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Zumbado-Corrales M, Esquivel-Rodríguez J. EvoSeg: Automated Electron Microscopy Segmentation through Random Forests and Evolutionary Optimization. Biomimetics (Basel) 2021; 6:biomimetics6020037. [PMID: 34206006 PMCID: PMC8293153 DOI: 10.3390/biomimetics6020037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/17/2021] [Accepted: 05/28/2021] [Indexed: 11/30/2022] Open
Abstract
Electron Microscopy Maps are key in the study of bio-molecular structures, ranging from borderline atomic level to the sub-cellular range. These maps describe the envelopes that cover possibly a very large number of proteins that form molecular machines within the cell. Within those envelopes, we are interested to find what regions correspond to specific proteins so that we can understand how they function, and design drugs that can enhance or suppress a process that they are involved in, along with other experimental purposes. A classic approach by which we can begin the exploration of map regions is to apply a segmentation algorithm. This yields a mask where each voxel in 3D space is assigned an identifier that maps it to a segment; an ideal segmentation would map each segment to one protein unit, which is rarely the case. In this work, we present a method that uses bio-inspired optimization, through an Evolutionary-Optimized Segmentation algorithm, to iteratively improve upon baseline segments obtained from a classical approach, called watershed segmentation. The cost function used by the evolutionary optimization is based on an ideal segmentation classifier trained as part of this development, which uses basic structural information available to scientists, such as the number of expected units, volume and topology. We show that a basic initial segmentation with the additional information allows our evolutionary method to find better segmentation results, compared to the baseline generated by the watershed.
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2
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Terashi G, Kagaya Y, Kihara D. MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. J Chem Inf Model 2020; 60:2634-2643. [PMID: 32197044 DOI: 10.1021/acs.jcim.9b01110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yuki Kagaya
- Graduate School of Information Sciences, Tohoku University, Aramaki Aza, Aoba 6-3-09, Aoba-Ku, Sendai, Miyagi 980-8579, Japan
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Computer Science, Purdue University, West Lafayette, Indiana 47907, United States
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3
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Terwilliger TC, Adams PD, Afonine PV, Sobolev OV. Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge. J Struct Biol 2018; 204:338-343. [PMID: 30063987 PMCID: PMC6163059 DOI: 10.1016/j.jsb.2018.07.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/11/2018] [Accepted: 07/27/2018] [Indexed: 11/27/2022]
Abstract
A recently-developed method for identifying a compact, contiguous region representing the unique part of a density map was applied to 218 Cryo-EM maps with resolutions of 4.5 Å or better. The key elements of the segmentation procedure are (1) identification of all regions of density above a threshold and (2) choice of a unique set of these regions, taking symmetry into consideration, that maximize connectivity and compactness. This segmentation approach was then combined with tools for automated map sharpening and model-building to generate models for the 12 maps in the 2016 Cryo-EM Model Challenge in a fully automated manner. The resulting models have completeness from 24% to 82% and RMS distances from reference interpretations of 0.6 Å-2.1 Å.
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Affiliation(s)
- Thomas C Terwilliger
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87544, USA.
| | - Paul D Adams
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Pavel V Afonine
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA; Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China
| | - Oleg V Sobolev
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
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4
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Weiss GL, Medeiros JM, Pilhofer M. In Situ Imaging of Bacterial Secretion Systems by Electron Cryotomography. Methods Mol Biol 2018; 1615:353-375. [PMID: 28667625 DOI: 10.1007/978-1-4939-7033-9_27] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The unique property of electron cryotomography (ECT) is its capability to resolve the structure of macromolecular machines in their cellular context. The integration of ECT data with high-resolution structures of purified subcomplexes and live-cell fluorescence light microscopy can generate pseudo-atomic models that lead to a mechanistic understanding across size and time scales. Recent advances in electron detection, sample thinning, data acquisition, and data processing have significantly enhanced the applicability and performance of ECT. Here we describe a detailed workflow for an ECT experiment, including cell culture, vitrification, data acquisition, data reconstruction, tomogram analysis, and subtomogram averaging. This protocol provides an entry point to the technique for students and researchers and indicates the many possible variations arising from specific target properties and the available instrumentation.
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Affiliation(s)
- Gregor L Weiss
- Department of Biology, ETH Zürich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - João M Medeiros
- Department of Biology, ETH Zürich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Martin Pilhofer
- Department of Biology, ETH Zürich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093, Zürich, Switzerland.
