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Article ; Online: Characterization of membrane protein function by solid-state NMR spectroscopy.

Baker, Lindsay A / Baldus, Marc

2014 Volume 27, Page(s) 48–55

Abstract: Membrane proteins are an important class of biological molecules whose association with lipid bilayers and intrinsic molecular mobility can complicate their structural study by high-resolution methods. As different experimental techniques require ... ...

Abstract	Membrane proteins are an important class of biological molecules whose association with lipid bilayers and intrinsic molecular mobility can complicate their structural study by high-resolution methods. As different experimental techniques require different membrane mimetics, it can be challenging to relate membrane protein structure to function. This review presents examples of the use of solid-state nuclear magnetic resonance spectroscopy (ssNMR) to correlate structure and function in membrane proteins with diverse biological roles, including signaling, transport, and enzymatic reactions. The types of ssNMR experiments, as well as sources of complementary information and implications for biology, will be discussed. An outlook towards extending ssNMR studies to cellular preparations will be given.
MeSH term(s)	Enzymes/metabolism ; Humans ; Kinetics ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Nuclear Magnetic Resonance, Biomolecular/methods ; Signal Transduction
Chemical Substances	Enzymes ; Membrane Proteins
Language	English
Publishing date	2014-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2014.03.009
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Article ; Online: Uncovering the Role of

El-Baba, Tarick J / Lutomski, Corinne A / Burnap, Sean A / Bolla, Jani R / Baker, Lindsay A / Baldwin, Andrew J / Struwe, Weston B / Robinson, Carol V

Journal of the American Chemical Society

2023 Volume 145, Issue 14, Page(s) 8021–8032

Abstract: Interactions between the SARS-CoV-2 Spike protein and ACE2 are one of the most scrutinized reactions of our time. Yet, questions remain as to the impact of glycans on mediating ACE2 dimerization and downstream interactions with Spike. Here, we address ... ...

Abstract	Interactions between the SARS-CoV-2 Spike protein and ACE2 are one of the most scrutinized reactions of our time. Yet, questions remain as to the impact of glycans on mediating ACE2 dimerization and downstream interactions with Spike. Here, we address these unanswered questions by combining a glycoengineering strategy with high-resolution native mass spectrometry (MS) to investigate the impact of
MeSH term(s)	Humans ; SARS-CoV-2/metabolism ; COVID-19 ; Angiotensin-Converting Enzyme 2/chemistry ; Protein Binding ; Mass Spectrometry ; Polysaccharides
Chemical Substances	spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Polysaccharides
Language	English
Publishing date	2023-03-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c00291
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Article ; Online: Electron cryo-tomography captures macromolecular complexes in native environments.

Baker, Lindsay A / Grange, Michael / Grünewald, Kay

Current opinion in structural biology

2017 Volume 46, Page(s) 149–156

Abstract: Transmission electron microscopy has a long history in cellular biology. Fixed and stained samples have been used for cellular imaging for over 50 years, but suffer from sample preparation induced artifacts. Electron cryo-tomography (cryoET) instead uses ...

Abstract	Transmission electron microscopy has a long history in cellular biology. Fixed and stained samples have been used for cellular imaging for over 50 years, but suffer from sample preparation induced artifacts. Electron cryo-tomography (cryoET) instead uses frozen-hydrated samples, without chemical modification, to determine the structure of macromolecular complexes in their native environment. Recent developments in electron microscopes and associated technologies have greatly expanded our ability to visualize cellular features and determine the structures of macromolecular complexes in situ. This review highlights the technological improvements and the new areas of biology these advances have made accessible. We discuss the potential of cryoET to reveal novel and significant biological information on the nanometer or subnanometer scale, and directions for further work.
MeSH term(s)	Animals ; Cryoelectron Microscopy/methods ; Humans ; Macromolecular Substances/chemistry ; Systems Integration
Chemical Substances	Macromolecular Substances
Language	English
Publishing date	2017
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2017.08.005
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Article ; Online: Edged watershed segmentation: a semi-interactive algorithm for segmentation of low-resolution maps from electron cryomicroscopy.

Baker, Lindsay A / Rubinstein, John L

Journal of structural biology

2011 Volume 176, Issue 1, Page(s) 127–132

Abstract: Electron cryomicroscopy (cryo-EM) allows for the structural analysis of large protein complexes that may be difficult to study by other means. Frequently, maps of complexes from cryo-EM are obtained at resolutions between 10 and 25Å. To aid in the ... ...

