Cross-Link Guided Molecular Modeling with ROSETTA

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Kahraman, Abdullah ^a   Herzog, Franz ^b   Leitner, Alexander ^a   Rosenberger, George ^a   Aebersold, Ruedi ^a,c   Malmström, Lars ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF MUNICH   (Germany)

^c UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MULTIPROTEIN COMPLEX;

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; MASS SPECTROMETRY; MOLECULAR DOCKING; MOLECULAR MODEL; PREDICTION; PROTEIN CROSS LINKING; PROTEIN DATA BANK; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; XLDB DATABASE;

CRYSTALLOGRAPHY, X-RAY; MASS SPECTROMETRY; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOFTWARE;

EID: 84884228178     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0073411     Document Type: Article

References (44)

1. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, et al. (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature. doi:10.1038/nature11503.
2. Wang X, Wei X, Thijssen B, Das J, Lipkin SM, et al. (2012) Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat Biotechnol 30: 159-164 doi:10.1038/nbt.2106.
3. Edwards A, (2009) Large-Scale Structural Biology of the Human Proteome. Annu Rev Biochem 78: 541-568 doi:10.1146/annurev.biochem.78.070907.103305.
4. Krissinel E, Henrick K, (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-797.
5. Mosca R, Pons C, Fernández-Recio J, Aloy P, (2009) Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments. PLoS Comput Biol 5: e1000490 doi:10.1371/journal.pcbi.1000490.
6. Herzog F, Kahraman A, Boehringer D, Mak R, Bracher A, et al. (2012) Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science 337: 1348-1352 doi:10.1126/science.1221483.
7. Rappsilber J, (2011) The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. Journal of Structural biology 173: 530-540 doi:10.1016/j.jsb.2010.10.014.
8. Chen ZA, Jawhari A, Fischer L, Buchen C, Tahir S, et al. (2010) Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. Embo J 29: 717-726 doi:10.1038/emboj.2009.401.
9. Blattner C, Jennebach S, Herzog F, Mayer A, Cheung ACM, et al. (2011) Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Gene Dev 25: 2093-2105 doi:10.1101/gad.17363311.
10. Bohn S, Beck F, Sakata E, Walzthoeni T, Beck M, et al. (2010) Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution. Proc Natl Acad Sci U S A 107: 20992-20997 doi:10.1073/pnas.1015530107.
11. Lasker K, Forster F, Bohn S, Walzthoeni T, Villa E, et al. (2012) Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach Vol. 109: 1380-1387.
12. Trnka MJ, Burlingame AL, (2010) Topographic Studies of the GroEL-GroES Chaperonin Complex by Chemical Cross-linking Using Diformyl Ethynylbenzene. Mol Cell Proteomics 9: 2306-2317 doi:10.1074/mcp.M110.003764.
13. 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 U S A. doi:10.1073/pnas.1119472109.
14. Leitner A, Joachimiak LA, Bracher A, Mönkemeyer L, Walzthoeni T, et al. (2012) The Molecular Architecture of the Eukaryotic Chaperonin TRiC/CCT. Structure/Folding and Design: 1-12. doi:10.1016/j.str.2012.03.007.
15. Mädler S, Bich C, Touboul D, Zenobi R, (2009) Chemical cross-linking with NHS esters: a systematic study on amino acid reactivities. J Mass Spectrom 44: 694-706 doi:10.1002/jms.1544.
16. Leitner A, Walzthoeni T, Kahraman A, Herzog F, Rinner O, et al. (2010) Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Molecular & cellular proteomics: MCP 9: 1634-1649 doi:10.1074/mcp.R000001-MCP201.
17. Mayne SLN, Patterton H-G, (2011) Bioinformatics tools for the structural elucidation of multi-subunit protein complexes by mass spectrometric analysis of protein-protein cross-links. Brief Bioinform 12: 660-671 doi:10.1093/bib/bbq087.
18. Leitner A, Reischl R, Walzthoeni T, Herzog F, Bohn S, et al. (2012) Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Molecular & cellular proteomics: MCP 11: M111.014126 doi:10.1074/mcp.M111.014126.
19. Luo J, Fishburn J, Hahn S, Ranish J, (2012) An integrated chemical cross-linking and mass spectrometry approach to study protein complex architecture and function. Molecular & cellular proteomics: MCP 11: M111.008318 doi:10.1074/mcp.M111.008318.