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5
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Li B, Fooksa M, Heinze S, Meiler J. Finding the needle in the haystack: towards solving the protein-folding problem computationally. Crit Rev Biochem Mol Biol 2018; 53:1-28. [PMID: 28976219 PMCID: PMC6790072 DOI: 10.1080/10409238.2017.1380596] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/22/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022]
Abstract
Prediction of protein tertiary structures from amino acid sequence and understanding the mechanisms of how proteins fold, collectively known as "the protein folding problem," has been a grand challenge in molecular biology for over half a century. Theories have been developed that provide us with an unprecedented understanding of protein folding mechanisms. However, computational simulation of protein folding is still difficult, and prediction of protein tertiary structure from amino acid sequence is an unsolved problem. Progress toward a satisfying solution has been slow due to challenges in sampling the vast conformational space and deriving sufficiently accurate energy functions. Nevertheless, several techniques and algorithms have been adopted to overcome these challenges, and the last two decades have seen exciting advances in enhanced sampling algorithms, computational power and tertiary structure prediction methodologies. This review aims at summarizing these computational techniques, specifically conformational sampling algorithms and energy approximations that have been frequently used to study protein-folding mechanisms or to de novo predict protein tertiary structures. We hope that this review can serve as an overview on how the protein-folding problem can be studied computationally and, in cases where experimental approaches are prohibitive, help the researcher choose the most relevant computational approach for the problem at hand. We conclude with a summary of current challenges faced and an outlook on potential future directions.
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Affiliation(s)
- Bian Li
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Michaela Fooksa
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, TN, USA
| | - Sten Heinze
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
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6
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Baldwin PR, Tan YZ, Eng ET, Rice WJ, Noble AJ, Negro CJ, Cianfrocco MA, Potter CS, Carragher B. Big data in cryoEM: automated collection, processing and accessibility of EM data. Curr Opin Microbiol 2017; 43:1-8. [PMID: 29100109 DOI: 10.1016/j.mib.2017.10.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/27/2017] [Accepted: 10/09/2017] [Indexed: 11/24/2022]
Abstract
The scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ∼10-100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope of data acquisition, methods for automation, and use of cloud storage and computing.
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Affiliation(s)
- Philip R Baldwin
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Yong Zi Tan
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Edward T Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - William J Rice
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Alex J Noble
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Carl J Negro
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Michael A Cianfrocco
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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7
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Ali RA, Mehdi AM, Rothnagel R, Hamilton NA, Gerle C, Landsberg MJ, Hankamer B. RAZA: A Rapid 3D z-crossings algorithm to segment electron tomograms and extract organelles and macromolecules. J Struct Biol 2017; 200:73-86. [PMID: 29032142 DOI: 10.1016/j.jsb.2017.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 11/30/2022]
Abstract
Resolving the 3D architecture of cells to atomic resolution is one of the most ambitious challenges of cellular and structural biology. Central to this process is the ability to automate tomogram segmentation to identify sub-cellular components, facilitate molecular docking and annotate detected objects with associated metadata. Here we demonstrate that RAZA (Rapid 3D z-crossings algorithm) provides a robust, accurate, intuitive, fast, and generally applicable segmentation algorithm capable of detecting organelles, membranes, macromolecular assemblies and extrinsic membrane protein domains. RAZA defines each continuous contour within a tomogram as a discrete object and extracts a set of 3D structural fingerprints (major, middle and minor axes, surface area and volume), enabling selective, semi-automated segmentation and object extraction. RAZA takes advantage of the fact that the underlying algorithm is a true 3D edge detector, allowing the axes of a detected object to be defined, independent of its random orientation within a cellular tomogram. The selectivity of object segmentation and extraction can be controlled by specifying a user-defined detection tolerance threshold for each fingerprint parameter, within which segmented objects must fall and/or by altering the number of search parameters, to define morphologically similar structures. We demonstrate the capability of RAZA to selectively extract subgroups of organelles (mitochondria) and macromolecular assemblies (ribosomes) from cellular tomograms. Furthermore, the ability of RAZA to define objects and their contours, provides a basis for molecular docking and rapid tomogram annotation.
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Affiliation(s)
- Rubbiya A Ali
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Ahmed M Mehdi
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD, Australia; Department of Electrical Engineering, University of Engineering and Technology, Lahore, Punjab, Pakistan
| | - Rosalba Rothnagel
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nicholas A Hamilton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Christoph Gerle
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Michael J Landsberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Ben Hankamer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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8
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Kuzu G, Keskin O, Nussinov R, Gursoy A. PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Acta Crystallogr D Struct Biol 2016; 72:1137-1148. [PMID: 27710935 PMCID: PMC5053140 DOI: 10.1107/s2059798316013541] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/23/2016] [Indexed: 12/29/2022] Open
Abstract
The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.