Abstract	Electron cryomicroscopy (cryo-EM) allows for the structural analysis of large protein complexes that may be difficult to study by other means. Frequently, maps of complexes from cryo-EM are obtained at resolutions between 10 and 25Å. To aid in the interpretation of these medium- to low-resolution maps, they may be subdivided into three-dimensional segments representing subunits or subcomplexes. This division is often accomplished using a manual segmentation approach. While extremely useful, manual segmentation is subjective. We have developed a novel semi-interactive segmentation algorithm that can incorporate prior knowledge of subunit composition or structure without biasing the boundaries between subunits or subcomplexes. This algorithm has been characterized with experimental and simulated cryo-EM density maps at resolutions between 10 and 25Å.
MeSH term(s)	Algorithms ; Computer Simulation ; Cryoelectron Microscopy/methods ; Models, Molecular ; Multiprotein Complexes/chemistry
Chemical Substances	Multiprotein Complexes
Language	English
Publishing date	2011-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2011.06.012
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Article ; Online: Radiation damage in electron cryomicroscopy.

Baker, Lindsay A / Rubinstein, John L

Methods in enzymology

2010 Volume 481, Page(s) 371–388

Abstract: In an electron microscope, the electron beam used to determine the structures of biological tissues, cells, and molecules destroys the specimen as the image is acquired. This destruction occurs before a statistically well-defined image can be obtained ... ...

Abstract	In an electron microscope, the electron beam used to determine the structures of biological tissues, cells, and molecules destroys the specimen as the image is acquired. This destruction occurs before a statistically well-defined image can be obtained and is consequently the fundamental limit to resolution in biological electron cryomicroscopy (cryo-EM). Damage from the destructive interaction of electrons with frozen-hydrated specimens occurs in three stages: primary damage, as electrons ionize the sample, break bonds, and produce secondary electrons and free radicals; secondary damage, as the secondary electrons and free radicals migrate through the specimen and cause further chemical reactions; and tertiary damage, as hydrogen gas is evolved within the sample, causing gross morphological changes to the specimen. The deleterious effects of radiation are minimized in cryo-EM by limiting the exposure of the specimen to incident electrons and cooling the sample to reduce secondary damage. This review emphasizes practical considerations for minimizing radiation damage, including measurement of electron exposure, estimation of absorbed doses of energy, selection of microscope voltage and specimen temperature, and selection of electron exposure to optimize images.
MeSH term(s)	Cryoelectron Microscopy/methods ; Radiation
Language	English
Publishing date	2010
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1557-7988 ; 0076-6879
ISSN (online)	1557-7988
ISSN	0076-6879
DOI	10.1016/S0076-6879(10)81015-8
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Article ; Online: Cryo-SOFI enabling low-dose super-resolution correlative light and electron cryo-microscopy.

Moser, Felipe / Pražák, Vojtěch / Mordhorst, Valerie / Andrade, Débora M / Baker, Lindsay A / Hagen, Christoph / Grünewald, Kay / Kaufmann, Rainer

Proceedings of the National Academy of Sciences of the United States of America

2019 Volume 116, Issue 11, Page(s) 4804–4809

Abstract: Correlative light and electron cryo-microscopy (cryo-CLEM) combines information from the specific labeling of fluorescence cryo-microscopy (cryo-FM) with the high resolution in environmental context of electron cryo-microscopy (cryo-EM). Exploiting super- ...

Abstract	Correlative light and electron cryo-microscopy (cryo-CLEM) combines information from the specific labeling of fluorescence cryo-microscopy (cryo-FM) with the high resolution in environmental context of electron cryo-microscopy (cryo-EM). Exploiting super-resolution methods for cryo-FM is advantageous, as it enables the identification of rare events within the environmental background of cryo-EM at a sensitivity and resolution beyond that of conventional methods. However, due to the need for relatively high laser intensities, current super-resolution cryo-CLEM methods require cryo-protectants or support films which can severely reduce image quality in cryo-EM and are not compatible with many samples, such as mammalian cells. Here, we introduce cryogenic super-resolution optical fluctuation imaging (cryo-SOFI), a low-dose super-resolution imaging scheme based on the SOFI principle. As cryo-SOFI does not require special sample preparation, it is fully compatible with conventional cryo-EM specimens, and importantly, it does not affect the quality of cryo-EM imaging. By applying cryo-SOFI to a variety of biological application examples, we demonstrate resolutions up to ∼135 nm, an improvement of up to three times compared with conventional cryo-FM, while maintaining the specimen in a vitrified state for subsequent cryo-EM. Cryo-SOFI presents a general solution to the problem of specimen devitrification in super-resolution cryo-CLEM. It does not require a complex optical setup and can easily be implemented in any existing cryo-FM system.
MeSH term(s)	Animals ; Cell Line ; Cryoelectron Microscopy/methods ; Endoplasmic Reticulum/ultrastructure ; Humans ; Microscopy, Fluorescence ; Mitochondria/ultrastructure
Language	English
Publishing date	2019-02-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1810690116
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Article ; Online: DNA origami signposts for identifying proteins on cell membranes by electron cryotomography.

