Beta-sheet detection and representation from medium resolution Cryo-EM density maps

2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013

Volumn , Issue , 2013, Pages 764-770

  Si, Dong ^a   He, Jing ^a  

^a ECS Building   (United States)

Author keywords

3d surface; Beta sheet; Electron cryo microscopy; Helix; Local structure tensor; Local thickness; Polynomial model; Protein; Secondary structure; Skeleton

Indexed keywords

3D SURFACE; BETA-SHEET; ELECTRON CRYO MICROSCOPIES; HELIX; LOCAL STRUCTURE TENSORS; LOCAL THICKNESS; POLYNOMIAL MODELING; SECONDARY STRUCTURES; SKELETON;

MATHEMATICAL MODELS; MEDICAL IMAGING; PROTEINS; THREE DIMENSIONAL;

BIOINFORMATICS;

EID: 84888176775     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/2506583.2506707     Document Type: Conference Paper

References (38)

1. Bottcher, B., Wynne, S. A. and Crowther, R. A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature, 386, 6620 (Mar 6 1997), 88-91.
2. Mancini, E. J., Clarke, M., Gowen, B. E., Rutten, T. and Fuller, S. D. Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus. Mol Cell, 5, 2 (Feb 2000), 255-266.
3. Zhou, Z. H., Dougherty, M., Jakana, J., He, J., Rixon, F. J. and Chiu, W. Seeing the herpesvirus capsid at 8.5 A. Science, 288, 5467 (May 5 2000), 877-880.
4. van Heel, M., Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, M. and Patwardhan, A. Single-particle electron cryo-microscopy: Towards atomic resolution. Quarterly reviews of biophysics, 33, 4 (Nov 2000), 307-369.
5. Zhou, Z. H. Towards atomic resolution structural determination by single-particle cryo-electron microscopy. Curr Opin Struct Biol, 18, 2 (Apr 2008), 218-228.
6. Hryc, C . F ., Chen, D. H. and C hiu, W . N ear-Atomic- Resolution Cryo-EM for Molecular Virology. Curr Opin Virol, 1, 2 (Aug 1 2011), 110-117.
7. Zhang, R., Hryc, C. F., Cong, Y., Liu, X. G., Jakana, J., Gorchakov, R., Baker, M. L., Weaver, S. C. and Chiu, W. 4.4 angstrom cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus. Embo J, 30, 18 (Sep 14 2011), 3854-3863.
8. Settembre, E. C., Chen, J. Z., Dormitzer, P. R., Grigorieff, N. and Harrison, S. C. Atomic model of an infectious rotavirus particle. Embo J, 30, 2 (Jan 19 2011), 408-416.
9. Daban, J. R. Electron microscopy and atomic force microscopy studies of chromatin and metaphase chromosome structure. Micron, 42, 8 (Dec 2011), 733-750.
10. Grigorieff, N. and Harrison, S. C. Near-atomic resolution reconstructions of icosahedral viruses from electron cryomicroscopy. Curr Opin Struct Biol, 21, 2 (Apr 2011), 265-273.
11. Chiu, W., Baker, M. L., Jiang, W., Dougherty, M. and Schmid, M. F. Electron cryomicroscopy of biological machines at subnanometer resolution. Structure, 13, 3 (Mar 2005), 363-372.
12. Zhou, Z. H. Atomic resolution cryo electron microscopy of macromolecular complexes. Advances in protein chemistry and structural biology, 82(Apr 2011), 1-35.
13. Lawson, C. L., Baker, M. L., Best, C., Bi, C., Dougherty, M., Feng, P., van Ginkel, G., Devkota, B., Lagerstedt, I., Ludtke, S. J., Newman, R. H., Oldfield, T. J., Rees, I., Sahni, G., Sala, R., Velankar, S., Warren, J., Westbrook, J. D., Henrick, K., Kleywegt, G. J., Berman, H. M. and Chiu, W. EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res, 39, Database issue (Jan 2011), 456-464.
14. Al Nasr, K., Ranjan, D., Zubair, M. and He, J. Ranking Valid Topologies of the Secondary Structure Elements Using a Constraint Graph. J Bioinform Comput B, 9, 3 (Jun 2011), 415- 430.
15. Lindert, S., Alexander, N., Wotzel, N., Karakas, M., Stewart, P. L. and Meiler, J. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps. Structure, 20, 3 (Mar 7 2012), 464-478.
16. 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. Modeling protein structure at near atomic resolutions with Gorgon. J Struct Biol, 174, 2 (May 2011), 360-373.
