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Items: 9

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.

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.

3.

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.

4.

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.

5.

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
6.

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.

7.

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
8.

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
9.

(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

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