skip to main content
10.1145/2975167.2975183acmconferencesArticle/Chapter ViewAbstractPublication PagesbcbConference Proceedingsconference-collections
research-article

Automatic Detection of Beta-barrel from Medium Resolution Cryo-EM Density Maps

Published: 02 October 2016 Publication History

Abstract

Cryo-electron microscopy (Cryo-EM) has become central to the study of large-scale molecular interactions and has produced three-dimensional (3D) density maps at various resolutions. Secondary structure element (SSE) identification from volumetric protein density maps is critical for de novo backbone structure derivation in cryo-EM. Multiple methods have been developed to detect helix and β-sheet from density maps at medium resolutions (~5-10Å). β-barrel as a special β-sheet structure has been found in many proteins. However, currently there are no methods aimed to automatically and accurately extract the β-barrel as a complete chunk of density from cryo-EM map of β-barrel protein. We present an effective approach, BarrelMiner, to automatically extract the β-barrel region from cryo-EM density maps based on the conspicuous cylindrical shape of β-barrel. BarrelMiner has been tested using ten simulated density maps at 10Å resolution and seven experimental cryo-EM maps between 5.5Å and 8.25Å resolution. The result suggests that BarrelMiner can be used for the detection of β-barrel from medium resolution cryo-EM density maps of β-barrel proteins.

