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Xia X, Sung PY, Martynowycz MW, Gonen T, Roy P, Zhou ZH. RNA genome packaging and capsid assembly of bluetongue virus visualized in host cells. Cell 2024; 187:2236-2249.e17. [PMID: 38614100 DOI: 10.1016/j.cell.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 10/18/2023] [Accepted: 03/07/2024] [Indexed: 04/15/2024]
Abstract
Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques of high-resolution cryoelectron microscopy (cryo-EM), cellular cryoelectron tomography (cryo-ET), and structure-guided mutagenesis to investigate genome packaging and capsid assembly of bluetongue virus (BTV), a member of the Reoviridae family of dsRNA viruses. A total of eleven assembly states of BTV capsid were captured, with resolutions up to 2.8 Å, with most visualized in the host cytoplasm. ATPase VP6 was found underneath the vertices of capsid shell protein VP3 as an RNA-harboring pentamer, facilitating RNA packaging. RNA packaging expands the VP3 shell, which then engages middle- and outer-layer proteins to generate infectious virions. These revealed "duality" characteristics of the BTV assembly mechanism reconcile previous contradictory co-assembly and core-filling models and provide insights into the mysterious RNA packaging and capsid assembly of Reoviridae members and beyond.
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Affiliation(s)
- Xian Xia
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Po-Yu Sung
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Michael W Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Polly Roy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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2
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Bardin AA, Haymaker A, Banihashemi F, Lin JYS, Martynowycz MW, Nannenga BL. Focused ion beam milling and MicroED structure determination of metal-organic framework crystals. Ultramicroscopy 2024; 257:113905. [PMID: 38086288 PMCID: PMC10843726 DOI: 10.1016/j.ultramic.2023.113905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
We report new advancements in the determination and high-resolution structural analysis of beam-sensitive metal organic frameworks (MOFs) using microcrystal electron diffraction (MicroED) coupled with focused ion beam milling at cryogenic temperatures (cryo-FIB). A microcrystal of the beam-sensitive MOF, ZIF-8, was ion-beam milled in a thin lamella approximately 150 nm thick. MicroED data were collected from this thin lamella using an energy filter and a direct electron detector operating in counting mode. Using this approach, we achieved a greatly improved resolution of 0.59 Å with a minimal total exposure of only 0.64 e-/A2. These innovations not only improve model statistics but also further demonstrate that ion-beam milling is compatible with beam-sensitive materials, augmenting the capabilities of electron diffraction in MOF research.
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Affiliation(s)
- Andrey A Bardin
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States; Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, United States
| | - Alison Haymaker
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States; Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, United States
| | - Fateme Banihashemi
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States
| | - Jerry Y S Lin
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States
| | - Michael W Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States.
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States; Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, United States.
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3
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Haymaker A, Bardin AA, Gonen T, Martynowycz MW, Nannenga BL. Structure determination of a DNA crystal by MicroED. Structure 2023; 31:1499-1503.e2. [PMID: 37541248 PMCID: PMC10805983 DOI: 10.1016/j.str.2023.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 08/06/2023]
Abstract
Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In this study, we apply MicroED to DNA crystals, which have not been previously analyzed using this technique. We utilized the d(CGCGCG)2 DNA duplex as a model sample and employed cryo-FIB milling to create thin lamella for diffraction data collection. The MicroED data collection and subsequent processing resulted in a 1.10 Å resolution structure of the d(CGCGCG)2 DNA, demonstrating the successful application of cryo-FIB milling and MicroED to the investigation of nucleic acid crystals.
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Affiliation(s)
- Alison Haymaker
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Andrey A Bardin
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael W Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Brent L Nannenga
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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4
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Hattne J, Clabbers MTB, Martynowycz MW, Gonen T. Electron counting with direct electron detectors in MicroED. Structure 2023; 31:1504-1509.e1. [PMID: 37992709 PMCID: PMC10756876 DOI: 10.1016/j.str.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/30/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023]
Abstract
The combination of high sensitivity and rapid readout makes it possible for electron-counting detectors to record cryogenic electron microscopy data faster and more accurately without increasing the number of electrons used for data collection. This is especially useful for MicroED of macromolecular crystals where the strength of the diffracted signal at high resolution is comparable to the surrounding background. The ability to decrease fluence also alleviates concerns about radiation damage which limits the information that can be recovered from a diffraction measurement. The major concern with electron-counting direct detectors lies at the low end of the resolution spectrum: their limited linear range makes strong low-resolution reflections susceptible to coincidence loss and careful data collection is required to avoid compromising data quality. Nevertheless, these cameras are increasingly deployed in cryo-EM facilities, and several have been successfully used for MicroED. Provided coincidence loss can be minimized, electron-counting detectors bring high potential rewards.