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Affiliation(s)
- Guray Kuzu
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, 34450 Istanbul, Turkey
- Chemical and Biological Engineering, College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Attila Gursoy
- Computer Engineering, Koc University, 34450 Istanbul, Turkey
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9
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Chen M, Baldwin PR, Ludtke SJ, Baker ML. De Novo modeling in cryo-EM density maps with Pathwalking. J Struct Biol 2016; 196:289-298. [PMID: 27436409 DOI: 10.1016/j.jsb.2016.06.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 11/26/2022]
Abstract
As electron cryo-microscopy (cryo-EM) can now frequently achieve near atomic resolution, accurate interpretation of these density maps in terms of atomistic detail has become paramount in deciphering macromolecular structure and function. However, there are few software tools for modeling protein structure from cryo-EM density maps in this resolution range. Here, we present an extension of our original Pathwalking protocol, which can automatically trace a protein backbone directly from a near-atomic resolution (3-6Å) density map. The original Pathwalking approach utilized a Traveling Salesman Problem solver for backbone tracing, but manual adjustment was still required during modeling. In the new version, human intervention is minimized and we provide a more robust approach for backbone modeling. This includes iterative secondary structure identification, termini detection and the ability to model multiple subunits without prior segmentation. Overall, the new Pathwalking procedure provides a more complete and robust tool for annotating protein structure function in near-atomic resolution density maps.
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Affiliation(s)
- Muyuan Chen
- Program in Structural and Computational Biology and Molecular Biophysics, United States; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Philip R Baldwin
- Department of Psychology, United States; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Matthew L Baker
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States.
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10
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Bettadapura R, Rasheed M, Vollrath A, Bajaj C. PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps. PLoS Comput Biol 2015; 11:e1004289. [PMID: 26469938 PMCID: PMC4607507 DOI: 10.1371/journal.pcbi.1004289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 04/14/2015] [Indexed: 11/30/2022] Open
Abstract
There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.
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Affiliation(s)
- Radhakrishna Bettadapura
- Radhakrishna Bettadapura Computational Visualization Center/Department of Mechanical Engineering, University of Texas at Austin, Austin, Texas, United States of America
| | - Muhibur Rasheed
- Muhibur Rasheed Computational Visualization Center/Department of Mechanical Engineering, University of Texas at Austin, Austin, Texas, United States of America
| | - Antje Vollrath
- Antje Vollrath Institut Computational Mathematics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Chandrajit Bajaj
- Chandrajit Bajaj Computational Visualization Center/Institute of Computational Engineering & Sciences/Department of Computer Science, University of Texas at Austin, Austin, Texas, United States of America
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Zhang Q, Cha D, Bajaj C. Quality Partitioned Meshing of Multi-material Objects. PROCEDIA ENGINEERING 2015; 124:187-199. [PMID: 27563367 PMCID: PMC4994976 DOI: 10.1016/j.proeng.2015.10.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/29/2022]
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12
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Georges AD, Hashem Y, Buss SN, Jossinet F, Zhang Q, Liao HY, Fu J, Jobe A, Grassucci RA, Langlois R, Bajaj C, Westhof E, Madison-Antenucci S, Frank J. High-resolution Cryo-EM Structure of the Trypanosoma brucei Ribosome: A Case Study. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/978-1-4614-9521-5_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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13
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Hashem Y, des Georges A, Fu J, Buss SN, Jossinet F, Jobe A, Zhang Q, Liao HY, Grassucci RA, Bajaj C, Westhof E, Madison-Antenucci S, Frank J. High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature 2013; 494:385-9. [PMID: 23395961 DOI: 10.1038/nature11872] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 12/21/2012] [Indexed: 12/12/2022]
Abstract
Ribosomes, the protein factories of living cells, translate genetic information carried by messenger RNAs into proteins, and are thus involved in virtually all aspects of cellular development and maintenance. The few available structures of the eukaryotic ribosome reveal that it is more complex than its prokaryotic counterpart, owing mainly to the presence of eukaryote-specific ribosomal proteins and additional ribosomal RNA insertions, called expansion segments. The structures also differ among species, partly in the size and arrangement of these expansion segments. Such differences are extreme in kinetoplastids, unicellular eukaryotic parasites often infectious to humans. Here we present a high-resolution cryo-electron microscopy structure of the ribosome of Trypanosoma brucei, the parasite that is transmitted by the tsetse fly and that causes African sleeping sickness. The atomic model reveals the unique features of this ribosome, characterized mainly by the presence of unusually large expansion segments and ribosomal-protein extensions leading to the formation of four additional inter-subunit bridges. We also find additional rRNA insertions, including one large rRNA domain that is not found in other eukaryotes. Furthermore, the structure reveals the five cleavage sites of the kinetoplastid large ribosomal subunit (LSU) rRNA chain, which is known to be cleaved uniquely into six pieces, and suggests that the cleavage is important for the maintenance of the T. brucei ribosome in the observed structure. We discuss several possible implications of the large rRNA expansion segments for the translation-regulation process. The structure could serve as a basis for future experiments aimed at understanding the functional importance of these kinetoplastid-specific ribosomal features in protein-translation regulation, an essential step towards finding effective and safe kinetoplastid-specific drugs.