References

[1]
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.
[2]
Zhou, Z. H. Atomic resolution cryo electron microscopy of macromolecular complexes. Adv Protein Chem Struct Biol, 82 (2011), 1--35.
[3]
Callaway, E. The revolution will not be crystallized: a new method sweeps through structural biology. Nature, 525, 7568 (September 2015), 172--174.
[4]
Liu, Z., Guo, F., Wang, F., Li, T. C. and Jiang, W. 2.9 A Resolution Cryo-EM 3D Reconstruction of Close-Packed Virus Particles. Structure, 24, 2 (Feb 2 2016), 319--328.
[5]
Bartesaghi, A., Merk, A., Banerjee, S., Matthies, D., Wu, X., Milne, J. L. and Subramaniam, S. 2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor. Science, 348, 6239 (Jun 5 2015), 1147--1151.
[6]
Agirrezabala, X., Schreiner, E., Trabuco, L. G., Lei, J., Ortiz-Meoz, R. F., Schulten, K., Green, R. and Frank, J. Structural insights into cognate versus near-cognate discrimination during decoding. The EMBO Journal, 30, 8 (March 4 2011), 1497--1507.
[7]
Zhou, A., Rohou, A., Schep, D. G., Bason, J. V., Montgomery, M. G., Walker, J. E., Grigorieff, N. and Rubinstein, J. L. Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM. eLife, 4 (2015), e10180.
[8]
Schroder, G. F., Brunger, A. T. and Levitt, M. Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure, 15, 12 (Dec 2007), 1630--1641.
[9]
Chan, K. Y., Trabuco, L. G., Schreiner, E. and Schulten, K. Cryo-Electron Microscopy Modeling by the Molecular Dynamics Flexible Fitting Method. Biopolymers, 97, 9 (Sep 2012), 678--686.
[10]
Topf, M., Lasker, K., Webb, B., Wolfson, H., Chiu, W. and Sali, A. Protein structure fitting and refinement guided by cryo-EM density. Structure, 16, 2 (Feb 2008), 295--307.
[11]
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. Journal of Structural Biology, 174, 2 (2011), 360--373.
[12]
Lindert, S., Alexander, N., Wotzel, N., Karaka, M., Stewart, P. L. and Meiler, J. EM-Fold: De Novo Atomic-Detail Protein Structure Determination from Medium-Resolution Density Maps. Structure (London, England: 1993), 20 (2012), 464--478.
[13]
Nasr, K. A., Chen, L., Ranjan, D., Zubair, M., Si, D. and He, J. A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps. In Proceedings of the Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics (Wshington DC, USA, 2013). ACM.
[14]
Nasr, K. A., Chen, L., Si, D., Ranjan, D., Zubair, M. and He, J. Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions. In Proceedings of the Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (Orlando, Florida, 2012). ACM.
[15]
Biswas, A., Si, D., Al Nasr, K., Ranjan, D., Zubair, M. and He, J. Improved efficiency in cryo-EM secondary structure topology determination from inaccurate data. Journal of bioinformatics and computational biology, 10, 3 (Jun 2012), 1242006.
[16]
He, J. and Si, D. Towards De Novo Folding of Protein Structures from Cryo-EM 3D Images at Medium Resolutions. In Proceedings of the Robotics: Science and Systems Conference (University of California Berkeley, USA, July 12-July 16, 2014).
[17]
Wang, R. Y., Kudryashev, M., Li, X., Egelman, E. H., Basler, M., Cheng, Y., Baker, D. and DiMaio, F. De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nature methods, 12, 4 (Apr 2015), 335--338.
[18]
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 2001), 1033--1044.
[19]
Del Palu, A., He, J., Pontelli, E. and Lu, Y. Identification of Alpha-Helices from Low Resolution Protein Density Maps. In Proceedings of the Proceeding of Computational Systems Bioinformatics Conference(CSB) (Stanford, CA, 2006).
[20]
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.
[21]
Si, D., Ji, S., Nasr, K. A. and He, J. A machine learning approach for the identification of protein secondary structure elements from electron cryo-microscopy density maps. Biopolymers, 97, 9 (Sep 2012), 698--708.
[22]
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.
[23]
Zeyun, Y. and Bajaj, C. Computational Approaches for Automatic Structural Analysis of Large Biomolecular Complexes. Computational Biology and Bioinformatics, IEEE/ACM Transactions on, 5, 4 (2008), 568--582.
[24]
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.
[25]
Si, D. and He, J. Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps. In Proceedings of the Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics (Wshington DC, USA, 2013). ACM.
[26]
He, J., Si, D. and Arab, M. Detection of Secondary Structures from 3D Protein Images of Medium Resolutions and its Challenges. Image and Graphics, Springer International Publishing, 9812, 13 (2015), 147--155.
[27]
Si, D. and He, J. Modeling Protein Structure Features from Three Dimensional Cryo-EM Images. In Proceedings of the Modeling, Simulation, and Visualization Capstone Conference (Suffolk VA, April 17, 2014).
[28]
Si, D. Computational development for secondary structure detection from three-dimensional images of cryo-electron microscopy. Ph.D. dissertation, Old Dominion University, 2015.
[29]
Zhou, Z. H. Towards atomic resolution structural determination by single-particle cryo-electron microscopy. Current Opinion in Structural Biology, 18, 2 (Apr 2008), 218--228.
[30]
Baker, M. L., Baker, M. R., Hryc, C. F., Ju, T. and Chiu, W. Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps. Biopolymers, 97, 9 (Sep 2012), 655--668.
[31]
Si, D. and He, J. Tracing Beta Strands Using StrandTwister from Cryo-EM Density Maps at Medium Resolutions. Structure, 22, 11 (2014), 1665--1676.
[32]
Si, D. and He, J. Orientations of beta-strand traces and near maximum twist. In Proceedings of the Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (Newport Beach, California, 2014). ACM.
[33]
Chothia, C. Conformation of twisted beta-pleated sheets in proteins. J Mol Biol, 75, 2 (Apr 5 1973), 295--302.
[34]
Cherezov, V., Liu, W., Derrick, J. P., Luan, B., Aksimentiev, A., Katritch, V. and Caffrey, M. In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin. Proteins, 71, 1 (Apr 2008), 24--34.
[35]
McLachlan, A. D. Gene duplications in the structural evolution of chymotrypsin. J Mol Biol, 128, 1 (Feb 15 1979), 49--79.
[36]
Si, D. and He, J. Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels. In Proceedings of the 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (Chicago IL, 26-30 Aug. 2014, 2014).
[37]
Murzin, A. G., Lesk, A. M. and Chothia, C. Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis. J Mol Biol, 236, 5 (Mar 11 1994), 1369--1381.
[38]
Murzin, A. G., Lesk, A. M. and Chothia, C. Principles determining the structure of beta-sheet barrels in proteins. II. The observed structures. J Mol Biol, 236, 5 (Mar 11 1994), 1382--1400.
[39]
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.
[40]
Tolonen, E., Bueno, B., Kulshreshta, S., Cieplak, P., Argaez, M., Velazquez, L. and Stec, B. Allosteric transition and binding of small molecule effectors causes curvature change in central beta-sheets of selected enzymes. Journal of molecular modeling, 17, 4 (Apr 2011), 899--911.
[41]
Lasters, I., Wodak, S. J., Alard, P. and van Cutsem, E. Structural principles of parallel beta-barrels in proteins. Proceedings of the National Academy of Sciences of the United States of America, 85, 10 (May 1988), 3338--3342.
[42]
Koh, E. and Kim, T. Minimal surface as a model of beta-sheets. Proteins, 61, 3 (Nov 15 2005), 559--569.
[43]
Fischler, M. A. and Bolles, R. C. Random sample consensus: a paradigm for model fitting with applications to image analysis and automated cartography. Commun. ACM, 24, 6 (1981), 381--395.
[44]
Torr, P. H. S. and Zisserman, A. MLESAC: A New Robust Estimator with Application to Estimating Image Geometry. Computer Vision and Image Understanding, 78, 1 (April 2000), 138--156.
[45]
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C. and Ferrin, T. E. UCSF Chimera--a visualization system for exploratory research and analysis. Journal of computational chemistry, 25, 13 (Oct 2004), 1605--1612.
[46]
Choi, S., Kim, T. and Yu, W. Performance Evaluation of RANSAC Family. In Proceedings of the British Machine Vision Conference (London, 2009).
[47]
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.