Silvester, Emma / Vollmer, Benjamin / Pražák, Vojtěch / Vasishtan, Daven / Machala, Emily A / Whittle, Catheryne / Black, Susan / Bath, Jonathan / Turberfield, Andrew J / Grünewald, Kay / Baker, Lindsay A

Cell

2021 Volume 184, Issue 4, Page(s) 1110–1121.e16

Abstract: Electron cryotomography (cryoET), an electron cryomicroscopy (cryoEM) modality, has changed our understanding of biological function by revealing the native molecular details of membranes, viruses, and cells. However, identification of individual ... ...

Abstract	Electron cryotomography (cryoET), an electron cryomicroscopy (cryoEM) modality, has changed our understanding of biological function by revealing the native molecular details of membranes, viruses, and cells. However, identification of individual molecules within tomograms from cryoET is challenging because of sample crowding and low signal-to-noise ratios. Here, we present a tagging strategy for cryoET that precisely identifies individual protein complexes in tomograms without relying on metal clusters. Our method makes use of DNA origami to produce "molecular signposts" that target molecules of interest, here via fluorescent fusion proteins, providing a platform generally applicable to biological surfaces. We demonstrate the specificity of signpost origami tags (SPOTs) in vitro as well as their suitability for cryoET of membrane vesicles, enveloped viruses, and the exterior of intact mammalian cells.
MeSH term(s)	Animals ; Aptamers, Nucleotide/chemistry ; Biophysical Phenomena ; Cell Line ; Cell Membrane/ultrastructure ; Cryoelectron Microscopy ; DNA/ultrastructure ; Electron Microscope Tomography ; Female ; Fluorescence ; Humans ; Nanoparticles/ultrastructure
Chemical Substances	Aptamers, Nucleotide ; DNA (9007-49-2)
Language	English
Publishing date	2021-02-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.01.033
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Article ; Online: Angle determination for side views in single particle electron microscopy.

Baker, Lindsay A / Rubinstein, John L

Journal of structural biology

2008 Volume 162, Issue 2, Page(s) 260–270

Abstract: In order to build a first model in single particle electron microscopy the relative angular orientation of each image of a protein complex must be determined. These orientations can be described by three Eulerian angles. Images of complexes that present ... ...

Abstract	In order to build a first model in single particle electron microscopy the relative angular orientation of each image of a protein complex must be determined. These orientations can be described by three Eulerian angles. Images of complexes that present the same view can be aligned in two-dimensions and averaged in order to increase their signal-to-noise ratio. Based on these averaged images, several standard approaches exist for determining Euler angles for randomly oriented projection images. The common lines and angular reconstitution methods work well for particles with symmetry while the random conical tilting and related orthogonal tilt reconstruction methods work in most cases but require the acquisition of tilt pairs of images. For the situation where views of particles can be identified that are rotations about a single axis parallel to the grid, an alternative algorithm to determine the orientations of class averages without the need to acquire tilt pairs can be applied. This type of view of a complex is usually called a side view. This paper describes the detailed workings and characterization of an algorithm, named rotational analysis, which uses real-space fiducial markers derived from the averages themselves to determine the Euler angles for side views. We demonstrate how this algorithm works in practice by applying it to a data set of images of affinity-purified bovine mitochondrial ATP synthase.
MeSH term(s)	Algorithms ; Animals ; Cattle ; Image Processing, Computer-Assisted ; Microscopy, Electron/instrumentation ; Microscopy, Electron/methods ; Mitochondrial Proton-Translocating ATPases/chemistry ; Multiprotein Complexes/chemistry
Chemical Substances	Multiprotein Complexes ; Mitochondrial Proton-Translocating ATPases (EC 3.6.3.-)
Language	English
Publishing date	2008-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2008.01.001
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Article ; Online: The use of sonicated lipid vesicles for mass spectrometry of membrane protein complexes.

