Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2017, Article ID 1793213, 9 pages
https://doi.org/10.1155/2017/1793213
Research Article

Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps

1Division of Computing and Software Systems, University of Washington Bothell, Bothell, WA 98011, USA
2Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA

Correspondence should be addressed to Jing He; ude.udo.sc@ehj

Received 15 September 2016; Accepted 8 December 2016; Published 10 January 2017

Academic Editor: Slavica Jonic

Copyright © 2017 Dong Si and Jing He. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. W. Chiu, M. L. Baker, W. Jiang, M. Dougherty, and M. F. Schmid, “Electron cryomicroscopy of biological machines at subnanometer resolution,” Structure, vol. 13, no. 3, pp. 363–372, 2005. View at Publisher · View at Google Scholar · View at Scopus
  2. Z. H. Zhou, “Atomic resolution cryo electron microscopy of macromolecular complexes,” Advances in Protein Chemistry and Structural Biology, vol. 82, pp. 1–35, 2011. View at Publisher · View at Google Scholar · View at Scopus
  3. Z. Liu, F. Guo, F. Wang, T.-C. Li, and W. Jiang, “2.9 Å resolution cryo-EM 3D reconstruction of close-packed virus particles,” Structure, vol. 24, no. 2, pp. 319–328, 2016. View at Publisher · View at Google Scholar · View at Scopus
  4. A. Bartesaghi, A. Merk, S. Banerjee et al., “2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor,” Science, vol. 348, no. 6239, pp. 1147–1151, 2015. View at Publisher · View at Google Scholar · View at Scopus
  5. M. G. Rossmann, “Fitting atomic models into electron-microscopy maps,” Acta Crystallographica Section D: Biological Crystallography, vol. 56, no. 10, pp. 1341–1349, 2000. View at Publisher · View at Google Scholar · View at Scopus
  6. L. G. Trabuco, E. Villa, K. Mitra, J. Frank, and K. Schulten, “Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics,” Structure, vol. 16, no. 5, pp. 673–683, 2008. View at Publisher · View at Google Scholar · View at Scopus
  7. G. F. Schröder, A. T. Brunger, and M. Levitt, “Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution,” Structure, vol. 15, no. 12, pp. 1630–1641, 2007. View at Publisher · View at Google Scholar · View at Scopus
  8. K.-Y. Chan, L. G. Trabuco, E. Schreiner, and K. Schulten, “Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method,” Biopolymers, vol. 97, no. 9, pp. 678–686, 2012. View at Publisher · View at Google Scholar · View at Scopus
  9. M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu, and A. Sali, “Protein structure fitting and refinement guided by cryo-EM density,” Structure, vol. 16, no. 2, pp. 295–307, 2008. View at Publisher · View at Google Scholar · View at Scopus
  10. K. Al Nasr, D. Ranjan, M. Zubair, L. Chen, and J. He, “Solving the secondary structure matching problem in de novo modeling using a constrained K-shortest path graph algorithm,” IEEE Transaction of Computational Biology and Bioinformatics, vol. 11, no. 2, pp. 419–430, 2014. View at Publisher · View at Google Scholar
  11. M. L. Baker, S. S. Abeysinghe, S. Schuh et al., “Modeling protein structure at near atomic resolutions with Gorgon,” Journal of Structural Biology, vol. 174, no. 2, pp. 360–373, 2011. View at Publisher · View at Google Scholar · View at Scopus
  12. S. Lindert, N. Alexander, N. Wötzel, M. Karakaş, P. L. Stewart, and J. Meiler, “EM-Fold: de novo atomic-detail protein structure determination from medium-resolution density maps,” Structure, vol. 20, no. 3, pp. 464–478, 2012. View at Publisher · View at Google Scholar · View at Scopus
  13. K. Al Nasr and J. He, “Constrained cyclic coordinate descent—beyond the protein loop closure problem,” Robotica, vol. 34, no. 8, pp. 1777–1790, 2016. View at Google Scholar
  14. D. Si, S. Ji, K. A. Nasr, and J. He, “A machine learning approach for the identification of protein secondary structure elements from electron cryo-microscopy density maps,” Biopolymers, vol. 97, no. 9, pp. 698–708, 2012. View at Publisher · View at Google Scholar · View at Scopus
