Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking

Structure

Volumn 20, Issue 3, 2012, Pages 450-463

  Baker, Mariah R ^a   Rees, Ian ^a   Ludtke, Steven J ^a   Chiu, Wah ^a   Baker, Matthew L ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; DATA BASE; ELECTRON MICROSCOPY; MOLECULAR MODEL; PATHWALKING; PRIORITY JOURNAL; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; CRYOELECTRON MICROSCOPY; CRYSTALLOGRAPHY, X-RAY; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MOLECULAR BIOLOGY; PROTEIN FOLDING; SOFTWARE;

EID: 84857925824     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2012.01.008     Document Type: Article

References (50)

1. Abeysinghe, S., Ju, T., Baker, M.L., and Chiu, W. (2008a). Shape modeling and matching in identifying 3D protein structures. Comput. Aided Des. 40, 708-720.
2. Abeysinghe, S.S., and Ju, T. (2009). Interactive skeletonization of intensity volumes. Vis. Comput. 25, 627-635.
3. Abeysinghe, S.S., Baker, M.L., Chiu, W., and Ju, T. (2008b). Segmentation-free skeletonization of grayscale volumes for shape understanding. Proceedings of the IEEE International Conference on Shape Modeling and Applications, 63-71.
4. Alber, F., Dokudovskaya, S., Veenhoff, L.M., Zhang, W., Kipper, J., Devos, D., Suprapto, A., Karni-Schmidt, O., Williams, R., Chait, B.T., et al. (2007). Determining the architectures of macromolecular assemblies. Nature 450, 683-694. (Pubitemid 350207700)
5. Applegate, D.L. (2006). The traveling salesman problem: a computational study (Princeton: Princeton University Press).
6. Baker, M.L., Ju, T., and Chiu, W. (2007). Identification of secondary structure elements in intermediate-resolution density maps. Structure 15, 7-19. (Pubitemid 46073771)
7. Baker, M.L., Zhang, J., Ludtke, S.J., and Chiu, W. (2010a). Cryo-EM of macromolecular assemblies at near-atomic resolution. Nat. Protoc. 5, 1697-1708.
8. Baker, M.L., Baker, M.R., Hryc, C.F., and Dimaio, F. (2010b). Analyses of subnanometer resolution cryo-EM density maps. Methods Enzymol. 483, 1-29.
9. Baker, M.L., Abeysinghe, S.S., Schuh, S., Coleman, R.A., Abrams, A., Marsh, M.P., Hryc, C.F., Ruths, T., Chiu, W., and Ju, T. (2011). Modeling protein structure at near atomic resolutions with Gorgon. J. Struct. Biol. 174, 360-373.
10. Baumeister, W., and Steven, A.C. (2000). Macromolecular electron microscopy in the era of structural genomics. Trends Biochem. Sci. 25, 624-631.
11. Blundell, T.L., and Johnson, L.N. (1976). Protein crystallography (New York: Academic Press).
12. Bradley, P., Malmström, L., Qian, B., Schonbrun, J., Chivian, D., Kim, D.E., Meiler, J., Misura, K.M.S., and Baker, D. (2005). Free modeling with Rosetta in CASP6. Proteins 61 (Suppl 7), 128-134. (Pubitemid 43069966)
13. Chaudhry, C., Horwich, A.L., Brunger, A.T., and Adams, P.D. (2004). Exploring the structural dynamics of the E. coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. J. Mol. Biol. 342, 229-245. (Pubitemid 39094518)
14. Chen, D.H., Baker, M.L., Hryc, C.F., Dimaio, F., Jakana, J., Wu, W., Dougherty, M., Haase-Pettingell, C., Schmid, M.F., Jiang, W., et al. (2011). Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proc. Natl. Acad. Sci. USA 108, 1355-1360.
15. Chiu, W., Baker, M.L., and Almo, S.C. (2006). Structural biology of cellular machines. Trends Cell Biol. 16, 144-150. (Pubitemid 43358002)
16. Cohen, S.X., Morris, R.J., Fernandez, F.J., Ben Jelloul, M., Kakaris, M., Parthasarathy, V., Lamzin, V.S., Kleywegt, G.J., and Perrakis, A. (2004). Towards complete validated models in the next generation of ARP/wARP. Acta Crystallogr. D Biol. Crystallogr. 60, 2222-2229. (Pubitemid 41742774)
17. Cong, Y., Baker, M.L., Jakana, J., Woolford, D., Miller, E.J., Reissmann, S., Kumar, R.N., Redding-Johanson, A.M., Batth, T.S., Mukhopadhyay, A., et al. (2010). 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement. Proc. Natl. Acad. Sci. USA 107, 4967-4972.
18. Cowtan, K. (2006). The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D Biol. Crystallogr. 62, 1002-1011.
19. DiMaio, F., Tyka, M.D., Baker, M.L., Chiu, W., and Baker, D. (2009). Refinement of protein structures into low-resolution density maps using Rosetta. J. Mol. Biol. 392, 181-190.
20. Emsley, P., Lohkamp, B., Scott, W.G., and Cowtan, K. (2010). Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501.
21. Frank, J. (2002). Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 31, 303-319.
22. Grigorieff, N., and Harrison, S.C. (2011). Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy. Curr. Opin. Struct. Biol. 21, 265-273.
23. Helgstrand, C., Wikoff, W.R., Duda, R.L., Hendrix, R.W., Johnson, J.E., and Liljas, L. (2003). The refined structure of a protein catenane: the HK97 bacteriophage capsid at 3.44 A resolution. J. Mol. Biol. 334, 885-899. (Pubitemid 37485678)