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Affiliation(s)
- Yaser Hashem
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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14
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Burger V, Chennubhotla C. Nhs: network-based hierarchical segmentation for cryo-electron microscopy density maps. Biopolymers 2012; 97:732-41. [PMID: 22696408 PMCID: PMC3483038 DOI: 10.1002/bip.22041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cryo-electron microscopy (cryo-EM) experiments yield low-resolution (3-30 Å) 3D-density maps of macromolecules. These density maps are segmented to identify structurally distinct proteins, protein domains, and subunits. Such partitioning aids the inference of protein motions and guides fitting of high-resolution atomistic structures. Cryo-EM density map segmentation has traditionally required tedious and subjective manual partitioning or semisupervised computational methods, whereas validation of resulting segmentations has remained an open problem in this field. We introduce a network-based hierarchical segmentation (Nhs) method, that provides a multi-scale partitioning, reflecting local and global clustering, while requiring no user input. This approach models each map as a graph, where map voxels constitute nodes and weighted edges connect neighboring voxels. Nhs initiates Markov diffusion (or random walk) on the weighted graph. As Markov probabilities homogenize through diffusion, an intrinsic segmentation emerges. We validate the segmentations with ground-truth maps based on atomistic models. When implemented on density maps in the 2010 Cryo-EM Modeling Challenge, Nhs efficiently and objectively partitions macromolecules into structurally and functionally relevant subregions at multiple scales.
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Affiliation(s)
- Virginia Burger
- Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh School of Medicine
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine
| | - Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine
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15
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Zhang Q, Bettadapura R, Bajaj C. Macromolecular structure modeling from 3D EM using VolRover 2.0. Biopolymers 2012; 97:709-31. [PMID: 22696407 DOI: 10.1002/bip.22052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We review tools for structure identification and model-based refinement from three-dimensional electron microscopy implemented in our in-house software package, VOLROVER 2.0. For viral density maps with icosahedral symmetry, we segment the capsid, polymeric, and monomeric subunits using techniques based on automatic symmetry detection and multidomain fast marching. For large biomolecules without symmetry information, we again use our multidomain fast-marching method with manual or fit-based multiseeding to segment meaningful substructures. In either case, we subject the resulting segmented subunit to secondary structure detection when the EM resolution is sufficiently high, and rigid-body structure fitting when the corresponding X-ray structure is available. Secondary structure elements are identified by three techniques: our earlier volume-based and boundary-based skeletonization methods as well as a new method, currently in development, based on solving the grassfire flow equation. For rigid-body fitting, we adapt our earlier fast Fourier-based correlation scheme F2Dock. Our reported segmentation, secondary structure elements identification, and rigid-body fitting techniques, implemented in VOLROVER 2.0 are applied to the PSB 2011 cryo-EM modeling challenge data, and our results are briefly compared to similar results submitted from other research groups. The comparisons show that our techniques are equally capable of segmenting relatively accurate subunits from a viral or protein assembly, and that high segmentation quality leads in turn to higher-quality results of secondary structure elements identification and correlation-based rigid-body fitting. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 709-731, 2012.
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Affiliation(s)
- Qin Zhang
- Institute for Computational Engineering and Sciences, The University of Texas, Austin, TX 78712, USA
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16
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Pintilie G, Chiu W. Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in cryo-EM density maps. Biopolymers 2012; 97:742-60. [PMID: 22696409 DOI: 10.1002/bip.22074] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Segmentation and docking are useful methods for the discovery of molecular components in electron cryo-microscopy (cryo-EM) density maps of macromolecular complexes. In this article, we describe the segmentation and docking methods implemented in Segger. For 11 targets posted in the 2010 cryo-EM challenge, we segmented the regions corresponding to individual molecular components using Segger. We then used the segmented regions to guide rigid-body docking of individual components. Docking results were evaluated by comparing the docked components with published structures, and by calculation of several scores, such as atom inclusion, density occupancy, and geometry clash. The accuracy of the component segmentation using Segger and other methods was assessed by comparing segmented regions with docked components.
