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Jiang X, Seidler M, Butterfoss GL, Luo X, Yu T, Xuan S, Prendergast D, Zuckermann RN, Balsara NP. Atomic-Scale Corrugations in Crystalline Polypeptoid Nanosheets Revealed by Three-Dimensional Cryogenic Electron Microscopy. ACS Macro Lett 2023; 12:632-638. [PMID: 37099693 DOI: 10.1021/acsmacrolett.3c00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Amphiphilic molecules that can crystallize often form molecularly thin nanosheets in aqueous solutions. The possibility of atomic-scale corrugations in these structures has not yet been recognized. We have studied the self-assembly of amphiphilic polypeptoids, a family of bio-inspired polymers that can self-assemble into various crystalline nanostructures. Atomic-scale structure of the crystals in these systems has been inferred using both X-ray diffraction and electron microscopy. Here we use cryogenic electron microscopy to determine the in-plane and out-of-plane structures of a crystalline nanosheet. Data were collected as a function of tilt angle and analyzed using a hybrid single-particle crystallographic approach. The analysis reveals that adjacent rows of peptoid chains, which are separated by 4.5 Å in the plane of the nanosheet, are offset by 6 Å in the direction perpendicular to the plane of the nanosheet. These atomic-scale corrugations lead to a doubling of the unit cell dimension from 4.5 to 9 Å. Our work provides an alternative interpretation for the observed Å X-ray diffraction peak often reported in polypeptoid crystals.
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Affiliation(s)
- Xi Jiang
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Morgan Seidler
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Xubo Luo
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tianyi Yu
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Sunting Xuan
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David Prendergast
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ronald N Zuckermann
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Nitash P Balsara
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
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2
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Dunstone MA, de Marco A. Cryo-electron tomography: an ideal method to study membrane-associated proteins. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630150 DOI: 10.1098/rstb.2016.0210] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cryo-electron tomography (cryo-ET) is a three-dimensional imaging technique that makes it possible to analyse the structure of complex and dynamic biological assemblies in their native conditions. The latest technological and image processing developments demonstrate that it is possible to obtain structural information at nanometre resolution. The sample preparation required for the cryo-ET technique does not require the isolation of a protein and other macromolecular complexes from its native environment. Therefore, cryo-ET is emerging as an important tool to study the structure of membrane-associated proteins including pores.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Michelle A Dunstone
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia.,Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia .,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
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3
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Martynowycz MW, Gonen T. From electron crystallography of 2D crystals to MicroED of 3D crystals. Curr Opin Colloid Interface Sci 2018; 34:9-16. [PMID: 30166936 PMCID: PMC6112780 DOI: 10.1016/j.cocis.2018.01.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron crystallography is widespread in material science applications, but for biological samples its use has been restricted to a handful of examples where two-dimensional (2D) crystals or helical samples were studied either by electron diffraction and/or imaging. Electron crystallography in cryoEM, was developed in the mid-1970s and used to solve the structure of several membrane proteins and some soluble proteins. In 2013, a new method for cryoEM was unveiled and named Micro-crystal Electron Diffraction, or MicroED, which is essentially three-dimensional (3D) electron crystallography of microscopic crystals. This method uses truly 3D crystals, that are about a billion times smaller than those typically used for X-ray crystallography, for electron diffraction studies. There are several important differences and some similarities between electron crystallography of 2D crystals and MicroED. In this review, we describe the development of these techniques, their similarities and differences, and offer our opinion of future directions in both fields.