24. Helsgaun, K. (2009). General k-opt submoves for the Lin-Kernighan TSP heuristic. Mathematical Programming Computation 1, 119-163.
25. Hryc, C.F., Chen, D.H., and Chiu, W. (2011). Near-atomic resolution cryo-EM for molecular virology. Curr Opin Virol 1, 110-117.
26. Jiang, W., Baker, M.L., Ludtke, S.J., and Chiu, W. (2001). Bridging the information gap: computational tools for intermediate resolution structure interpretation. J. Mol. Biol. 308, 1033-1044. (Pubitemid 32574375)
27. Jiang, W., Baker, M.L., Jakana, J., Weigele, P.R., King, J., and Chiu, W. (2008). Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature 451, 1130-1134. (Pubitemid 351317451)
28. Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119.
29. Ju, T., Baker, M.L., and Chiu, W. (2007). Computing a family of skeletons of volumetric models for shape description. Comput. Aided Des. 39, 352-360. (Pubitemid 46726282)
30. Kleywegt, G.J. (1997). Validation of protein models from Calpha coordinates alone. J. Mol. Biol. 273, 371-376.
31. Lawler, E.L. (1985). The Traveling salesman problem: a guided tour of combinatorial optimization (New York: Wiley).
32. Liu, X., Jiang, W., Jakana, J., and Chiu, W. (2007). Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. J. Struct. Biol. 160, 11-27. (Pubitemid 47405231)
33. Liu, X., Zhang, Q., Murata, K., Baker, M.L., Sullivan, M.B., Fu, C., Dougherty, M.T., Schmid, M.F., Osburne, M.S., Chisholm, S.W., and Chiu, W. (2010). Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nat. Struct. Mol. Biol. 17, 830-836.
34. Ludtke, S.J., Baker, M.L., Chen, D.-H.H., Song, J.-L.L., Chuang, D.T., and Chiu, W. (2008). De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 16, 441-448. (Pubitemid 351324126)
35. Mathieu, M., Petitpas, I., Navaza, J., Lepault, J., Kohli, E., Pothier, P., Prasad, B.V., Cohen, J., and Rey, F.A. (2001). Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion. EMBO J. 20, 1485-1497. (Pubitemid 32299386)
36. Murata, K., Mitsuoka, K., Hirai, T., Walz, T., Agre, P., Heymann, J.B., Engel, A., and Fujiyoshi, Y. (2000). Structural determinants of water permeation through aquaporin-1. Nature 407, 599-605.
37. Nakagawa, A., Miyazaki, N., Taka, J., Naitow, H., Ogawa, A., Fujimoto, Z., Mizuno, H., Higashi, T., Watanabe, Y., Omura, T., et al. (2003). The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins. Structure 11, 1227-1238. (Pubitemid 37214885)
38. Nguyen, M.N., Tan, K.P., and Madhusudhan, M.S. (2011). CLICK-topology-independent comparison of biomolecular 3D structures. Nucleic Acids Res. 39 (Web Server issue), W24-W28.
39. Pereira, J.H., Ralston, C.Y., Douglas, N.R., Meyer, D., Knee, K.M., Goulet, D.R., King, J.A., Frydman, J., and Adams, P.D. (2010). Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J. Biol. Chem. 285, 27958-27966.
40. Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612.
41. Pintilie, G.D., Zhang, J., Goddard, T.D., Chiu, W., and Gossard, D.C. (2010). Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J. Struct. Biol. 170, 427-438.
42. Sali, A., and Kuriyan, J. (1999). Challenges at the frontiers of structural biology. Trends Cell Biol. 9, M20-M24.
43. Sali, A., Glaeser, R., Earnest, T., and Baumeister, W. (2003). From words to literature in structural proteomics. Nature 422, 216-225. (Pubitemid 36362759)
44. Schröder, G.F., Brunger, A.T., and Levitt, M. (2007). Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure 15, 1630-1641. (Pubitemid 350213409)
45. Schuette, J.C., Murphy, F.V., 4th, Kelley, A.C., Weir, J.R., Giesebrecht, J., Connell, S.R., Loerke, J., Mielke, T., Zhang, W., Penczek, P.A., et al. (2009). GTPase activation of elongation factor EF-Tu by the ribosome during decoding. EMBO J. 28, 755-765.
46. Tang, G., Peng, L., Baldwin, P.R., Mann, D.S., Jiang, W., Rees, I., and Ludtke, S.J. (2007). EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38-46. (Pubitemid 44880785)
47. Zhang, J., Baker, M.L., Schröder, G.F., Douglas, N.R., Reissmann, S., Jakana, J., Dougherty, M., Fu, C.J., Levitt, M., Ludtke, S.J., et al. (2010a). Mechanism of folding chamber closure in a group II chaperonin. Nature 463, 379-383.
48. Zhang, X., Settembre, E., Xu, C., Dormitzer, P.R., Bellamy, R., Harrison, S.C., and Grigorieff, N. (2008). Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc. Natl. Acad. Sci. USA 105, 1867-1872. (Pubitemid 351439431)
49. Zhang, X., Jin, L., Fang, Q., Hui, W.H., and Zhou, Z.H. (2010b). 3.3 A cryo-EM structure of a nonenveloped virus reveals a priming mechanism for cell entry. Cell 141, 472-482.
50. Zhou, Z.H. (2008). Towards atomic resolution structural determination by single-particle cryo-electron microscopy. Curr. Opin. Struct. Biol. 18, 218-228.