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Affiliation(s)
- Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Max T B Clabbers
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael W Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Martynowycz MW, Andreev K, Mor A, Gidalevitz D. Cancer-Associated Gangliosides as a Therapeutic Target for Host Defense Peptide Mimics. Langmuir 2023; 39:12541-12549. [PMID: 37647566 DOI: 10.1021/acs.langmuir.3c01008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Aberrant levels of glycolipids expressed on cellular surfaces are characteristic of different types of cancers. The oligomer of acylated lysine (OAK) mimicking antimicrobial peptides displays in vitro activity against human and murine melanoma cell lines with upregulated GD3 and GM3 gangliosides. Herein, we demonstrate the capability of OAK to intercalate into the sialo-oligosaccharides of DPPC/GD3 and DPPC/GM3 lipid monolayers using X-ray scattering. The lack of insertion into monolayers containing phosphatidylserine suggests that the mechanism of action by OAKs against glycosylated lipid membranes is not merely driven by charge effects. The fluorescence microscopy data demonstrates the membrane-lytic activity of OAK. Understanding the molecular basis for selectivity toward GD3 and GM3 gangliosides by antimicrobial lipopeptides will contribute to the development of novel therapies to cure melanoma and other malignancies.
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Affiliation(s)
- Michael W Martynowycz
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, 10 W 35th Street, Chicago, Illinois 60616, United States
| | - Konstantin Andreev
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, 10 W 35th Street, Chicago, Illinois 60616, United States
| | - Amram Mor
- Department of Biotechnology and Food Engineering, Technion─Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - David Gidalevitz
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, 10 W 35th Street, Chicago, Illinois 60616, United States
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Shiriaeva A, Martynowycz MW, Nicolas WJ, Cherezov V, Gonen T. MicroED structure of the human vasopressin 1B receptor. bioRxiv 2023:2023.07.05.547888. [PMID: 37461729 PMCID: PMC10350018 DOI: 10.1101/2023.07.05.547888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The small size and flexibility of G protein-coupled receptors (GPCRs) have long posed a significant challenge to determining their structures for research and therapeutic applications. Single particle cryogenic electron microscopy (cryoEM) is often out of reach due to the small size of the receptor without a signaling partner. Crystallization of GPCRs in lipidic cubic phase (LCP) often results in crystals that may be too small and difficult to analyze using X-ray microcrystallography at synchrotron sources or even serial femtosecond crystallography at X-ray free electron lasers. Here, we determine the previously unknown structure of the human vasopressin 1B receptor (V1BR) using microcrystal electron diffraction (MicroED). To achieve this, we grew V1BR microcrystals in LCP and transferred the material directly onto electron microscopy grids. The protein was labeled with a fluorescent dye prior to crystallization to locate the microcrystals using cryogenic fluorescence microscopy, and then the surrounding material was removed using a plasma-focused ion beam to thin the sample to a thickness amenable to MicroED. MicroED data from 14 crystalline lamellae were used to determine the 3.2 Å structure of the receptor in the crystallographic space group P 1. These results demonstrate the use of MicroED to determine previously unknown GPCR structures that, despite significant effort, were not tractable by other methods.
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Affiliation(s)
- Anna Shiriaeva
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Michael W. Martynowycz
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
| | - William J. Nicolas
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
| | - Vadim Cherezov
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Tamir Gonen
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
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Gillman C, Nicolas WJ, Martynowycz MW, Gonen T. Design and implementation of suspended drop crystallization. IUCrJ 2023; 10:S2052252523004141. [PMID: 37223996 DOI: 10.1107/s2052252523004141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/10/2023] [Indexed: 05/26/2023]
Abstract
In this work, a novel crystal growth method termed suspended drop crystallization has been developed. Unlike traditional methods, this technique involves mixing protein and precipitant directly on an electron microscopy grid without any additional support layers. The grid is then suspended within a crystallization chamber designed in-house, allowing for vapor diffusion to occur from both sides of the drop. A UV-transparent window above and below the grid enables the monitoring of crystal growth via light, UV or fluorescence microscopy. Once crystals have formed, the grid can be removed and utilized for X-ray crystallography or microcrystal electron diffraction (MicroED) directly without having to manipulate the crystals. To demonstrate the efficacy of this method, crystals of the enzyme proteinase K were grown and its structure was determined by MicroED following focused ion beam/scanning electron microscopy milling to render the sample thin enough for cryoEM. Suspended drop crystallization overcomes many of the challenges associated with sample preparation, providing an alternative workflow for crystals embedded in viscous media, sensitive to mechanical stress and/or subject to preferred orientation on electron microscopy grids.