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Affiliation(s)
- Michael W Martynowycz
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA.,Howard Hughes Medical Institute, Departments of Physiology and Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, California 90095, USA
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4
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Pramanik S, Kutzner A, Heese K. 3D Structure, Dimerization Modeling, and Lead Discovery by Ligand-protein Interaction Analysis of p60 Transcription Regulator Protein (p60TRP). Mol Inform 2015; 35:99-108. [DOI: 10.1002/minf.201500035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 05/20/2015] [Indexed: 12/28/2022]
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5
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Uddin YM, Schmidt-Krey I. Inducing two-dimensional crystallization of membrane proteins by dialysis for electron crystallography. Methods Enzymol 2015; 557:351-62. [PMID: 25950973 DOI: 10.1016/bs.mie.2014.12.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron crystallography is an electron cryo-microscopy (cryo-EM) method that is particularly suitable for structure-function studies of small membrane proteins, which are crystallized in two-dimensional (2D) arrays for subsequent cryo-EM data collection and image processing. This approach allows for structural analysis of membrane proteins in a close-to-native, phospholipid bilayer environment. The process of growing 2D crystals from purified membrane proteins by dialysis detergent removal is described in this chapter. A short section covers screening for and identifying 2D crystals by transmission electron microscopy, and in the last section, optimization of the purification to obtain crystals of higher quality is discussed.
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Affiliation(s)
- Yusuf M Uddin
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ingeborg Schmidt-Krey
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA.
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6
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Pramanik S, Kutzner A, Heese K. Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17). Tumour Biol 2014; 36:239-49. [PMID: 25234718 DOI: 10.1007/s13277-014-2620-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 09/09/2014] [Indexed: 12/30/2022] Open
Abstract
FAM72A (p17) is a novel neuronal protein that has been linked to tumorigenic effects in non-neuronal tissue. Using state of the art in silico physicochemical analyses (e.g., I-TASSER, RaptorX, and Modeller), we determined the three-dimensional (3D) protein structure of FAM72A and further identified potential ligand-protein interactions. Our data indicate a Zn(2+)/Fe(3+)-containing 3D protein structure, based on a 3GA3_A model template, which potentially interacts with the organic molecule RSM ((2s)-2-(acetylamino)-N-methyl-4-[(R)-methylsulfinyl] butanamide). The discovery of RSM may serve as potential lead for further anti-FAM72A drug screening tests in the pharmaceutical industry because interference with FAM72A's activities via RSM-related molecules might be a novel option to influence the tumor suppressor protein p53 signaling pathways for the treatment of various types of cancers.
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Affiliation(s)
- Subrata Pramanik
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea
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7
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8
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Johnson MC, Schmidt-Krey I. Two-dimensional crystallization by dialysis for structural studies of membrane proteins by the cryo-EM method electron crystallography. Methods Cell Biol 2013; 113:325-37. [PMID: 23317909 DOI: 10.1016/b978-0-12-407239-8.00015-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Two-dimensional (2D) crystals of integral membrane proteins, comprising ordered protein reconstituted into a synthetic lipid bilayer, can be induced to form from detergent solubilized and purified membrane protein sources via the addition of exogenous lipid and the subsequent removal of the solubilizing detergent. This is most commonly accomplished by dialysis of a small volume of ternary protein-detergent-lipid mixture against a large volume of buffer, and can be carried out using common, easily available materials. Following successful crystallization, electron crystallographic data obtained by electron cryo-microscopy (cryo-EM) of vitrified 2D crystals can be used to determine the structure of the lipid bilayer-embedded integral membrane protein.
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Affiliation(s)
- Matthew C Johnson
- Georgia Institute of Technology, School of Biology, Atlanta, GA, USA
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9
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Ruigrok VJB, Levisson M, Hekelaar J, Smidt H, Dijkstra BW, van der Oost J. Characterization of aptamer-protein complexes by X-ray crystallography and alternative approaches. Int J Mol Sci 2012; 13:10537-10552. [PMID: 22949878 PMCID: PMC3431876 DOI: 10.3390/ijms130810537] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/09/2012] [Accepted: 08/17/2012] [Indexed: 12/11/2022] Open
Abstract
Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (K(D)). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions.
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Affiliation(s)
- Vincent J. B. Ruigrok
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
| | - Mark Levisson
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
| | - Johan Hekelaar
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands; E-Mails: (J.H.); (B.W.D.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
| | - Bauke W. Dijkstra
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands; E-Mails: (J.H.); (B.W.D.)
