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Chemical cross-linking coupled with mass spectrometry (CXMS) identifies protein residues that are close in space, and has been increasingly used for modeling the structures of protein complexes. Here we show that a single structure is usually sufficient to account for the intermolecular cross-links identified for a stable complex with sub-µmol/L binding affinity. In contrast, we show that the distance between two cross-linked residues in the different subunits of a transient or fleeting complex may exceed the maximum length of the cross-linker used, and the cross-links cannot be fully accounted for with a unique complex structure. We further show that the seemingly incompatible cross-links identified with high confidence arise from alternative modes of protein-protein interactions. By converting the intermolecular cross-links to ambiguous distance restraints, we established a rigid-body simulated annealing refinement protocol to seek the minimum set of conformers collectively satisfying the CXMS data. Hence we demonstrate that CXMS allows the depiction of the ensemble structures of protein complexes and elucidates the interaction dynamics for transient and fleeting complexes.
Baumli S, Lolli G, Lowe ED, Troiani S, Rusconi L, Bullock AN, Debreczeni JE, Knapp S, Johnson LN, (2008) The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation.EMBO J 27:1907-1918
Berg OG, Winter RB, Von Hippel PH, (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.Biochemistry (Mosc) 20:6929-6948
Fawzi NL, Doucleff M, Suh JY, Clore GM, (2010) Mechanistic details of a protein–protein association pathway revealed by paramagnetic relaxation enhancement titration measurements.Proc Natl Acad Sci USA 107:1379-1384
Gabdoulline RR, Wade RC, (2002) Biomolecular diffusional association.Curr Opin Struct Biol 12:204-213
Garrett DS, Seok YJ, Peterkofsky A, Gronenborn AM, Clore GM, (1999) Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr.Nat Struct Biol 6:166-173
Herzog F, Kahraman A, Boehringer D, Mak R, Bracher A, Walzthoeni T, Leitner A, Beck M, Hartl FU, Ban N, Malmstrom L, Aebersold R, (2012) Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry.Science 337:1348-1352
Jiang L, Stanevich V, Satyshur KA, Kong M, Watkins GR, Wadzinski BE, Sengupta R, Xing Y, (2013) Structural basis of protein phosphatase 2A stable latency.Nat Commun 4:1699
Jones S, Thornton JM, (1996) Principles of protein–protein interactions.Proc Natl Acad Sci USA 93:13-20
Kahraman A, Malmstrom L, Aebersold R, (2011) Xwalk: computing and visualizing distances in cross-linking experiments.Bioinformatics 27:2163-2164
Kahraman A, Herzog F, Leitner A, Rosenberger G, Aebersold R, Malmstrom L, (2013) Cross-link guided molecular modeling with ROSETTA.PLoS One 8:e73411
Kalisman N, Adams CM, Levitt M, (2012) Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling.Proc Natl Acad Sci USA 109:2884-2889
Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J, (2011) A structure-based benchmark for protein–protein binding affinity.Protein Sci 20:482-491
Lasker K, Forster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W, (2012) Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach.Proc Natl Acad Sci USA 109:1380-1387
Lee YJ, (2009) Probability-based shotgun cross-linking sites analysis.J Am Soc Mass Spectrom 20:1896-1899
Leitner A, Joachimiak LA, Unverdorben P, Walzthoeni T, Frydman J, Forster F, Aebersold R, (2014) Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes.Proc Natl Acad Sci USA 111:9455-9460
Liu Z, Zhang WP, Xing Q, Ren X, Liu M, Tang C, (2012) Noncovalent dimerization of ubiquitin.Angew Chem Int Ed Engl 51:469-472
Liu Z, Gong Z, Dong X, Tang C, (2016) Transient protein–protein interactions visualized by solution NMR.Biochim Biophys Acta 1864(1):115-122
Lossl P, Kolbel K, Tanzler D, Nannemann D, Ihling CH, Keller MV, Schneider M, Zaucke F, Meiler J, Sinz A, (2014) Analysis of nidogen-1/laminin gamma1 interaction by cross-linking, mass spectrometry, and computational modeling reveals multiple binding modes.PLoS One 9:e112886