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Affiliation(s)
- Cody Gillman
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles, CA, USA
| | - William J Nicolas
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles, CA, USA
| | - Michael W Martynowycz
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles, CA, USA
| | - Tamir Gonen
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles, CA, USA
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8
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Hattne J, Clabbers MTB, Martynowycz MW, Gonen T. Electron-counting in MicroED. bioRxiv 2023:2023.06.29.547123. [PMID: 37425889 PMCID: PMC10327187 DOI: 10.1101/2023.06.29.547123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The combination of high sensitivity and rapid readout makes it possible for electron-counting detectors to record cryogenic electron microscopy data faster and more accurately without increasing the exposure. This is especially useful for MicroED of macromolecular crystals where the strength of the diffracted signal at high resolution is comparable to the surrounding background. The ability to decrease the exposure also alleviates concerns about radiation damage which limits the information that can be recovered from a diffraction measurement. However, the dynamic range of electron-counting detectors requires careful data collection to avoid errors from coincidence loss. Nevertheless, these detectors are increasingly deployed in cryo-EM facilities, and several have been successfully used for MicroED. Provided coincidence loss can be minimized, electron-counting detectors bring high potential rewards.
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Affiliation(s)
- Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Max T. B. Clabbers
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Physiology, University of California, Los Angeles, CA 90095
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Haymaker A, Bardin AA, Gonen T, Martynowycz MW, Nannenga BL. Structure determination of a DNA crystal by MicroED. bioRxiv 2023:2023.04.25.538338. [PMID: 37163108 PMCID: PMC10168392 DOI: 10.1101/2023.04.25.538338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In this study, we apply MicroED to DNA crystals, which have not been previously analyzed using this technique. We utilized the d(CGCGCG) 2 DNA duplex as a model sample and employed cryo-FIB milling to create thin lamella for diffraction data collection. The MicroED data collection and subsequent processing resulted in a 1.10 Å resolution structure of the d(CGCGCG) 2 DNA, demonstrating the successful application of cryo-FIB milling and MicroED to the investigation of nucleic acid crystals.
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10
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Gillman C, Nicolas WJ, Martynowycz MW, Gonen T. Design and implementation of suspended drop crystallization. bioRxiv 2023:2023.03.28.534639. [PMID: 37034794 PMCID: PMC10081258 DOI: 10.1101/2023.03.28.534639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We have developed a novel crystal growth method known as suspended drop crystallization. Unlike traditional methods, this technique involves mixing protein and precipitant directly on an electron microscopy grid without any additional support layers. The grid is then suspended within a crystallization chamber which we designed, allowing for vapor diffusion to occur from both sides of the drop. A UV transparent window above and below the grid enables the monitoring of crystal growth via light, UV, or fluorescence microscopy. Once crystals have formed, the grid can be removed and utilized for x-ray crystallography or microcrystal electron diffraction (MicroED) directly without having to manipulate the crystals. To demonstrate the efficacy of this method, we grew crystals of the enzyme proteinase K and determined its structure by MicroED following FIB/SEM milling to render the sample thin enough for cryoEM. Suspended drop crystallization overcomes many of the challenges associated with sample preparation, providing an alternative workflow for crystals embedded in viscous media, sensitive to mechanical stress, and/or suffering from preferred orientation on EM grids.
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Affiliation(s)
- Cody Gillman
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - William J. Nicolas
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles CA, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
| | - Michael W. Martynowycz
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles CA, USA
| | - Tamir Gonen
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
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Martynowycz MW, Shiriaeva A, Clabbers MTB, Nicolas WJ, Weaver SJ, Hattne J, Gonen T. A robust approach for MicroED sample preparation of lipidic cubic phase embedded membrane protein crystals. Nat Commun 2023; 14:1086. [PMID: 36841804 PMCID: PMC9968316 DOI: 10.1038/s41467-023-36733-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/15/2023] [Indexed: 02/26/2023] Open
Abstract
Crystallizing G protein-coupled receptors (GPCRs) in lipidic cubic phase (LCP) often yields crystals suited for the cryogenic electron microscopy (cryoEM) method microcrystal electron diffraction (MicroED). However, sample preparation is challenging. Embedded crystals cannot be targeted topologically. Here, we use an integrated fluorescence light microscope (iFLM) inside of a focused ion beam and scanning electron microscope (FIB-SEM) to identify fluorescently labeled GPCR crystals. Crystals are targeted using the iFLM and LCP is milled using a plasma focused ion beam (pFIB). The optimal ion source for preparing biological lamellae is identified using standard crystals of proteinase K. Lamellae prepared using either argon or xenon produced the highest quality data and structures. MicroED data are collected from the milled lamellae and the structures are determined. This study outlines a robust approach to identify and mill membrane protein crystals for MicroED and demonstrates plasma ion-beam milling is a powerful tool for preparing biological lamellae.
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Affiliation(s)
- Michael W Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Anna Shiriaeva
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Max T B Clabbers
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - William J Nicolas
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Sara J Weaver
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA. .,Department of Physiology, University of California, Los Angeles, CA, 90095, USA.