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
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10
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Gualtieri EJ, Guo F, Kissick DJ, Jose J, Kuhn RJ, Jiang W, Simpson GJ. Detection of membrane protein two-dimensional crystals in living cells. Biophys J 2011; 100:207-14. [PMID: 21190673 DOI: 10.1016/j.bpj.2010.10.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/14/2010] [Accepted: 10/18/2010] [Indexed: 12/11/2022] Open
Abstract
It is notoriously difficult to grow membrane protein crystals and solve membrane protein structures. Improved detection and screening of membrane protein crystals are needed. We have shown here that second-order nonlinear optical imaging of chiral crystals based on second harmonic generation can provide sensitive and selective detection of two-dimensional protein crystalline arrays with sufficiently low background to enable crystal detection within the membranes of live cells. The method was validated using bacteriorhodopsin crystals generated in live Halobacterium halobium bacteria and confirmed by electron microscopy from the isolated crystals. Additional studies of alphavirus glycoproteins indicated the presence of localized crystalline domains associated with virus budding from mammalian cells. These results suggest that in vivo crystallization may provide a means for expediting membrane protein structure determination for proteins exhibiting propensities for two-dimensional crystal formation.
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Affiliation(s)
- E J Gualtieri
- Department of Chemistry, Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
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11
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Structural bioinformatics: deriving biological insights from protein structures. Interdiscip Sci 2010; 2:347-66. [PMID: 21153779 DOI: 10.1007/s12539-010-0045-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/18/2010] [Accepted: 06/21/2010] [Indexed: 12/27/2022]
Abstract
Structural bioinformatics can be described as an approach that will help decipher biological insights from protein structures. As an important component of structural biology, this area promises to provide a high resolution understanding of biology by assisting comprehension and interpretation of a large amount of structural data. Biological function of protein molecules can be inferred from their three-dimensional structures by comparing structures, classifying them and transferring function from a related protein or family. It is well known now that the structure space of protein molecules is more conserved than the sequence space, making it important to seek functional associations at the structural level. An added advantage of structural bioinformatics over simpler sequence-based methods is that the former also provides ultimate insights into the mechanisms by which various biological events take place. A bird's eye-view of the different aspects of structural bioinformatics is given here along with various recent advances in the area including how knowledge obtained from structural bioinformatics can be applied in drug discovery.
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12
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Sander B, Golas MM. Visualization of bionanostructures using transmission electron microscopical techniques. Microsc Res Tech 2010; 74:642-63. [DOI: 10.1002/jemt.20963] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Accepted: 10/01/2010] [Indexed: 11/10/2022]
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13
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Kolb U, Gorelik TE, Mugnaioli E, Stewart A. Structural Characterization of Organics Using Manual and Automated Electron Diffraction. POLYM REV 2010. [DOI: 10.1080/15583724.2010.494238] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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14
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Preparation of 2D Crystals of Membrane Proteins for High-Resolution Electron Crystallography Data Collection. Methods Enzymol 2010; 481:25-43. [DOI: 10.1016/s0076-6879(10)81001-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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15
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Neiner D, Okamoto NL, Yu P, Leonard S, Condron CL, Toney MF, Ramasse QM, Browning ND, Kauzlarich SM. Synthesis and Characterization of K8−x(H2)ySi46. Inorg Chem 2009; 49:815-22. [DOI: 10.1021/ic9004592] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Cathie L. Condron
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Michael F. Toney
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Quentin M. Ramasse
- National Center of Electron Microscopy, Lawrence Berkeley Laboratory, 1 Cyclotron Road, Berkeley, California 94270
| | - Nigel D. Browning
- Department of Chemical Engineering and Materials Science
- National Center of Electron Microscopy, Lawrence Berkeley Laboratory, 1 Cyclotron Road, Berkeley, California 94270
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
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16
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Massover WH. On the experimental use of light metal salts for negative staining. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2008; 14:126-137. [PMID: 18312717 DOI: 10.1017/s1431927608080033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 07/21/2007] [Indexed: 05/26/2023]
Abstract
All common negative stains are salts of heavy metals. To remedy several technical defects inherent in the use of heavy metal compounds, this study investigates whether salts of the light metals sodium, magnesium, and aluminum can function as negative stains. Screening criteria require aqueous solubility at pH 7.0, formation of a smooth amorphous layer upon drying, and transmission electron microscope imaging of the 87-A (8.7-nm) lattice periodicity in thin catalase crystals. Six of 23 salts evaluated pass all three screens; detection of the protein shell in ferritin macromolecules indicates that light metal salts also provide negative staining of single particle specimens. Appositional contrast is less than that given by heavy metal negative stains; image density can be raised by increasing electron phase contrast and by selecting salts with phosphate or sulfate anions, thereby adding strong scattering from P or S atoms. Low-dose electron diffraction of catalase crystals negatively stained with 200 mM magnesium sulfate shows Bragg spots extending out to 4.4 A. Future experimental use of sodium phosphate buffer and magnesium sulfate for negative staining is anticipated, particularly in designing new cocktail (multicomponent) negative stains able to support and protect protein structure to higher resolution levels than are currently achieved.