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Affiliation(s)
- Grigore Pintilie
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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18
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Abstract
In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images. In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets. Then, we discuss three key categories of image analysis tasks, namely segmentation, registration, and annotation. We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain.
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Affiliation(s)
| | | | - Hanchuan Peng
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
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Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:49-90. [PMID: 22297510 DOI: 10.1007/978-1-4614-0980-9_4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The past few decades have seen tremendous advances in single-particle electron -cryo-microscopy (cryo-EM). The field has matured to the point that near-atomic resolution density maps can be generated for icosahedral viruses without the need for crystallization. In parallel, substantial progress has been made in determining the structures of nonicosahedrally arranged proteins in viruses by employing either single-particle cryo-EM or cryo-electron tomography (cryo-ET). Implicit in this course have been the availability of a new generation of electron cryo-microscopes and the development of the computational tools that are essential for generating these maps and models. This methodology has enabled structural biologists to analyze structures in increasing detail for virus particles that are in different morphogenetic states. Furthermore, electron imaging of frozen, hydrated cells, in the process of being infected by viruses, has also opened up a new avenue for studying virus structures "in situ". Here we present the common techniques used to acquire and process cryo-EM and cryo-ET data and discuss their implications for structural virology both now and in the future.
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Abstract
A universal goal in studying the structures of macromolecules and macromolecular complexes by means of electron cryo-microscopy (cryo-TEM) and three-dimensional (3D) image reconstruction is the derivation of a reliable atomic or pseudoatomic model. Such a model provides the foundation for exploring in detail the mechanisms by which biomolecules function. Though a variety of highly ordered, symmetric specimens such as 2D crystals, helices, and icosahedral virus capsids have been studied by these methods at near-atomic resolution, until recently, numerous challenges have made it difficult to achieve sub-nanometer resolution with large (≥~500Å), asymmetric molecules such as the tailed bacteriophages. After briefly reviewing some of the history behind the development of asymmetric virus reconstructions, we use recent structural studies of the prolate phage ϕ29 as an example to illustrate the step-by-step procedures used to compute an asymmetric reconstruction at sub-nanometer resolution. In contrast to methods that have been employed to study other asymmetric complexes, we demonstrate how symmetries in the head and tail components of the phage can be exploited to obtain the structure of the entire phage in an expedited, stepwise process. Prospects for future enhancements to the procedures currently employed are noted in the concluding section.
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Abstract
Three-dimensional (3D) cryoelectron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Databank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB), and the National Center for Macromolecular Imaging (NCMI), is a "one-stop shop" resource for global deposition and retrieval of cryo-EM map, model, and associated metadata. The resource unifies public access to the two major EM Structural Data archives: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.
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Affiliation(s)
- Catherine L Lawson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, USA
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22
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Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W. EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res 2010; 39:D456-64. [PMID: 20935055 PMCID: PMC3013769 DOI: 10.1093/nar/gkq880] [Citation(s) in RCA: 192] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global ‘one-stop shop’ resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.
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Affiliation(s)
- Catherine L Lawson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA.
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23
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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 2010; 170:427-38. [PMID: 20338243 DOI: 10.1016/j.jsb.2010.03.007] [Citation(s) in RCA: 284] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 03/14/2010] [Accepted: 03/16/2010] [Indexed: 01/01/2023]
Abstract
Cryo-electron microscopy produces 3D density maps of molecular machines, which consist of various molecular components such as proteins and RNA. Segmentation of individual components in such maps is a challenging task, and is mostly accomplished interactively. We present an approach based on the immersive watershed method and grouping of the resulting regions using progressively smoothed maps. The method requires only three parameters: the segmentation threshold, a smoothing step size, and the number of smoothing steps. We first apply the method to maps generated from molecular structures and use a quantitative metric to measure the segmentation accuracy. The method does not attain perfect accuracy, however it produces single or small groups of regions that roughly match individual proteins or subunits. We also present two methods for fitting of structures into density maps, based on aligning the structures with single regions or small groups of regions. The first method aligns centers and principal axes, whereas the second aligns centers and then rotates the structure to find the best fit. We describe both interactive and automated ways of using these two methods. Finally, we show segmentation and fitting results for several experimentally-obtained density maps.