17. Jiang, W., Baker, M. L., Ludtke, S. J. and Chiu, W. Bridging the information gap: computational tools for intermediate resolution structure interpretation. J Mol Biol, 308, 5 (May 18 2001), 1033-1044.
18. Del Palu, A., He, J., Pontelli, E. and Lu, Y. Identification of Alpha-Helices from Low Resolution Protein Density Maps. Computational systems bioinformatics/Life Sciences Society. Computational Systems Bioinformatics Conference(2006), 89-98.
19. Baker, M. L., Ju, T. and Chiu, W. Identification of secondary structure elements in intermediate-resolution density maps. Structure, 15, 1 (Jan 2007), 7-19.
20. Lasker, K., Dror, O., Shatsky, M., Nussinov, R. and Wolfson, H. J. EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps. IEEE/ACM Trans Comput Biol Bioinform, 4, 1 (Jan-Mar 2007), 28-39.
21. Yu, Z. and Bajaj, C. Computational approaches for automatic structural analysis of large biomolecular complexes. IEEE/ACM Trans Comput Biol Bioinform, 5, 4 (Oct-Dec 2008), 568-582.
22. Ma, L ., Reisert, M. and Burkhardt, H.R ENNSH: A N ovel alpha-Helices Identification Approach for Intermediate Resolution Electron Density Maps. IEEE/ACM Trans Comput Biol Bioinform, 9, 1 (Jan-Feb 2011), 228-239.
23. Rusu, M. and Wriggers, W. Evolutionary bidirectional expansion for the tracing of alpha helices in cryo-electron microscopy reconstructions. J Struct Biol, 177, 2 (Feb 2012), 410- 419.
24. Si, D., Ji, S., Nasr, K. A. and He, J . A machine l earning approach for the identification of protein secondary structure elements from electron cryo-microscopy density maps. Biopolymers, 97, 9 (Sep 2012), 698-708.
25. Bajaj, C., Goswami, S. and Zhang, Q. Detection of secondary and supersecondary structures of proteins from cryo-electron microscopy. J Struct Biol, 177, 2 (Feb 2012), 367-381.
26. Kong, Y. and Ma, J. A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps. J Mol Biol, 332, 2 (Sep 12 2003), 399-413.
27. Pauling, L. and Corey, R. B. The pleated sheet, a new layer configuration of polypeptide chains. Proceedings of the National Academy of Sciences of the United States of America, 37, 5 (May 1951), 251-256.
28. Chothia, C. Conformation of twisted beta-pleated sheets in proteins. J Mol Biol, 75, 2 (Apr 5 1973), 295-302.
29. Salemme, F. R. Conformational and geometrical properties of beta-sheets in proteins. III. Isotropically stressed configurations. J Mol Biol, 146, 1 (Feb 15 1981), 143-156.
30. Novotny, J., Bruccoleri, R. E. and Newell, J. Twisted hyperboloid (Strophoid) as a model of beta-barrels in proteins. J Mol Biol, 177, 3 (Aug 15 1984), 567-573.
31. Znamenskiy, D., Le Tuan, K., Poupon, A., Chomilier, J. and Mornon, J. P. Beta-sheet modeling by helical surfaces. Protein engineering, 13, 6 (Jun 2000), 407-412.
32. Koh, E. and Kim, T. Minimal surfaceas a model of betasheets. Proteins, 61, 3 (Nov 15 2005), 559-569.
33. Ju, T ., Baker, M. L. and Chiu, W . Computing a f amily o f skeletons of volumetric models for shape description. Comput Aided Des, 39, 5 (May 2007), 352-360.
34. Fernandez, J. J. and Li, S. An improved algorithm for anisotropic nonlinear diffusion for denoising cryo-tomograms. J Struct Biol, 144, 1-2 (Oct-Nov 2003), 152-161.
35. Hildebrand, T. and Ruegsegger, P. A new method for the model-independent assessment of thickness in three-dimensional images. J Microsc-Oxford, 185(Jan 1997), 67-75.
36. Saito, T. and Toriwaki, J. I. New Algorithms for Euclidean Distance Transformation of an N-Dimensional Digitized Picture with Applications. Pattern Recogn, 27, 11 (Nov 1994), 1551- 1565.
37. Taylor, W. R. and Aszodi, A. Protein geometry, classification, topology and symmetry : A computational analysis of structure. Institute of Physics Pub., Bristol, 2005.
38. Ludtke, S. J., Baldwin, P. R. and Chiu, W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol, 128, 1 (Dec 1 1999), 82-97.