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Affiliation(s)
- William H Massover
- Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA.
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17
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Müller DJ, Wu N, Palczewski K. Vertebrate membrane proteins: structure, function, and insights from biophysical approaches. Pharmacol Rev 2008; 60:43-78. [PMID: 18321962 DOI: 10.1124/pr.107.07111] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Membrane proteins are key targets for pharmacological intervention because they are vital for cellular function. Here, we analyze recent progress made in the understanding of the structure and function of membrane proteins with a focus on rhodopsin and development of atomic force microscopy techniques to study biological membranes. Membrane proteins are compartmentalized to carry out extra- and intracellular processes. Biological membranes are densely populated with membrane proteins that occupy approximately 50% of their volume. In most cases membranes contain lipid rafts, protein patches, or paracrystalline formations that lack the higher-order symmetry that would allow them to be characterized by diffraction methods. Despite many technical difficulties, several crystal structures of membrane proteins that illustrate their internal structural organization have been determined. Moreover, high-resolution atomic force microscopy, near-field scanning optical microscopy, and other lower resolution techniques have been used to investigate these structures. Single-molecule force spectroscopy tracks interactions that stabilize membrane proteins and those that switch their functional state; this spectroscopy can be applied to locate a ligand-binding site. Recent development of this technique also reveals the energy landscape of a membrane protein, defining its folding, reaction pathways, and kinetics. Future development and application of novel approaches during the coming years should provide even greater insights to the understanding of biological membrane organization and function.
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Affiliation(s)
- Daniel J Müller
- Biotechnology Center, University of Technology, Dresden, Germany
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18
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Garduño E, Wong-Barnum M, Volkmann N, Ellisman MH. Segmentation of electron tomographic data sets using fuzzy set theory principles. J Struct Biol 2008; 162:368-79. [PMID: 18358741 DOI: 10.1016/j.jsb.2008.01.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 01/25/2008] [Accepted: 01/30/2008] [Indexed: 11/24/2022]
Abstract
In electron tomography the reconstructed density function is typically corrupted by noise and artifacts. Under those conditions, separating the meaningful regions of the reconstructed density function is not trivial. Despite development efforts that specifically target electron tomography manual segmentation continues to be the preferred method. Based on previous good experiences using a segmentation based on fuzzy logic principles (fuzzy segmentation) where the reconstructed density functions also have low signal-to-noise ratio, we applied it to electron tomographic reconstructions. We demonstrate the usefulness of the fuzzy segmentation algorithm evaluating it within the limits of segmenting electron tomograms of selectively stained, plastic embedded spiny dendrites. The results produced by the fuzzy segmentation algorithm within the framework presented are encouraging.
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Affiliation(s)
- Edgar Garduño
- Depto. Ciencias de la Computación, Instituto de Investigaciones en Matermáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Circuito Escolar S/N, Cd. Universitaria, C.P. 04510, Mexico City, Mexico.