  15. A. Biswas, D. Si, K. Al Nasr, D. Ranjan, M. Zubair, and J. He, “Improved efficiency in Cryo-Em secondary structure topology determination from inaccurate data,” Journal of Bioinformatics and Computational Biology, vol. 10, no. 3, Article ID 1242006, 2012. View at Publisher · View at Google Scholar · View at Scopus
  16. A. Biswas, D. Ranjan, M. Zubair, S. Zeil, K. Al Nasr, and J. He, “An effective computational method incorporating multiple secondary structure predictions in topology determination for cryo-EM images,” in Proceedings of the IEEE/ACM Transactions on Computational Biology and Bioinformatics, March 2016. View at Publisher · View at Google Scholar · View at Scopus
  17. K. Al Nasr, D. Ranjan, M. Zubair, and J. He, “Ranking valid topologies of the secondary structure elements using a constraint graph,” Journal of Bioinformatics and Computational Biology, vol. 9, no. 3, pp. 415–430, 2011. View at Publisher · View at Google Scholar · View at Scopus
  18. W. Jiang, M. L. Baker, S. J. Ludtke, and W. Chiu, “Bridging the information gap: computational tools for intermediate resolution structure interpretation,” Journal of Molecular Biology, vol. 308, no. 5, pp. 1033–1044, 2001. View at Publisher · View at Google Scholar · View at Scopus
  19. A. Dal Palu, J. He, E. Pontelli, and Y. Lu, “Identification of α-helices from low resolution protein density maps,” in Proceeding of the Computational Systems Bioinformatics Conference(CSB '06), pp. 89–98, 2006.
  20. M. L. Baker, T. Ju, and W. Chiu, “Identification of secondary structure elements in intermediate-resolution density maps,” Structure, vol. 15, no. 1, pp. 7–19, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. M. Rusu and W. Wriggers, “Evolutionary bidirectional expansion for the tracing of alpha helices in cryo-electron microscopy reconstructions,” Journal of Structural Biology, vol. 177, no. 2, pp. 410–419, 2012. View at Publisher · View at Google Scholar · View at Scopus
  22. Z. Yu and C. Bajaj, “Computational approaches for automatic structural analysis of large biomolecular complexes,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, no. 4, pp. 568–582, 2008. View at Publisher · View at Google Scholar · View at Scopus
  23. Y. Kong and J. Ma, “A structural-informatics approach for mining β-sheets: locating sheets in intermediate-resolution density maps,” Journal of Molecular Biology, vol. 332, no. 2, pp. 399–413, 2003. View at Publisher · View at Google Scholar · View at Scopus
  24. D. Si and J. He, “Beta-sheet detection and representation from medium resolution cryo-EM density maps,” in Proceedings of the 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (BCB '13), pp. 764–770, ACM, September 2013. View at Publisher · View at Google Scholar · View at Scopus
  25. J. He, D. Si, and M. Arab, “Detection of secondary structures from 3D protein images of medium resolutions and its challenges,” in Image and Graphics: 8th International Conference, ICIG 2015, Tianjin, China, August 13–16, 2015, Proceedings, Part II, vol. 9218 of Lecture Notes in Computer Science, pp. 147–155, Springer, Berlin, Germany, 2015. View at Publisher · View at Google Scholar
  26. Z. H. Zhou, “Towards atomic resolution structural determination by single-particle cryo-electron microscopy,” Current Opinion in Structural Biology, vol. 18, no. 2, pp. 218–228, 2008. View at Publisher · View at Google Scholar · View at Scopus
  27. M. L. Baker, M. R. Baker, C. F. Hryc, T. Ju, and W. Chiu, “Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps,” Biopolymers, vol. 97, no. 9, pp. 655–668, 2012. View at Publisher · View at Google Scholar · View at Scopus
  28. D. Si and J. He, “Tracing beta strands using strandtwister from cryo-EM density maps at medium resolutions,” Structure, vol. 22, no. 11, pp. 1665–1676, 2014. View at Publisher · View at Google Scholar · View at Scopus