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12
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Clabbers MTB, Martynowycz MW, Hattne J, Nannenga BL, Gonen T. Electron-counting MicroED data with the K2 and K3 direct electron detectors. J Struct Biol 2022; 214:107886. [PMID: 36044956 PMCID: PMC9999727 DOI: 10.1016/j.jsb.2022.107886] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 12/30/2022]
Abstract
Microcrystal electron diffraction (MicroED) uses electron cryo-microscopy (cryo-EM) to collect diffraction data from small crystals during continuous rotation of the sample. As a result of advances in hardware as well as methods development, the data quality has continuously improved over the past decade, to the point where even macromolecular structures can be determined ab initio. Detectors suitable for electron diffraction should ideally have fast readout to record data in movie mode, and high sensitivity at low exposure rates to accurately report the intensities. Direct electron detectors are commonly used in cryo-EM imaging for their sensitivity and speed, but despite their availability are generally not used in diffraction. Primary concerns with diffraction experiments are the dynamic range and coincidence loss, which will corrupt the measurement if the flux exceeds the count rate of the detector. Here, we describe instrument setup and low-exposure MicroED data collection in electron-counting mode using K2 and K3 direct electron detectors and show that the integrated intensities can be effectively used to solve structures of two macromolecules between 1.2 Å and 2.8 Å resolution. Even though a beam stop was not used with the K3 studies we did not observe damage to the camera. As these cameras are already available in many cryo-EM facilities, this provides opportunities for users who do not have access to dedicated facilities for MicroED.
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Affiliation(s)
- Max T B Clabbers
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States
| | - Michael W Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States
| | - Johan Hattne
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Arizona State University, Tempe, AZ, United States; Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States; Department of Physiology, University of California, Los Angeles CA 90095, United States.
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Clabbers MT, Martynowycz MW, Hattne J, Gonen T. Hydrogens and hydrogen-bond networks in macromolecular MicroED data. J Struct Biol X 2022; 6:100078. [PMID: 36507068 PMCID: PMC9731847 DOI: 10.1016/j.yjsbx.2022.100078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Microcrystal electron diffraction (MicroED) is a powerful technique utilizing electron cryo-microscopy (cryo-EM) for protein structure determination of crystalline samples too small for X-ray crystallography. Electrons interact with the electrostatic potential of the sample, which means that the scattered electrons carry information about the charged state of atoms and provide relatively stronger contrast for visualizing hydrogen atoms. Accurately identifying the positions of hydrogen atoms, and by extension the hydrogen bonding networks, is of importance for understanding protein structure and function, in particular for drug discovery. However, identification of individual hydrogen atom positions typically requires atomic resolution data, and has thus far remained elusive for macromolecular MicroED. Recently, we presented the ab initio structure of triclinic hen egg-white lysozyme at 0.87 Å resolution. The corresponding data were recorded under low exposure conditions using an electron-counting detector from thin crystalline lamellae. Here, using these subatomic resolution MicroED data, we identified over a third of all hydrogen atom positions based on strong difference peaks, and directly visualize hydrogen bonding interactions and the charged states of residues. Furthermore, we find that the hydrogen bond lengths are more accurately described by the inter-nuclei distances than the centers of mass of the corresponding electron clouds. We anticipate that MicroED, coupled with ongoing advances in data collection and refinement, can open further avenues for structural biology by uncovering the hydrogen atoms and hydrogen bonding interactions underlying protein structure and function.
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Affiliation(s)
- Max T.B. Clabbers
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Michael W. Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Johan Hattne
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States,Department of Physiology, University of California, Los Angeles, CA 90095, United States,Corresponding author at: Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States.
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14
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Dayeen FR, Brandner BA, Martynowycz MW, Kucuk K, Foody MJ, Bu W, Hall SB, Gidalevitz D. Effects of cholesterol on the structure and collapse of DPPC monolayers. Biophys J 2022; 121:3533-3541. [PMID: 35841141 PMCID: PMC9515002 DOI: 10.1016/j.bpj.2022.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/02/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Cholesterol induces faster collapse by compressed films of pulmonary surfactant. Because collapse prevents films from reaching the high surface pressures achieved in the alveolus, most therapeutic surfactants remove or omit cholesterol. The studies here determined the structural changes by which cholesterol causes faster collapse by films of dipalmitoyl phosphatidylcholine, used as a simple model for the functional alveolar film. Measurements of isobaric collapse, with surface pressure held constant at 52 mN/m, showed that cholesterol had little effect until the mol fraction of cholesterol, Xchol, exceeded 0.20. Structural measurements of grazing incidence X-ray diffraction at ambient laboratory temperatures and a surface pressure of 44 mN/m, just below the onset of collapse, showed that the major structural change in an ordered phase occurred at lower Xchol. A centered rectangular unit cell with tilted chains converted to an untilted hexagonal structure over the range of Xchol = 0.0-0.1. For Xchol = 0.1-0.4, the ordered structure was nearly invariant; the hexagonal unit cell persisted, and the spacing of the chains was essentially unchanged. That invariance strongly suggests that above Xchol = 0.1, cholesterol partitions into a disordered phase, which coexists with the ordered domains. The phase rule requires that for a binary film with coexisting phases, the stoichiometries of the ordered and disordered regions must remain constant. Added cholesterol must increase the area of the disordered phase at the expense of the ordered regions. X-ray scattering from dipalmitoyl phosphatidylcholine/cholesterol fit with that prediction. The data also show a progressive decrease in the size of crystalline domains. Our results suggest that cholesterol promotes adsorption not by altering the unit cell of the ordered phase but by decreasing both its total area and the size of individual crystallites.