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19
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Zou X, Hovmöller S. Electron crystallography: imaging and single-crystal diffraction from powders. Acta Crystallogr A 2007; 64:149-60. [DOI: 10.1107/s0108767307060084] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 11/16/2007] [Indexed: 11/10/2022] Open
Abstract
The study of crystals at atomic level by electrons – electron crystallography – is an important complement to X-ray crystallography. There are two main advantages of structure determinations by electron crystallography compared to X-ray diffraction: (i) crystals millions of times smaller than those needed for X-ray diffraction can be studied and (ii) the phases of the crystallographic structure factors, which are lost in X-ray diffraction, are present in transmission-electron-microscopy (TEM) images. In this paper, some recent developments of electron crystallography and its applications, mainly on inorganic crystals, are shown. Crystal structures can be solved to atomic resolution in two dimensions as well as in three dimensions from both TEM images and electron diffraction. Different techniques developed for electron crystallography, including three-dimensional reconstruction, the electron precession technique and ultrafast electron crystallography, are reviewed. Examples of electron-crystallography applications are given. There is in principle no limitation to the complexity of the structures that can be solved by electron crystallography.
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20
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Zeng X, Stahlberg H, Grigorieff N. A maximum likelihood approach to two-dimensional crystals. J Struct Biol 2007; 160:362-74. [PMID: 17964808 PMCID: PMC2147720 DOI: 10.1016/j.jsb.2007.09.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 09/05/2007] [Accepted: 09/14/2007] [Indexed: 11/24/2022]
Abstract
Maximum likelihood (ML) processing of transmission electron microscopy images of protein particles can produce reconstructions of superior resolution due to a reduced reference bias. We have investigated a ML processing approach to images centered on the unit cells of two-dimensional (2D) crystal images. The implemented software makes use of the predictive lattice node tracking in the MRC software, which is used to window particle stacks. These are then noise-whitened and subjected to ML processing. Resulting ML maps are translated into amplitudes and phases for further processing within the 2dx software package. Compared with ML processing for randomly oriented single particles, the required computational costs are greatly reduced as the 2D crystals restrict the parameter search space. The software was applied to images of negatively stained or frozen hydrated 2D crystals of different crystal order. We find that the ML algorithm is not free from reference bias, even though its sensitivity to noise correlation is lower than for pure cross-correlation alignment. Compared with crystallographic processing, the newly developed software yields better resolution for 2D crystal images of lower crystal quality, and it performs equally well for well-ordered crystal images.
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Affiliation(s)
- Xiangyan Zeng
- Molecular & Cellular Biology, University of California at Davis, 1 Shields Ave., Davis, CA 95616, USA
| | - Henning Stahlberg
- Molecular & Cellular Biology, University of California at Davis, 1 Shields Ave., Davis, CA 95616, USA
| | - Nikolaus Grigorieff
- Howard Hughes Medical Institute and Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
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21
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Chiu PL, Pagel MD, Evans J, Chou HT, Zeng X, Gipson B, Stahlberg H, Nimigean CM. The structure of the prokaryotic cyclic nucleotide-modulated potassium channel MloK1 at 16 A resolution. Structure 2007; 15:1053-64. [PMID: 17850745 PMCID: PMC2000844 DOI: 10.1016/j.str.2007.06.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Revised: 06/11/2007] [Accepted: 06/14/2007] [Indexed: 11/24/2022]
Abstract
The gating ring of cyclic nucleotide-modulated channels is proposed to be either a two-fold symmetric dimer of dimers or a four-fold symmetric tetramer based on high-resolution structure data of soluble cyclic nucleotide-binding domains and functional data on intact channels. We addressed this controversy by obtaining structural data on an intact, full-length, cyclic nucleotide-modulated potassium channel, MloK1, from Mesorhizobium loti, which also features a putative voltage-sensor. We present here the 3D single-particle structure by transmission electron microscopy and the projection map of membrane-reconstituted 2D crystals of MloK1 in the presence of cAMP. Our data show a four-fold symmetric arrangement of the CNBDs, separated by discrete gaps. A homology model for full-length MloK1 suggests a vertical orientation for the CNBDs. The 2D crystal packing in the membrane-embedded state is compatible with the S1-S4 domains in the vertical "up" state.