  29. C. Chothia, “Conformation of twisted β-pleated sheets in proteins,” Journal of Molecular Biology, vol. 75, no. 2, pp. 295–302, 1973. View at Publisher · View at Google Scholar · View at Scopus
  30. J. S. Richardson, “The anatomy and taxonomy of protein structure,” Advances in Protein Chemistry, vol. 34, pp. 167–339, 1981. View at Publisher · View at Google Scholar · View at Scopus
  31. J. S. Richardson and D. C. Richardson, “Interpretation of electron density maps,” Methods in Enzymology, vol. 115, pp. 189–206, 1985. View at Publisher · View at Google Scholar · View at Scopus
  32. V. Cherezov, W. Liu, J. P. Derrick et al., “In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin,” Proteins: Structure, Function and Genetics, vol. 71, no. 1, pp. 24–34, 2008. View at Publisher · View at Google Scholar · View at Scopus
  33. A. D. McLachlan, “Gene duplications in the structural evolution of chymotrypsin,” Journal of Molecular Biology, vol. 128, no. 1, pp. 49–79, 1979. View at Publisher · View at Google Scholar · View at Scopus
  34. A. G. Murzin, A. M. Lesk, and C. Chothia, “Principles determining the structure of β-sheet barrels in proteins I. A theoretical analysis,” Journal of Molecular Biology, vol. 236, no. 5, pp. 1369–1381, 1994. View at Publisher · View at Google Scholar · View at Scopus
  35. A. G. Murzin, A. M. Lesk, and C. Chothia, “Principles determining the structure of β-sheet barrels in proteins II. The observed structures,” Journal of Molecular Biology, vol. 236, no. 5, pp. 1382–1400, 1994. View at Publisher · View at Google Scholar · View at Scopus
  36. T. Páli and D. Marsh, “Tilt, twist, and coiling in β-barrel membrane proteins: relation to infrared dichroism,” Biophysical Journal, vol. 80, no. 6, pp. 2789–2797, 2001. View at Publisher · View at Google Scholar · View at Scopus
  37. G. E. Schulz, “The structure of bacterial outer membrane proteins,” Biochimica et Biophysica Acta (BBA)—Biomembranes, vol. 1565, no. 2, pp. 308–317, 2002. View at Publisher · View at Google Scholar · View at Scopus
  38. S. J. Ludtke, P. R. Baldwin, and W. Chiu, “EMAN: semiautomated software for high-resolution single-particle reconstructions,” Journal of Structural Biology, vol. 128, no. 1, pp. 82–97, 1999. View at Publisher · View at Google Scholar · View at Scopus
  39. D. Si and J. He, “Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels,” in Proceedings of the 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC '14), pp. 3941–3944, Chicago, Ill, USA., August 2014. View at Publisher · View at Google Scholar · View at Scopus
  40. J. Novotný, R. E. Bruccoleri, and J. Newell, “Twisted hyperboloid (strophoid) as a model of β-barrels in proteins,” Journal of Molecular Biology, vol. 177, no. 3, pp. 567–573, 1984. View at Publisher · View at Google Scholar
  41. E. Tolonen, B. Bueno, S. Kulshreshta et al., “Allosteric transition and binding of small molecule effectors causes curvature change in central β-sheets of selected enzymes,” Journal of Molecular Modeling, vol. 17, no. 4, pp. 899–911, 2011. View at Publisher · View at Google Scholar · View at Scopus
  42. I. Lasters, S. J. Wodak, P. Alard, and E. van Cutsem, “Structural principles of parallel beta-barrels in proteins,” Proceedings of the National Academy of Sciences of the United States of America, vol. 85, no. 10, pp. 3338–3342, 1988. View at Publisher · View at Google Scholar · View at Scopus
  43. E. Koh and T. Kim, “Minimal surface as a model of β-sheets,” Proteins: Structure, Function and Genetics, vol. 61, no. 3, pp. 559–569, 2005. View at Publisher · View at Google Scholar · View at Scopus
  44. M. A. Lomize, A. L. Lomize, I. D. Pogozheva, and H. I. Mosberg, “OPM: orientations of proteins in membranes database,” Bioinformatics, vol. 22, no. 5, pp. 623–625, 2006. View at Publisher · View at Google Scholar · View at Scopus
  45. S. Zeil, J. Kovacs, W. Wriggers, and J. He, “A method to compare an atomic model or a structure and its Cryo-EM image at the central axis of a helix,” Journal of Computational Biology, vol. 24, no. 1, pp. 52–67, 2017. View at Google Scholar