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Affiliation(s)
- Fazle R Dayeen
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, Illinois
| | - Bret A Brandner
- Pulmonary & Critical Care Medicine, Oregon Health & Science University, Portland, Oregon
| | - Michael W Martynowycz
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California
| | - Kamil Kucuk
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, Illinois
| | - Michael J Foody
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois
| | - Wei Bu
- NSF's ChemMatCARS, Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Stephen B Hall
- Pulmonary & Critical Care Medicine, Oregon Health & Science University, Portland, Oregon.
| | - David Gidalevitz
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, Illinois.
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15
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Martynowycz MW, Clabbers MTB, Hattne J, Gonen T. Ab initio phasing macromolecular structures using electron-counted MicroED data. Nat Methods 2022; 19:724-729. [PMID: 35637302 PMCID: PMC9184278 DOI: 10.1038/s41592-022-01485-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/07/2022] [Indexed: 12/31/2022]
Abstract
Structures of two globular proteins were determined ab initio using microcrystal electron diffraction (MicroED) data that were collected on a direct electron detector in counting mode. Microcrystals were identified using a scanning electron microscope (SEM) and thinned with a focused ion beam (FIB) to produce crystalline lamellae of ideal thickness. Continuous-rotation data were collected using an ultra-low exposure rate to enable electron counting in diffraction. For the first sample, triclinic lysozyme extending to a resolution of 0.87 Å, an ideal helical fragment of only three alanine residues provided initial phases. These phases were improved using density modification, allowing the entire atomic structure to be built automatically. A similar approach was successful on a second macromolecular sample, proteinase K, which is much larger and diffracted to a resolution of 1.5 Å. These results demonstrate that macromolecules can be determined to sub-ångström resolution by MicroED and that ab initio phasing can be successfully applied to counting data.
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Affiliation(s)
- Michael W. Martynowycz
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Max T. B. Clabbers
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Johan Hattne
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Department of Physiology, University of California, Los Angeles, CA, USA.
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16
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Abstract
The relationship between sample thickness and quality of data obtained is investigated by microcrystal electron diffraction (MicroED). Several electron microscopy (EM) grids containing proteinase K microcrystals of similar sizes from the same crystallization batch were prepared. Each grid was transferred into a focused ion beam and a scanning electron microscope in which the crystals were then systematically thinned into lamellae between 95- and 1,650-nm thick. MicroED data were collected at either 120-, 200-, or 300-kV accelerating voltages. Lamellae thicknesses were expressed in multiples of the corresponding inelastic mean free path to allow the results from different acceleration voltages to be compared. The quality of the data and subsequently determined structures were assessed using standard crystallographic measures. Structures were reliably determined with similar quality from crystalline lamellae up to twice the inelastic mean free path. Lower resolution diffraction was observed at three times the mean free path for all three accelerating voltages, but the data quality was insufficient to yield structures. Finally, no coherent diffraction was observed from lamellae thicker than four times the calculated inelastic mean free path. This study benchmarks the ideal specimen thickness with implications for all cryo-EM methods.
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Affiliation(s)
- Michael W Martynowycz
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Max T B Clabbers
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Johan Unge
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Johan Hattne
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Tamir Gonen
- HHMI, University of California, Los Angeles, CA 90095;
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Physiology, University of California, Los Angeles, CA 90095
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17
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Abstract
We present an in-depth protocol to reproducibly prepare crystalline lamellae from protein crystals for subsequent microcrystal electron diffraction (MicroED) experiments. This protocol covers typical soluble proteins and membrane proteins embedded in dense media. Following these steps will allow the user to prepare crystalline lamellae for protein structure determination by MicroED. For complete details on the use and execution of this protocol, please refer to Martynowycz et al. (2019a, 2020a).