Chorev, Dror S / Tang, Haiping / Rouse, Sarah L / Bolla, Jani Reddy / von Kügelgen, Andriko / Baker, Lindsay A / Wu, Di / Gault, Joseph / Grünewald, Kay / Bharat, Tanmay A M / Matthews, Stephen J / Robinson, Carol V

Nature protocols

2020 Volume 15, Issue 5, Page(s) 1690–1706

Abstract: Recent applications of mass spectrometry (MS) to study membrane protein complexes are yielding valuable insights into the binding of lipids and their structural and functional roles. To date, most native MS experiments with membrane proteins are based on ...

Abstract	Recent applications of mass spectrometry (MS) to study membrane protein complexes are yielding valuable insights into the binding of lipids and their structural and functional roles. To date, most native MS experiments with membrane proteins are based on detergent solubilization. Many insights into the structure and function of membrane proteins have been obtained using detergents; however, these can promote local lipid rearrangement and can cause fluctuations in the oligomeric state of protein complexes. To overcome these problems, we developed a method that does not use detergents or other chemicals. Here we report a detailed protocol that enables direct ejection of protein complexes from membranes for analysis by native MS. Briefly, lipid vesicles are prepared directly from membranes of different sources and subjected to sonication pulses. The resulting destabilized vesicles are concentrated, introduced into a mass spectrometer and ionized. The mass of the observed protein complexes is determined and this information, in conjunction with 'omics'-based strategies, is used to determine subunit stoichiometry as well as cofactor and lipid binding. Within this protocol, we expand the applications of the method to include peripheral membrane proteins of the S-layer and amyloid protein export machineries overexpressed in membranes from which the most abundant components have been removed. The described experimental procedure takes approximately 3 d from preparation to MS. The time required for data analysis depends on the complexity of the protein assemblies embedded in the membrane under investigation.
MeSH term(s)	Cytoplasmic Vesicles ; Mass Spectrometry/methods ; Membrane Proteins/analysis ; Sonication
Chemical Substances	Membrane Proteins
Language	English
Publishing date	2020-04-01
Publishing country	England
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-020-0303-y
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Article ; Online: Cellular Electron Cryo-Tomography to Study Virus-Host Interactions.

Quemin, Emmanuelle R J / Machala, Emily A / Vollmer, Benjamin / Pražák, Vojtěch / Vasishtan, Daven / Rosch, Rene / Grange, Michael / Franken, Linda E / Baker, Lindsay A / Grünewald, Kay

Annual review of virology

2020 Volume 7, Issue 1, Page(s) 239–262

Abstract: Viruses are obligatory intracellular parasites that reprogram host cells upon infection to produce viral progeny. Here, we review recent structural insights into virus-host interactions in bacteria, archaea, and eukaryotes unveiled by cellular electron ... ...

Abstract	Viruses are obligatory intracellular parasites that reprogram host cells upon infection to produce viral progeny. Here, we review recent structural insights into virus-host interactions in bacteria, archaea, and eukaryotes unveiled by cellular electron cryo-tomography (cryoET). This advanced three-dimensional imaging technique of vitreous samples in near-native state has matured over the past two decades and proven powerful in revealing molecular mechanisms underlying viral replication. Initial studies were restricted to cell peripheries and typically focused on early infection steps, analyzing surface proteins and viral entry. Recent developments including cryo-thinning techniques, phase-plate imaging, and correlative approaches have been instrumental in also targeting rare events inside infected cells. When combined with advances in dedicated image analyses and processing methods, details of virus assembly and egress at (sub)nanometer resolution were uncovered. Altogether, we provide a historical and technical perspective and discuss future directions and impacts of cryoET for integrative structural cell biology analyses of viruses.
MeSH term(s)	Cryoelectron Microscopy/methods ; Electron Microscope Tomography/methods ; Host Microbial Interactions ; Humans ; Image Processing, Computer-Assisted ; Imaging, Three-Dimensional/instrumentation ; Imaging, Three-Dimensional/methods ; Virus Replication ; Viruses/ultrastructure
Language	English
Publishing date	2020-07-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2764224-0
ISSN	2327-0578 ; 2327-056X
ISSN (online)	2327-0578
ISSN	2327-056X
DOI	10.1146/annurev-virology-021920-115935
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