Cited By

View all
  • (2022) Integrating model simulation tools and cryo‐electron microscopy WIREs Computational Molecular Science10.1002/wcms.164213:3Online publication date: 21-Nov-2022
  • (2018)Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray TracingJournal of Computational Biology10.1089/cmb.2017.015525:3(326-336)Online publication date: Mar-2018
  • (2018)GPU Accelerated Ray Tracing for the Beta-Barrel Detection from Three-Dimensional Cryo-EM MapsBioinformatics Research and Applications10.1007/978-3-319-94968-0_20(217-226)Online publication date: 13-Jul-2018
  • Show More Cited By

Recommendations

Comments

Information & Contributors

Information

Published In

cover image ACM Conferences
BCB '16: Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics
October 2016
675 pages
ISBN:9781450342254
DOI:10.1145/2975167
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than the author(s) must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected].

Sponsors

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 02 October 2016

Permissions

Request permissions for this article.

Check for updates

Author Tags

  1. Electron cryo-microscopy
  2. beta-barrel
  3. cryo-EM
  4. density map
  5. feature detection
  6. geometric modeling
  7. protein
  8. secondary structure
  9. three-dimensional image processing

Qualifiers

  • Research-article
  • Research
  • Refereed limited

Conference

BCB '16
Sponsor:

Acceptance Rates

Overall Acceptance Rate 254 of 885 submissions, 29%

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • Downloads (Last 12 months)0
  • Downloads (Last 6 weeks)0
Reflects downloads up to 20 Jan 2025

Other Metrics

Citations

Cited By

View all
  • (2022) Integrating model simulation tools and cryo‐electron microscopy WIREs Computational Molecular Science10.1002/wcms.164213:3Online publication date: 21-Nov-2022
  • (2018)Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray TracingJournal of Computational Biology10.1089/cmb.2017.015525:3(326-336)Online publication date: Mar-2018
  • (2018)GPU Accelerated Ray Tracing for the Beta-Barrel Detection from Three-Dimensional Cryo-EM MapsBioinformatics Research and Applications10.1007/978-3-319-94968-0_20(217-226)Online publication date: 13-Jul-2018
  • (2017)Genetic Algorithm Based Beta-Barrel Detection for Medium Resolution Cryo-EM Density MapsBioinformatics Research and Applications10.1007/978-3-319-59575-7_16(174-185)Online publication date: 31-May-2017

View Options

Login options

View options

PDF

View or Download as a PDF file.

PDF

eReader

View online with eReader.

eReader

Media

Figures

Other

Tables

Share

Share

Share this Publication link

Share on social media