20. Paramelle D, Miralles G, Subra G, Martinez J (2013) Chemical cross-linkers for protein structure studies by mass spectrometry. Proteomics. doi:10.1002/pmic.201200305.
21. Yang B, Wu Y-J, Zhu M, Fan S-B, Lin J, et al. (2012) Identification of cross-linked peptides from complex samples. Nat Methods 9: 904-906 doi:10.1038/nmeth.2099.
22. Walzthoeni T, Claassen M, Leitner A, Herzog F, Bohn S, et al. (2012) False discovery rate estimation for cross-linked peptides identified by mass spectrometry. Nat Methods 9: 901-903 doi:doi:10.1038/nmeth.2103.
23. Green N, Reisler E, Houk K, (2001) Quantitative evaluation of the lengths of homobifunctional protein cross-linking reagents used as molecular rulers. Protein Sci 10: 1293-1304.
24. Potluri S, Khan AA, Kuzminykh A, Bujnicki JM, Friedman AM, et al. (2004) Geometric analysis of cross-linkability for protein fold discrimination. Pac Symp Biocomput 9: 447-458.
25. Zelter A, Hoopmann MR, Vernon R, Baker D, MacCoss MJ, et al. (2010) Isotope Signatures Allow Identification of Chemically Cross-Linked Peptides by Mass Spectrometry: A Novel Method to Determine Interresidue Distances in Protein Structures through Cross-Linking. J Proteome Res 9: 3583-3589 doi:10.1021/pr1001115.
26. Kahraman A, Malmström L, Aebersold R, (2011) Xwalk: computing and visualizing distances in cross-linking experiments. Bioinformatics 27: 2163-2164 doi:10.1093/bioinformatics/btr348.
27. Söding J, Biegert A (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res.
28. Rice P, Longden I, Bleasby A, (2000) EMBOSS: The European molecular biology open software suite. Trends Genet 16: 276-277.
29. Kim D, Chivian D, Baker D, (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 32: W526-W531 doi:10.1093/nar/gkh468.
30. Jones D (1999) Protein secondary structure prediction based on position-specific scoring matrices 10.1006/jmbi.1999.3091: Journal of Molecular Biology {pipe} ScienceDirect.com. J Mol Biol.
31. Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
32. Team RDC (2010) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. Available: http://www.R-project.org.
33. Hubbard S, Thornton J (1993) Naccess. Department of Biochemistry and Molecular Biology, University College London: Computer Program.
34. Janin J, Bahadur RP, Chakrabarti P, (2008) Protein-protein interaction and quaternary structure. Q Rev Biophys 41: 133-180 doi:10.1017/S0033583508004708.
35. Kahraman A, Morris RJ, Laskowski RA, Thornton JM, (2007) Shape variation in protein binding pockets and their ligands. J Mol Biol 368: 283-301 doi:10.1016/j.jmb.2007.01.086.
36. Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM, (2010) On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins. Proteins 78: 1120-1136 doi:10.1002/prot.22633.
37. Gray J, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, et al. (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331: 281-299 doi:10.1016/S0022-2836(03)00670-3.
38. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40: D290-D301 doi:10.1093/nar/gkr1065.
39. Hwang H, Vreven T, Janin J, Weng Z, (2010) Protein-protein docking benchmark version 4.0. Proteins 78: 3111-3114 doi:10.1002/prot.22830.
40. Zheng C, Weisbrod CR, Chavez JD, Eng JK, Sharma V, et al. (2013) XLink-DB: Database and Software Tools for Storing and Visualizing Protein Interaction Topology Data. J Proteome Res 12: 1989-1995 doi:10.1021/pr301162j.
41. Baker EN, Anderson BF, Baker HM, Haridas M, Jameson GB, et al. (1991) Structure, function and flexibility of human lactoferrin. International Journal of Biological Macromolecules 13: 122-129.
42. Prickett T, Brautigan D, (2004) Overlapping binding sites in protein phosphatase 2A for association with regulatory A and alpha-4 (mTap42) subunits. J Biol Chem 279: 38912-38920 doi:10.1074/jbc.M401444200.
43. Shih ESC, Hwang M-J, (2012) On the use of distance constraints in protein-protein docking computations. Proteins 80: 194-205 doi:10.1002/prot.23179.
44. DeLano W (2002) The PyMOL Molecular Graphics System.