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Affiliation(s)
- Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
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18
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Martynowycz MW, Shiriaeva A, Ge X, Hattne J, Nannenga BL, Cherezov V, Gonen T. MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP. Proc Natl Acad Sci U S A 2021; 118:e2106041118. [PMID: 34462357 PMCID: PMC8433539 DOI: 10.1073/pnas.2106041118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs), or seven-transmembrane receptors, are a superfamily of membrane proteins that are critically important to physiological processes in the human body. Determining high-resolution structures of GPCRs without bound cognate signaling partners, such as a G protein, requires crystallization in lipidic cubic phase (LCP). GPCR crystals grown in LCP are often too small for traditional X-ray crystallography. These microcrystals are ideal for investigation by microcrystal electron diffraction (MicroED), but the gel-like nature of LCP makes traditional approaches to MicroED sample preparation insurmountable. Here, we show that the structure of a human A2A adenosine receptor can be determined by MicroED after converting the LCP into the sponge phase followed by focused ion-beam milling. We determined the structure of the A2A adenosine receptor to 2.8-Å resolution and resolved an antagonist in its orthosteric ligand-binding site, as well as four cholesterol molecules bound around the receptor. This study lays the groundwork for future structural studies of lipid-embedded membrane proteins by MicroED using single microcrystals that would be impossible with other crystallographic methods.
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Affiliation(s)
- Michael W Martynowycz
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Anna Shiriaeva
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Xuanrui Ge
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90007
| | - Johan Hattne
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Vadim Cherezov
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007;
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Tamir Gonen
- HHMI, University of California, Los Angeles, CA 90095;
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Physiology, University of California, Los Angeles, CA 90095
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19
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Abstract
A detailed protocol for preparing small molecule samples for microcrystal electron diffraction (MicroED) experiments is described. MicroED has been developed to solve structures of proteins and small molecules using standard electron cryo-microscopy (cryo-EM) equipment. In this way, small molecules, peptides, soluble proteins, and membrane proteins have recently been determined to high resolutions. Protocols are presented here for preparing grids of small-molecule pharmaceuticals using the drug carbamazepine as an example. Protocols for screening and collecting data are presented. Additional steps in the overall process, such as data integration, structure determination, and refinement are presented elsewhere. The time required to prepare the small-molecule grids is estimated to be less than 30 min.
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Affiliation(s)
- Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California Los Angeles,Department of Biological Chemistry, University of California Los Angeles
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California Los Angeles; Department of Biological Chemistry, University of California Los Angeles; Department of Physiology, University of California Los Angeles;
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20
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Abstract
Microcrystal electron diffraction (MicroED) enables atomic resolution structures to be determined from vanishingly small crystals. Soluble proteins typically grow crystals that are tens to hundreds of microns in size for X-ray crystallography. But membrane protein crystals often grow crystals that are too small for X-ray diffraction and yet too large for MicroED. These crystals are often formed in thick, viscous media that challenge traditional cryoEM grid preparation. Here, we describe two approaches for preparing membrane protein crystals for MicroED data collection: application of a crystal slurry directly to EM grids, and focused ion beam milling in a Scanning Electron Microscope (FIB-SEM). We summarize the case of preparing an ion channel, NaK, and the workflow of focused ion-beam milling. By milling away the excess media and crystalline material, crystals of any size may be prepared for MicroED. Finally, an energy filter may be used to help minimize inelastic scattering leading to lower noise on recorded images.
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Affiliation(s)
- Michael W. Martynowycz
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA.,Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA.,Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA. .,Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA. .,Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA.
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21
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Andreev K, Martynowycz MW, Kuzmenko I, Bu W, Hall SB, Gidalevitz D. Structural Changes in Films of Pulmonary Surfactant Induced by Surfactant Vesicles. Langmuir 2020; 36:13439-13447. [PMID: 33080138 PMCID: PMC8754419 DOI: 10.1021/acs.langmuir.0c01813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
When compressed by the shrinking alveolar surface area during exhalation, films of pulmonary surfactant in situ reduce surface tension to levels at which surfactant monolayers collapse from the surface in vitro. Vesicles of pulmonary surfactant added below these monolayers slow collapse. X-ray scattering here determined the structural changes induced by the added vesicles. Grazing incidence X-ray diffraction on monolayers of extracted calf surfactant detected an ordered phase. Mixtures of dipalmitoyl phosphatidylcholine and cholesterol, but not the phospholipid alone, mimic that structure. At concentrations that stabilize the monolayers, vesicles in the subphase had no effect on the unit cell, and X-ray reflection showed that the film remained monomolecular. The added vesicles, however, produced a concentration-dependent increase in the diffracted intensity. These results suggest that the enhanced resistance to collapse results from enlargement by the additional material of the ordered phase.
