteomics.

Petrotchenko EV, Borchers CH.

Adv Protein Chem Struct Biol. 2014;95:193-213. doi: 10.1016/B978-0-12-800453-1.00006-3.

PMID:
24985773
19.

(14)N(15)N DXMSMS Match program for the automated analysis of LC/ESI-MS/MS crosslinking data from experiments using (15)N metabolically labeled proteins.

Petrotchenko EV, Serpa JJ, Makepeace KA, Brodie NI, Borchers CH.

J Proteomics. 2014 Sep 23;109:104-10. doi: 10.1016/j.jprot.2014.06.014. Epub 2014 Jun 25.

PMID:
24972318
20.

Application of a fast sorting algorithm to the assignment of mass spectrometric cross-linking data.

Petrotchenko EV, Borchers CH.

Proteomics. 2014 Sep;14(17-18):1987-9. doi: 10.1002/pmic.201300486. Epub 2014 Jul 10.

PMID:
24895266
21.

The prolyl isomerase, FKBP25, interacts with RNA-engaged nucleolin and the pre-60S ribosomal subunit.

Gudavicius G, Dilworth D, Serpa JJ, Sessler N, Petrotchenko EV, Borchers CH, Nelson CJ.

RNA. 2014 Jul;20(7):1014-22. doi: 10.1261/rna.042648.113. Epub 2014 May 19.

22.

Analysis of protein structure by cross-linking combined with mass spectrometry.

Petrotchenko EV, Makepeace KA, Serpa JJ, Borchers CH.

Methods Mol Biol. 2014;1156:447-63. doi: 10.1007/978-1-4939-0685-7_30.

PMID:
24792007
23.

Super Spy variants implicate flexibility in chaperone action.

Quan S, Wang L, Petrotchenko EV, Makepeace KA, Horowitz S, Yang J, Zhang Y, Borchers CH, Bardwell JC.

Elife. 2014;3:e01584. doi: 10.7554/eLife.01584. Epub 2014 Feb 4.

24.

"Out-gel" tryptic digestion procedure for chemical cross-linking studies with mass spectrometric detection.

Petrotchenko EV, Serpa JJ, Cabecinha AN, Lesperance M, Borchers CH.

J Proteome Res. 2014 Feb 7;13(2):527-35. doi: 10.1021/pr400710q. Epub 2014 Jan 3.

PMID:
24354799
25.

Using isotopically-coded hydrogen peroxide as a surface modification reagent for the structural characterization of prion protein aggregates.

Serpa JJ, Makepeace KA, Borchers TH, Wishart DS, Petrotchenko EV, Borchers CH.

J Proteomics. 2014 Apr 4;100:160-6. doi: 10.1016/j.jprot.2013.11.020. Epub 2013 Dec 3.

PMID:
24316355
26.

Model of the Mediator middle module based on protein cross-linking.

Larivière L, Plaschka C, Seizl M, Petrotchenko EV, Wenzeck L, Borchers CH, Cramer P.

Nucleic Acids Res. 2013 Nov;41(20):9266-73. doi: 10.1093/nar/gkt704. Epub 2013 Aug 11.

27.

Structural and biochemical characterization of Plasmodium falciparum 12 (Pf12) reveals a unique interdomain organization and the potential for an antiparallel arrangement with Pf41.

Tonkin ML, Arredondo SA, Loveless BC, Serpa JJ, Makepeace KA, Sundar N, Petrotchenko EV, Miller LH, Grigg ME, Boulanger MJ.

J Biol Chem. 2013 May 3;288(18):12805-17. doi: 10.1074/jbc.M113.455667. Epub 2013 Mar 19.

28.

Using multiple structural proteomics approaches for the characterization of prion proteins.

Serpa JJ, Patterson AP, Pan J, Han J, Wishart DS, Petrotchenko EV, Borchers CH.

J Proteomics. 2013 Apr 9;81:31-42. doi: 10.1016/j.jprot.2012.10.008. Epub 2012 Oct 17.

PMID:
23085224
29.

Mass spectrometry-based structural proteomics.

Serpa JJ, Parker CE, Petrotchenko EV, Han J, Pan J, Borchers CH.

Eur J Mass Spectrom (Chichester). 2012;18(2):251-67. doi: 10.1255/ejms.1178. Review.

PMID:
22641729
30.

Use of proteinase K nonspecific digestion for selective and comprehensive identification of interpeptide cross-links: application to prion proteins.

Petrotchenko EV, Serpa JJ, Hardie DB, Berjanskii M, Suriyamongkol BP, Wishart DS, Borchers CH.

Mol Cell Proteomics. 2012 Jul;11(7):M111.013524. doi: 10.1074/mcp.M111.013524. Epub 2012 Mar 21.