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Abstract
Today, electron cryomicroscopy (cryo-EM) can routinely achieve subnanometer resolutions of complex macromolecular assemblies. From a density map, one can extract key structural and functional information using a variety of computational analysis tools. At subnanometer resolution, these tools make it possible to isolate individual subunits, identify secondary structures, and accurately fit atomic models. With several cryo-EM studies achieving resolutions beyond 5Å, computational modeling and feature recognition tools have been employed to construct backbone and atomic models of the protein components directly from a density map. In this chapter, we describe several common classes of computational tools that can be used to analyze and model subnanometer resolution reconstructions from cryo-EM. A general protocol for analyzing subnanometer resolution density maps is presented along with a full description of steps used in analyzing the 4.3Å resolution structure of Mm-cpn.
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Affiliation(s)
- Matthew L Baker
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
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25
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Norlén L, Oktem O, Skoglund U. Molecular cryo-electron tomography of vitreous tissue sections: current challenges. J Microsc 2009; 235:293-307. [PMID: 19754724 DOI: 10.1111/j.1365-2818.2009.03219.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electron tomography of vitreous tissue sections (tissue TOVIS) allows the study of the three-dimensional structure of molecular complexes in a near-native cellular context. Its usage is, however, limited by an unfortunate combination of noisy and incomplete data, by a technically demanding sample preparation procedure, and by a disposition for specimen degradation during data collection. Here we outline some major challenges as experienced from the application of TOVIS to human skin. We further consider a number of practical measures as well as theoretical approaches for its future development.
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Affiliation(s)
- L Norlén
- Department of Cell and Molecular Biology (CMB), Medical Nobel Institute, Karolinska Institute, Stockholm, Sweden.
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26
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Abstract
Single-particle electron microscopy (EM) can provide structural information for a large variety of biological molecules, ranging from small proteins to large macromolecular assemblies, without the need to produce crystals. The year 2008 has become a landmark year for single-particle EM as for the first time density maps have been produced at a resolution that made it possible to trace protein backbones or even to build atomic models. In this review, we highlight some of the recent successes achieved by single-particle EM and describe the individual steps involved in producing a density map by this technique. We also discuss some of the remaining challenges and areas, in which further advances would have a great impact on the results that can be achieved by single-particle EM.
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Affiliation(s)
- Yifan Cheng
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California-San Francisco, CA 94158, USA.
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27
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Heuser P, Langer GG, Lamzin VS. Interpretation of very low resolution X-ray electron-density maps using core objects. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:690-6. [PMID: 19564689 PMCID: PMC2703575 DOI: 10.1107/s090744490901991x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 05/25/2009] [Indexed: 11/11/2022]
Abstract
A novel approach to obtaining structural information from macromolecular X-ray data extending to resolutions as low as 20 A is presented. Following a simple map-segmentation procedure, the approximate shapes of the domains forming the structure are identified. A pattern-recognition comparative analysis of these shapes and those derived from the structures of domains from the PDB results in candidate structural models that can be used for a fit into the density map. It is shown that the placed candidate models can be employed for subsequent phase extension to higher resolution.
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Affiliation(s)
- Philipp Heuser
- Hamburg Unit, European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Hamburg 22603, Germany.
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28
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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. IEEE/NIH LIFE SCIENCE SYSTEMS AND APPLICATIONS WORKSHOP 2009; 2009:44-47. [PMID: 20556220 PMCID: PMC2885738 DOI: 10.1109/lissa.2009.4906705] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Segmentation of density maps obtained using cryo-electron microscopy (cryo-EM) is a challenging task, and is typically accomplished by time-intensive interactive methods. The goal of segmentation is to identify the regions inside the density map that correspond to individual components. We present a multi-scale segmentation method for accomplishing this task that requires very little user interaction. The method uses the concept of scale space, which is created by convolution of the input density map with a Gaussian filter. The latter process smoothes the density map. The standard deviation of the Gaussian filter is varied, with smaller values corresponding to finer scales and larger values to coarser scales. Each of the maps at different scales is segmented using the watershed method, which is very efficient, completely automatic, and does not require the specification of seed points. Some detail is lost in the smoothing process. A sharpening process reintroduces detail into the segmentation at the coarsest scale by using the segmentations at the finer scales. We apply the method to simulated density maps, where the exact segmentation (or ground truth) is known, and rigorously evaluate the accuracy of the resulting segmentations.