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Affiliation(s)
- Po-Lin Chiu
- Molecular and Cellular Biology, College of Biological Sciences, University of California-Davis, 1 Shields Avenue, Davis, CA 95616, USA
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22
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Gipson B, Zeng X, Stahlberg H. 2dx_merge: data management and merging for 2D crystal images. J Struct Biol 2007; 160:375-84. [PMID: 17967545 DOI: 10.1016/j.jsb.2007.09.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Revised: 08/29/2007] [Accepted: 09/06/2007] [Indexed: 10/22/2022]
Abstract
Electron crystallography of membrane proteins determines the structure of membrane-reconstituted and two-dimensionally (2D) crystallized membrane proteins by low-dose imaging with the transmission electron microscope, and computer image processing. We have previously presented the software system 2dx, for user-friendly image processing of 2D crystal images. Its central component 2dx_image is based on the MRC program suite, and allows the optionally fully automatic processing of one 2D crystal image. We present here the program 2dx_merge, which assists the user in the management of a 2D crystal image processing project, and facilitates the merging of the data from multiple images. The merged dataset can be used as a reference to re-process all images, which usually improves the resolution of the final reconstruction. Image processing and merging can be applied iteratively, until convergence is reached. 2dx is available under the GNU General Public License at http://2dx.org.
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Affiliation(s)
- Bryant Gipson
- Molecular and Cellular Biology, Briggs Hall, College of Biological Sciences, University of California at Davis, 1 Shields Avenue, Davis, CA 95616, USA
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Minor DL. The neurobiologist's guide to structural biology: a primer on why macromolecular structure matters and how to evaluate structural data. Neuron 2007; 54:511-33. [PMID: 17521566 PMCID: PMC3011226 DOI: 10.1016/j.neuron.2007.04.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Structural biology now plays a prominent role in addressing questions central to understanding how excitable cells function. Although interest in the insights gained from the definition and dissection of macromolecular anatomy is high, many neurobiologists remain unfamiliar with the methods employed. This primer aims to help neurobiologists understand approaches for probing macromolecular structure and where the limits and challenges remain. Using examples of macromolecules with neurobiological importance, the review covers X-ray crystallography, electron microscopy (EM), small-angle X-ray scattering (SAXS), and nuclear magnetic resonance (NMR) and biophysical methods with which these approaches are often paired: isothermal titration calorimetry (ITC), equilibrium analytical ultracentifugation, and molecular dynamics (MD).
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Affiliation(s)
- Daniel L Minor
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158-2330, USA.
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Gipson B, Zeng X, Zhang ZY, Stahlberg H. 2dx—User-friendly image processing for 2D crystals. J Struct Biol 2007; 157:64-72. [PMID: 17055742 DOI: 10.1016/j.jsb.2006.07.020] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 07/25/2006] [Accepted: 07/29/2006] [Indexed: 10/24/2022]
Abstract
Electron crystallography determines the structure of two-dimensional (2D) membrane protein crystals and other 2D crystal systems. Cryo-transmission electron microscopy records high-resolution electron micrographs, which require computer processing for three-dimensional structure reconstruction. We present a new software system 2dx, which is designed as a user-friendly, platform-independent software package for electron crystallography. 2dx assists in the management of an image-processing project, guides the user through the processing of 2D crystal images, and provides transparence for processing tasks and results. Algorithms are implemented in the form of script templates reminiscent of c-shell scripts. These templates can be easily modified or replaced by the user and can also execute modular stand-alone programs from the MRC software or from other image processing software packages. 2dx is available under the GNU General Public License at 2dx.org.
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Affiliation(s)
- Bryant Gipson
- Molecular and Cellular Biology, University of California at Davis, CA 95616, USA
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