31.

MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain.

Thambirajah AA, Ng MK, Frehlick LJ, Li A, Serpa JJ, Petrotchenko EV, Silva-Moreno B, Missiaen KK, Borchers CH, Adam Hall J, Mackie R, Lutz F, Gowen BE, Hendzel M, Georgel PT, Ausió J.

Nucleic Acids Res. 2012 Apr;40(7):2884-97. doi: 10.1093/nar/gkr1066. Epub 2011 Dec 5.

32.
33.

Crosslinking combined with mass spectrometry for structural proteomics.

Petrotchenko EV, Borchers CH.

Mass Spectrom Rev. 2010 Nov-Dec;29(6):862-76. doi: 10.1002/mas.20293. Review.

PMID:
20730915
34.

An isotopically coded CID-cleavable biotinylated cross-linker for structural proteomics.

Petrotchenko EV, Serpa JJ, Borchers CH.

Mol Cell Proteomics. 2011 Feb;10(2):M110.001420. doi: 10.1074/mcp.M110.001420. Epub 2010 Jul 9.

35.

ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite.

Petrotchenko EV, Borchers CH.

BMC Bioinformatics. 2010 Jan 28;11:64. doi: 10.1186/1471-2105-11-64.

36.
37.

BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics.

Petrotchenko EV, Xiao K, Cable J, Chen Y, Dokholyan NV, Borchers CH.

Mol Cell Proteomics. 2009 Feb;8(2):273-86. doi: 10.1074/mcp.M800265-MCP200. Epub 2008 Oct 6.

38.

Inhibition of APCCdh1 activity by Cdh1/Acm1/Bmh1 ternary complex formation.

Dial JM, Petrotchenko EV, Borchers CH.

J Biol Chem. 2007 Feb 23;282(8):5237-48. Epub 2006 Dec 18.

39.

Combining fluorescence detection and mass spectrometric analysis for comprehensive and quantitative analysis of redox-sensitive cysteines in native membrane proteins.

Petrotchenko EV, Pasek D, Elms P, Dokholyan NV, Meissner G, Borchers CH.

Anal Chem. 2006 Dec 1;78(23):7959-66.

PMID:
17134128
40.

Combined top-down and bottom-up proteomics identifies a phosphorylation site in stem-loop-binding proteins that contributes to high-affinity RNA binding.

Borchers CH, Thapar R, Petrotchenko EV, Torres MP, Speir JP, Easterling M, Dominski Z, Marzluff WF.

Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3094-9. Epub 2006 Feb 21.

41.

Isotopically coded cleavable cross-linker for studying protein-protein interaction and protein complexes.

Petrotchenko EV, Olkhovik VK, Borchers CH.

Mol Cell Proteomics. 2005 Aug;4(8):1167-79. Epub 2005 May 18.

42.
43.

Crystal structure of the human estrogen sulfotransferase-PAPS complex: evidence for catalytic role of Ser137 in the sulfuryl transfer reaction.

Pedersen LC, Petrotchenko E, Shevtsov S, Negishi M.

J Biol Chem. 2002 May 17;277(20):17928-32. Epub 2002 Mar 7.

44.

Structure and function of sulfotransferases.

Negishi M, Pedersen LG, Petrotchenko E, Shevtsov S, Gorokhov A, Kakuta Y, Pedersen LC.

Arch Biochem Biophys. 2001 Jun 15;390(2):149-57. Review.

PMID:
11396917
45.

Crystal structure-based studies of cytosolic sulfotransferase.

Yoshinari K, Petrotchenko EV, Pedersen LC, Negishi M.

J Biochem Mol Toxicol. 2001;15(2):67-75. Review.

PMID:
11284047
46.

The dimerization motif of cytosolic sulfotransferases.

Petrotchenko EV, Pedersen LC, Borchers CH, Tomer KB, Negishi M.

FEBS Lett. 2001 Feb 9;490(1-2):39-43.

47.

Crystal structure of SULT2A3, human hydroxysteroid sulfotransferase.

Pedersen LC, Petrotchenko EV, Negishi M.

FEBS Lett. 2000 Jun 9;475(1):61-4.

48.

Substrate gating confers steroid specificity to estrogen sulfotransferase.

Petrotchenko EV, Doerflein ME, Kakuta Y, Pedersen LC, Negishi M.

J Biol Chem. 1999 Oct 15;274(42):30019-22.

49.

The sulfuryl transfer mechanism. Crystal structure of a vanadate complex of estrogen sulfotransferase and mutational analysis.

Kakuta Y, Petrotchenko EV, Pedersen LC, Negishi M.

J Biol Chem. 1998 Oct 16;273(42):27325-30.

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