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Affiliation(s)
| | - Junjie Zhang
- Structural & Computational, Biology and Molecular, Biophysics, Baylor College of Medicine,
| | - Wah Chiu
- Structural & Computational, Biology and Molecular, Biophysics, Baylor College of Medicine,
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29
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Bajaj C, Goswami S. Modeling Cardiovascular Anatomy from Patient-Specific Imaging Data. COMPUTATIONAL METHODS IN APPLIED SCIENCES (SPRINGER) 2009; 13:1-28. [PMID: 20871793 PMCID: PMC2943643 DOI: 10.1007/978-1-4020-9086-8_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Chandrajit Bajaj
- Computational Visualization Center, Institute of Computational Engineering and Sciences, University of Texas, Austin Texas 78712
| | - Samrat Goswami
- Computational Visualization Center, Institute of Computational Engineering and Sciences, University of Texas, Austin Texas 78712
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30
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Yu Z, Bajaj C. Computational approaches for automatic structural analysis of large biomolecular complexes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2008; 5:568-582. [PMID: 18989044 DOI: 10.1109/tcbb.2007.70226] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We present computational solutions to two problems of macromolecular structure interpretation from reconstructed three-dimensional electron microscopy (3D-EM) maps of large bio-molecular complexes at intermediate resolution (5A-15 A). The two problems addressed are: 1) 3D structural alignment (matching) between identified and segmented 3D maps of structure units (e.g. trimeric configuration of proteins), and 2) the secondary structure identification of a segmented protein 3D map (i.e.locations of alpha-helices, beta-sheets). For problem 1, we present an efficient algorithm to correlate spatially (and structurally) two 3D maps of structure units. Besides providing a similarity score between structure units, the algorithm yields an effective technique for resolution refinement of repeated structure units, by 3D alignment and averaging. For problem 2, we present an efficient algorithm to compute eigenvalues and link eigenvectors of a Gaussian convoluted structure tensor derived from the protein 3D Map, thereby identifying and locating secondary structural motifs of proteins. The efficiency and performance of our approach is demonstrated on several experimentally reconstructed 3D maps of virus capsid shells from single-particle cryo-electron microscopy (cryo-EM), as well as computationally simulated protein structure density 3D maps generated from protein model entries in the Protein Data Bank.
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Affiliation(s)
- Zeyun Yu
- Department of Computer Science, University of Wisconsin, Milwaukee, WI 53211, USA.
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31
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Yu Z, Holst MJ, Hayashi T, Bajaj CL, Ellisman MH, McCammon JA, Hoshijima M. Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: bridging the gap between microscopic imaging and mathematical simulation. J Struct Biol 2008; 164:304-13. [PMID: 18835449 DOI: 10.1016/j.jsb.2008.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 10/21/2022]
Abstract
A general framework of image-based geometric processing is presented to bridge the gap between three-dimensional (3D) imaging that provides structural details of a biological system and mathematical simulation where high-quality surface or volumetric meshes are required. A 3D density map is processed in the order of image pre-processing (contrast enhancement and anisotropic filtering), feature extraction (boundary segmentation and skeletonization), and high-quality and realistic surface (triangular) and volumetric (tetrahedral) mesh generation. While the tool-chain described is applicable to general types of 3D imaging data, the performance is demonstrated specifically on membrane-bound organelles in ventricular myocytes that are imaged and reconstructed with electron microscopic (EM) tomography and two-photon microscopy (T-PM). Of particular interest in this study are two types of membrane-bound Ca(2+)-handling organelles, namely, transverse tubules (T-tubules) and junctional sarcoplasmic reticulum (jSR), both of which play an important role in regulating the excitation-contraction (E-C) coupling through dynamic Ca(2+) mobilization in cardiomyocytes.
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Affiliation(s)
- Zeyun Yu
- Department of Mathematics, University of California, San Diego, La Jolla, CA 92093, USA.
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32
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Alber F, Förster F, Korkin D, Topf M, Sali A. Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 2008; 77:443-77. [PMID: 18318657 DOI: 10.1146/annurev.biochem.77.060407.135530] [Citation(s) in RCA: 185] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To understand the cell, we need to determine the macromolecular assembly structures, which may consist of tens to hundreds of components. First, we review the varied experimental data that characterize the assemblies at several levels of resolution. We then describe computational methods for generating the structures using these data. To maximize completeness, resolution, accuracy, precision, and efficiency of the structure determination, a computational approach is required that uses spatial information from a variety of experimental methods. We propose such an approach, defined by its three main components: a hierarchical representation of the assembly, a scoring function consisting of spatial restraints derived from experimental data, and an optimization method that generates structures consistent with the data. This approach is illustrated by determining the configuration of the 456 proteins in the nuclear pore complex (NPC) from baker's yeast. With these tools, we are poised to integrate structural information gathered at multiple levels of the biological hierarchy--from atoms to cells--into a common framework.