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Affiliation(s)
- Konstantin Andreev
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Michael W Martynowycz
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, Illinois 60616, United States
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Ivan Kuzmenko
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Wei Bu
- The Center for Advanced Radiation Sources (CARS), University of Chicago, Chicago, Illinois 60637, United States
| | - Stephen B Hall
- Pulmonary & Critical Care Medicine, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - David Gidalevitz
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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22
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Martynowycz MW, Gonen T. Ligand Incorporation into Protein Microcrystals for MicroED by On-Grid Soaking. Structure 2020; 29:88-95.e2. [PMID: 33007196 DOI: 10.1016/j.str.2020.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/29/2020] [Accepted: 09/15/2020] [Indexed: 11/17/2022]
Abstract
A high throughout method for soaking ligands into protein microcrystals on TEM grids is presented. Every crystal on the grid is soaked simultaneously using only standard cryoelectron microscopy vitrification equipment. The method is demonstrated using proteinase K microcrystals soaked with the 5-amino-2,4,6-triodoisophthalic acid (I3C) magic triangle. A soaked microcrystal is milled to a thickness of approximately 200 nm using a focused ion beam, and MicroED data are collected. A high-resolution structure of the protein with four ligands at high occupancy is determined. Both the number of ligands bound and their occupancy is higher using on-grid soaking of microcrystals compared with much larger crystals treated similarly and investigated by X-ray crystallography. These results indicate that on-grid soaking ligands into microcrystals results in efficient uptake of ligands into protein microcrystals.
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Affiliation(s)
- Michael W Martynowycz
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA 90095, USA; Department of Physiology, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles CA90095, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA 90095, USA; Department of Physiology, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles CA90095, USA.
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23
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Richards LS, Millán C, Miao J, Martynowycz MW, Sawaya MR, Gonen T, Borges RJ, Usón I, Rodriguez JA. Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER. Acta Crystallogr D Struct Biol 2020; 76:703-712. [PMID: 32744252 PMCID: PMC7397493 DOI: 10.1107/s2059798320008049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO, a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE. The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.
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Affiliation(s)
- Logan S. Richards
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Jennifer Miao
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Rafael J. Borges
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
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24
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Wolff AM, Young ID, Sierra RG, Brewster AS, Martynowycz MW, Nango E, Sugahara M, Nakane T, Ito K, Aquila A, Bhowmick A, Biel JT, Carbajo S, Cohen AE, Cortez S, Gonzalez A, Hino T, Im D, Koralek JD, Kubo M, Lazarou TS, Nomura T, Owada S, Samelson AJ, Tanaka T, Tanaka R, Thompson EM, van den Bedem H, Woldeyes RA, Yumoto F, Zhao W, Tono K, Boutet S, Iwata S, Gonen T, Sauter NK, Fraser JS, Thompson MC. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. IUCrJ 2020; 7:306-323. [PMID: 32148858 PMCID: PMC7055375 DOI: 10.1107/s205225252000072x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.
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Affiliation(s)
- Alexander M. Wolff
- Graduate Program in Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Iris D. Young
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takanori Nakane
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazutaka Ito
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Laboratory for Drug Discovery, Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni-shi, Shizuoka 410-2321, Japan
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Justin T. Biel
- Graduate Program in Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sergio Carbajo
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Aina E. Cohen
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Saul Cortez
- Department of Biology, San Francisco State University, San Francisco, California, USA
| | - Ana Gonzalez
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Tomoya Hino
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho, Minami, Tottori 680-8552, Japan
- Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
| | - Dohyun Im
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jake D. Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Minoru Kubo
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | | | - Takashi Nomura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Avi J. Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Erin M. Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, California, USA
| | - Henry van den Bedem
- Bioscience Department, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Rahel A. Woldeyes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, California, USA
| | - Fumiaki Yumoto
- Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan
| | - Wei Zhao
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Sebastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA
- Department of Physiology, University of California, Los Angeles, Los Angeles, California, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Michael C. Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
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25
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Martynowycz MW, Hattne J, Gonen T. Experimental Phasing of MicroED Data Using Radiation Damage. Structure 2020; 28:458-464.e2. [PMID: 32023481 PMCID: PMC7313391 DOI: 10.1016/j.str.2020.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 10/24/2022]
Abstract
We previously demonstrated that microcrystal electron diffraction (MicroED) can be used to determine atomic-resolution structures from vanishingly small three-dimensional crystals. Here, we present an example of an experimentally phased structure using only MicroED data. The structure of a seven-residue peptide is solved starting from differences to the diffraction intensities induced by structural changes due to radiation damage. The same wedge of reciprocal space was recorded twice by continuous-rotation MicroED from a set of 11 individual crystals. The data from the first pass were merged to make a "low-dose dataset." The data from the second pass were similarly merged to form a "damaged dataset." Differences between these two datasets were used to identify a single heavy-atom site from a Patterson difference map, and initial phases were generated. Finally, the structure was completed by iterative cycles of modeling and refinement.