Marquart M, Walter J, Deisenhofer J, Bode W, Huber R, (1983) The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors.Acta Crystallogr B 39:480-490
Merkley ED, Rysavy S, Kahraman A, Hafen RP, Daggett V, Adkins JN, (2014) Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine–lysine distances.Protein Sci 23:747-759
Nilges M, (1995) Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities.J Mol Biol 245:645-660
Nooren IM, Thornton JM, (2003) Diversity of protein–protein interactions.EMBO J 22:3486-3492
Petrotchenko EV, Serpa JJ, Makepeace KA, Brodie NI, Borchers CH, (2014) (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.J Proteomics 109:104-110
Plaschka C, Lariviere L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P, (2015) Architecture of the RNA polymerase II-Mediator core initiation complex.Nature 518:376-380
Politis A, Stengel F, Hall Z, Hernandez H, Leitner A, Walzthoeni T, Robinson CV, Aebersold R, (2014) A mass spectrometry-based hybrid method for structural modeling of protein complexes.Nat Methods 11:403-406
Rappsilber J, (2011) The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes.J Struct Biol 173:530-540
Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M, Schmidt A, Mueller M, Aebersold R, (2008) Identification of cross-linked peptides from large sequence databases.Nat Methods 5:315-318
Schilder J, Ubbink M, (2013) Formation of transient protein complexes.Curr Opin Struct Biol 23:911-918
Schmidt C, Robinson CV, (2014) Dynamic protein ligand interactions—insights from MS.FEBS J 281:1950-1964
Schreiber G, Fersht AR, (1996) Rapid, electrostatically assisted association of proteins.Nat Struct Biol 3:427-431
Schwieters CD, Clore GM, (2002) Reweighted atomic densities to represent ensembles of NMR structures.J Biomol NMR 23:221-225
Schwieters CD, Kuszewski JJ, Clore GM, (2006) Using Xplor-NIH for NMR molecular structure determination.Prog Nucl Magn Reson Spectrosc 48:47-62
Suh JY, Tang C, Clore GM, (2007) Role of electrostatic interactions in transient encounter complexes in protein–protein association investigated by paramagnetic relaxation enhancement.J Am Chem Soc 129:12954-12955
Tang C, Iwahara J, Clore GM, (2006) Visualization of transient encounter complexes in protein–protein association.Nature 444:383-386
Tang C, Louis JM, Aniana A, Suh JY, Clore GM, (2008) Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease.Nature 455:U692-U693
Taverner T, Hall NE, O’Hair RA, Simpson RJ, (2002) Characterization of an antagonist interleukin-6 dimer by stable isotope labeling, cross-linking, and mass spectrometry.J Biol Chem 277:46487-46492
Thalassinos K, Pandurangan AP, Xu M, Alber F, Topf M, (2013) Conformational states of macromolecular assemblies explored by integrative structure calculation.Structure 21:1500-1508
Vijay-Kumar S, Bugg CE, Cook WJ, (1987) Structure of ubiquitin refined at 1.8 A resolution.J Mol Biol 194:531-544
Vinogradova O, Qin J, (2012) NMR as a unique tool in assessment and complex determination of weak protein–protein interactions.Top Curr Chem 326:35-45
Walzthoeni T, Leitner A, Stengel F, Aebersold R, (2013) Mass spectrometry supported determination of protein complex structure.Curr Opin Struct Biol 23:252-260
Xing Q, Huang P, Yang J, Sun JQ, Gong Z, Dong X, Guo DC, Chen SM, Yang YH, Wang Y, Yang MH, Yi M, Ding YM, Liu ML, Zhang WP, Tang C, (2014) Visualizing an ultra-weak protein–protein interaction in phosphorylation signaling.Angew Chem Int Ed Engl 53:11501-11505
Yang B, Wu YJ, Zhu M, Fan SB, Lin J, Zhang K, Li S, Chi H, Li YX, Chen HF, Luo SK, Ding YH, Wang LH, Hao Z, Xiu LY, Chen S, Ye K, He SM, Dong MQ, (2012) Identification of cross-linked peptides from complex samples.Nat Methods 9:904-906
Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE, (2011) Cross-linking measurements of in vivo protein complex topologies.Mol Cell Proteomics 10:M110 006841
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