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Affiliation(s)
- Frank Alber
- Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158-2330, USA.
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33
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BONGINI L, FANELLI D, SVENSSON S, GEDDA M, PIAZZA F, SKOGLUND U. Resolving the geometry of biomolecules imaged by cryo electron tomography. J Microsc 2007; 228:174-84. [DOI: 10.1111/j.1365-2818.2007.01839.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Salvi E, Cantele F, Zampighi L, Fain N, Pigino G, Zampighi G, Lanzavecchia S. JUST (Java User Segmentation Tool) for semi-automatic segmentation of tomographic maps. J Struct Biol 2007; 161:287-97. [PMID: 17707657 PMCID: PMC2692284 DOI: 10.1016/j.jsb.2007.06.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 05/16/2007] [Accepted: 06/21/2007] [Indexed: 10/23/2022]
Abstract
We are presenting a program for interactive segmentation of tomographic maps, based on objective criteria so as to yield reproducible results. The strategy starts with the automatic segmentation of the entire volume with the watershed algorithm in 3D. The watershed regions are clustered successively by supervised classification, allowing the segmentation of known organelles, such as membranes, vesicles and microtubules. These organelles are processed with topological models and input parameters manually derived from the tomograms. After known organelles are extracted from the volume, all other watershed regions can be organized into homogeneous assemblies on the basis of their densities. To complete the process, all voxels in the volume are assigned either to the background or individual structures, which can then be extracted for visualization with any rendering technique. The user interface of the program is written in Java, and computational routines are written in C. For some operations, involving the visualization of the tomogram, we refer to existing software, either open or commercial. While the program runs, a history file is created, that allows all parameters and other data to be saved for the purposes of comparison or exchange. Initially, the program was developed for the segmentation of synapses, and organelles belonging to these structures have thus far been the principal targets modeled with JUST. Since each organelle is clustered independently from the rest of the volume, however, the program can accommodate new models of different organelles as well as tomograms of other types of preparations of tissue, such as cytoskeletal components in vitreous ice.
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Affiliation(s)
- Eleonora Salvi
- Department of Structural Chemistry, School of Pharmacy, University of Milan, Italy
| | - Francesca Cantele
- Department of Structural Chemistry, School of Pharmacy, University of Milan, Italy
| | - Lorenzo Zampighi
- Department Physiology, UCLA School of Medicine, Los Angeles, California
| | - Nick Fain
- Department Neurobiology, UCLA School of Medicine, Los Angeles, California
| | - Gaia Pigino
- Department of Evolutionary Biology, University of Siena, Italy
| | - Guido Zampighi
- Department Neurobiology, UCLA School of Medicine, Los Angeles, California
- Department Jules Stein Eye Research Institute, UCLA School of Medicine, Los Angeles, California
| | - Salvatore Lanzavecchia
- Department of Structural Chemistry, School of Pharmacy, University of Milan, Italy
- Author for Correspondence: Salvatore Lanzavecchia, University of Milano, Dept. of Structural Chemistry, Via G. Venezian 21, 20133, Milano, Italy, Tel: (+39) 02 5031 4444, Fax: (+39) 02 5031 4454, e-mail:
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35
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Bajaj CL. AUTOMATIC STRUCTURE INTERPRETATION OF SINGLE PARTICLE CRYO-ELECTRON MICROSCOPY: FROM IMAGES TO PSUEDO-ATOMIC MODELS. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2007; 2007:236-239. [PMID: 19424455 PMCID: PMC2678009 DOI: 10.1109/isbi.2007.356832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Three dimensional Electron Microscopy (EM) and in particular single particle reconstruction using cryo-EM, has rapidly advanced over recent years, such that increasingly several macromolecular complexes can be resolved at subnanometer resolution (6-10 Å). This paper reviews some of the main volumetric image and geometric post-processing steps once a three dimensional EM map (henceforth a 3D map) has been reconstructed from single particle Cryo-EM, as essential steps in an enhanced and automated computational structure interpretation pipeline. In particular the paper addresses automated filtering, critical point calculations, symmetric and non-symmetric molecular domain segmentation, molecular surface selection, curation, and protein secondary structure (α- helices and β-sheets) elucidation from 3D maps.
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Affiliation(s)
- Chandrajit L Bajaj
- Department of Computer Sciences & Institute of Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712
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