Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps

Methods in Enzymology

Volumn 579, Issue , 2016, Pages 255-276

  DiMaio, F ^a   Chiu, W ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

CryoEM map derived model; Model optimization; Model validation

Indexed keywords

ALGORITHM; ATOM; CHEMICAL STRUCTURE; CRYOELECTRON MICROSCOPY; GEOMETRY; MACROMOLECULE; MOLECULAR MODEL; NEAR ATOMIC RESOLUTION ELECTRON CRYO MICROSCOPY; NONHUMAN; PROCESS OPTIMIZATION; SOFTWARE; STEREOCHEMISTRY; STRUCTURAL MODEL; BROMOVIRUS; DEVICES; IMAGE PROCESSING; PROCEDURES; PROTEIN CONFORMATION; STATISTICS AND NUMERICAL DATA; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE;

BACTERIAL PROTEIN; BETA GALACTOSIDASE; CAPSID PROTEIN; VIRUS ANTIGEN; VP6 PROTEIN, ROTAVIRUS;

ALGORITHMS; ANTIGENS, VIRAL; BACTERIAL PROTEINS; BETA-GALACTOSIDASE; BROMOVIRUS; CAPSID PROTEINS; CRYOELECTRON MICROSCOPY; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; SOFTWARE;

EID: 85020198001     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/bs.mie.2016.06.003     Document Type: Chapter

References (50)

1. Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., et al. PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica. Section D, Biological Crystallography 66 (2010), 213–221.
2. Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallographica. Section D, Biological Crystallography 68 (2012), 352–367.
3. Baker, M.L., Abeysinghe, S.S., Schuh, S., Coleman, R.A., Abrams, A., Marsh, M.P., et al. Modeling protein structure at near atomic resolutions with Gorgon. Journal of Structural Biology 174 (2011), 360–373.
4. Baker, M.L., Baker, M.R., Hryc, C.F., Ju, T., Chiu, W., Gorgon and pathwalking: Macromolecular modeling tools for subnanometer resolution density maps. Biopolymers 97 (2012), 655–668.
5. Baker, M.L., Hryc, C.F., Zhang, Q., Wu, W., Jakana, J., Haase-Pettingell, C., et al. Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Proceedings of the National Academy of Sciences of the United States of America 110 (2013), 12301–12306.
6. Baker, M.L., Ju, T., Chiu, W., Identification of secondary structure elements in intermediate-resolution density maps. Structure 15 (2007), 7–19.
7. Baker, M.R., Rees, I., Ludtke, S.J., Chiu, W., Baker, M.L., Constructing and validating initial Calpha models from subnanometer resolution density maps with pathwalking. Structure 20 (2012), 450–463.
8. Barad, B.A., Echols, N., Wang, R.Y., Cheng, Y., DiMaio, F., Adams, P.D., et al. EMRinger: Side chain-directed model and map validation for 3D cryo-electron microscopy. Nature Methods 12 (2015), 943–946.
9. Brown, A., Long, F., Nicholls, R.A., Toots, J., Emsley, P., Murshudov, G., Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions. Acta Crystallographica. Section D, Biological Crystallography 71 (2015), 136–153.
10. Brunger, A.T., Rice, L.M., Crystallographic refinement by simulated annealing: Methods and applications. Methods in Enzymology 277 (1997), 243–269.
11. Chen, V.B., Arendall, W.B. 3rd, Headd, J.J., Keedy, D.A., Immormino, R.M., Kapral, G.J., et al. MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallographica. Section D, Biological Crystallography 66 (2010), 12–21.
12. Chen M., Baldwin P. R., Ludtke S. J., & Baker M. L. (2016). De novo modeling of cryo-EM density maps with pathwalker, Journal of Structural Biology, (in press).
13. Chen, D.H., Madan, D., Weaver, J., Lin, Z., Schroder, G.F., Chiu, W., et al. Visualizing GroEL/ES in the act of encapsulating a folding protein. Cell 153 (2013), 1354–1365.
14. Chen, S., McMullan, G., Faruqi, A.R., Murshudov, G.N., Short, J.M., Scheres, S.H., et al. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135C (2013), 24–35.
15. Cole, C., Barber, J.D., Barton, G.J., The Jpred 3 secondary structure prediction server. Nucleic Acids Research 36 (2008), W197–W201.
16. Cowtan, K., The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallographica. Section D, Biological Crystallography 62 (2006), 1002–1011.
17. DiMaio, F., Song, Y., Li, X., Brunner, M.J., Xu, C., Conticello, V., et al. Atomic-accuracy models from 4.5-A cryo-electron microscopy data with density-guided iterative local refinement. Nature Methods 12 (2015), 361–365.
18. DiMaio, F., Zhang, J., Chiu, W., Baker, D., Cryo-EM model validation using independent map reconstructions. Protein Science: A Publication of the Protein Society 22 (2013), 865–868.
19. Emsley, P., Lohkamp, B., Scott, W.G., Cowtan, K., Features and development of Coot. Acta Crystallographica. Section D, Biological Crystallography 66 (2010), 486–501.
20. Falkner, B., Schroder, G.F., Cross-validation in cryo-EM-based structural modeling. Proceedings of the National Academy of Sciences of the United States of America 110 (2013), 8930–8935.
21. Fan, G., Baker, M.L., Wang, Z., Baker, M.R., Sinyagovskiy, P.A., Chiu, W., et al. Gating machinery of InsP3R channels revealed by electron cryomicroscopy. Nature 527 (2015), 336–341.
22. Galkin, V.E., Orlova, A., Vos, M.R., Schroder, G.F., Egelman, E.H., Near-atomic resolution for one state of F-actin. Structure 23 (2015), 173–182.
23. Headd, J.J., Echols, N., Afonine, P.V., Grosse-Kunstleve, R.W., Chen, V.B., Moriarty, N.W., et al. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallographica. Section D, Biological Crystallography 68 (2012), 381–390.
24. Henderson, R., Overview and future of single particle electron cryomicroscopy. Archives of Biochemistry and Biophysics 581 (2015), 19–24.
25. Henderson, R., Sali, A., Baker, M.L., Carragher, B., Devkota, B., Downing, K.H., et al. Outcome of the first electron microscopy validation task force meeting. Structure 20 (2012), 205–214.
26. Jiang, W., Baker, M.L., Jakana, J., Weigele, P.R., King, J., Chiu, W., Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature 451 (2008), 1130–1134.
27. Jiang, W., Baker, M.L., Ludtke, S.J., Chiu, W., Bridging the information gap: Computational tools for intermediate resolution structure interpretation. Journal of Molecular Biology 308 (2001), 1033–1044.
28. Kelley, L.A., Sternberg, M.J., Protein structure prediction on the Web: A case study using the Phyre server. Nature Protocols 4 (2009), 363–371.
29. Kudryashev, M., Wang, R.Y., Brackmann, M., Scherer, S., Maier, T., Baker, D., et al. Structure of the type VI secretion system contractile sheath. Cell 160 (2015), 952–962.
30. Kuhlbrandt, W., Biochemistry. The resolution revolution. Science 343 (2014), 1443–1444.
31. Lasker, K., Topf, M., Sali, A., Wolfson, H.J., Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. Journal of Molecular Biology 388 (2009), 180–194.
32. Lindert, S., Staritzbichler, R., Wotzel, N., Karakas, M., Stewart, P.L., Meiler, J., EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. Structure 17 (2009), 990–1003.
33. Nicholls, R.A., Long, F., Murshudov, G.N., Low-resolution refinement tools in REFMAC5. Acta Crystallographica. Section D, Biological Crystallography 68 (2012), 404–417.
34. Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., et al. UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry 25 (2004), 1605–1612.
35. Pintilie, G.D., Chen, D.H., Haase-Pettingell, C.A., King, J.A., Chiu, W., Resolution and probabilistic models of components in CryoEM maps of mature P22 bacteriophage. Biophysical Journal 110 (2016), 827–839.
36. Pintilie, G., Zhang, J., Chiu, W., Gossard, D., Identifying components in 3D density maps of protein nanomachines by multi-scale segmentation. IEEE/NIH Life Science Systems and Applications Workshop 2009 (2009), 44–47.
37. Pintilie, G.D., Zhang, J., Goddard, T.D., Chiu, W., Gossard, D.C., Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. Journal of Structural Biology 170 (2010), 427–438.
38. Rosenthal, P.B., Henderson, R., Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology 333 (2003), 721–745.
39. Scheres, S.H., Chen, S., Prevention of overfitting in cryo-EM structure determination. Nature Methods 9 (2012), 853–854.
40. Schroder, G.F., Levitt, M., Brunger, A.T., Super-resolution biomolecular crystallography with low-resolution data. Nature 464 (2010), 1218–1222.
41. Terwilliger, T.C., Read, R.J., Adams, P.D., Brunger, A.T., Afonine, P.V., Grosse-Kunstleve, R.W., et al. Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement. Acta Crystallographica. Section D, Biological Crystallography 68 (2012), 861–870.
42. Topf, M., Baker, M.L., Marti-Renom, M.A., Chiu, W., Sali, A., Refinement of protein structures by Iterative comparative modeling and cryoEM density fitting. Journal of Molecular Biology 357 (2006), 1655–1668.
43. Topf, M., Lasker, K., Webb, B., Wolfson, H., Chiu, W., Sali, A., Protein structure fitting and refinement guided by Cryo-EM density. Structure 16 (2008), 295–307.
44. Trabuco, L.G., Villa, E., Mitra, K., Frank, J., Schulten, K., Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16 (2008), 673–683.
45. Walls, A.C., Tortorici, M.A., Bosch, B.J., Frenz, B., Rottier, P.J., DiMaio, F., et al. Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer. Nature 531 (2016), 114–117.
46. Wang, Z., Hryc, C.F., Bammes, B., Afonine, P.V., Jakana, J., Chen, D.H., et al. An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Nature Communications, 5, 2014, 4808.
47. Wang, R.Y., Kudryashev, M., Li, X., Egelman, E.H., Basler, M., Cheng, Y., et al. De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nature Methods 12 (2015), 335–338.
48. Webb, B., Sali, A., Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics/Editoral Board, Andreas D Baxevanis [et al.] 47 (2014), 5.6.1–5.6.32.
49. Wriggers, W., Chacon, P., Modeling tricks and fitting techniques for multiresolution structures. Structure 9 (2001), 779–788.
50. Zhao, G., Perilla, J.R., Yufenyuy, E.L., Meng, X., Chen, B., Ning, J., et al. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 497 (2013), 643–646.