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Affiliation(s)
- Michael W Martynowycz
- Howard Hughes Medical Institute, Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Johan Hattne
- Howard Hughes Medical Institute, Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
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26
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Abstract
We previously engineered the β-subunit of tryptophan synthase (TrpB), which catalyzes the condensation of l-serine and indole to l-tryptophan, to synthesize a range of noncanonical amino acids from l-serine and indole derivatives or other nucleophiles. Here we employ directed evolution to engineer TrpB to accept 3-substituted oxindoles and form C-C bonds leading to new quaternary stereocenters. Initially, the variants that could use 3-substituted oxindoles preferentially formed N-C bonds on N1 of the substrate. Protecting N1 encouraged evolution toward C-alkylation, which persisted when protection was removed. Six generations of directed evolution resulted in TrpB Pfquat with a 400-fold improvement in activity for alkylation of 3-substituted oxindoles and the ability to selectively form a new, all-carbon quaternary stereocenter at the γ-position of the amino acid products. The enzyme can also alkylate and form all-carbon quaternary stereocenters on structurally similar lactones and ketones, where it exhibits excellent regioselectivity for the tertiary carbon. The configurations of the γ-stereocenters of two of the products were determined via microcrystal electron diffraction (MicroED), and we report the MicroED structure of a small molecule obtained using the Falcon III direct electron detector. Highly thermostable and expressed at >500 mg/L E. coli culture, TrpB Pfquat offers an efficient, sustainable, and selective platform for the construction of diverse noncanonical amino acids bearing all-carbon quaternary stereocenters.
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Affiliation(s)
- Markus Dick
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Nicholas S. Sarai
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, David Geffen School of Medicine, Departments of Biological Chemistry and Physiology, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Tamir Gonen
- Howard Hughes Medical Institute, David Geffen School of Medicine, Departments of Biological Chemistry and Physiology, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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27
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Hattne J, Martynowycz MW, Penczek PA, Gonen T. MicroED with the Falcon III direct electron detector. IUCrJ 2019; 6:921-926. [PMID: 31576224 PMCID: PMC6760445 DOI: 10.1107/s2052252519010583] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/25/2019] [Indexed: 05/06/2023]
Abstract
Microcrystal electron diffraction (MicroED) combines crystallography and electron cryo-microscopy (cryo-EM) into a method that is applicable to high-resolution structure determination. In MicroED, nanosized crystals, which are often intractable using other techniques, are probed by high-energy electrons in a transmission electron microscope. Diffraction data are recorded by a camera in movie mode: the nanocrystal is continuously rotated in the beam, thus creating a sequence of frames that constitute a movie with respect to the rotation angle. Until now, diffraction-optimized cameras have mostly been used for MicroED. Here, the use of a direct electron detector that was designed for imaging is reported. It is demonstrated that data can be collected more rapidly using the Falcon III for MicroED and with markedly lower exposure than has previously been reported. The Falcon III was operated at 40 frames per second and complete data sets reaching atomic resolution were recorded in minutes. The resulting density maps to 2.1 Å resolution of the serine protease proteinase K showed no visible signs of radiation damage. It is thus demonstrated that dedicated diffraction-optimized detectors are not required for MicroED, as shown by the fact that the very same cameras that are used for imaging applications in electron microscopy, such as single-particle cryo-EM, can also be used effectively for diffraction measurements.
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Affiliation(s)
- Johan Hattne
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Pawel A. Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Correspondence e-mail:
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28
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Martynowycz MW, Zhao W, Hattne J, Jensen GJ, Gonen T. Qualitative Analyses of Polishing and Precoating FIB Milled Crystals for MicroED. Structure 2019; 27:1594-1600.e2. [PMID: 31422911 DOI: 10.1016/j.str.2019.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/12/2019] [Accepted: 07/15/2019] [Indexed: 10/26/2022]
Abstract
Microcrystal electron diffraction (MicroED) leverages the strong interaction between matter and electrons to determine protein structures from vanishingly small crystals. This strong interaction limits the thickness of crystals that can be investigated by MicroED, mainly due to absorption. Recent studies have demonstrated that focused ion-beam (FIB) milling can thin crystals into ideal-sized lamellae; however, it is not clear how to best apply FIB milling for MicroED. Here, the effects of polishing the lamellae, whereby the last few nanometers are milled away using a low-current gallium beam, are explored in both the platinum-precoated and uncoated samples. Our results suggest that precoating samples with a thin layer of platinum followed by polishing the crystal surfaces prior to data collection consistently led to superior results as indicated by higher signal-to-noise ratio, higher resolution, and better refinement statistics. This study lays the foundation for routine and reproducible methodology for sample preparation in MicroED.
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Affiliation(s)
- Michael W Martynowycz
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA; Departments of Biological Chemistry and Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Wei Zhao
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA; Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Johan Hattne
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA; Departments of Biological Chemistry and Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Grant J Jensen
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA; Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA; Departments of Biological Chemistry and Physiology, University of California Los Angeles, Los Angeles, CA, USA.
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29
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Martynowycz MW, Hattne J, Gonen T. MicroED: tiny crystals, big opportunities. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319098982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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30
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Martynowycz MW, Rice A, Andreev K, Nobre TM, Kuzmenko I, Wereszczynski J, Gidalevitz D. Salmonella Membrane Structural Remodeling Increases Resistance to Antimicrobial Peptide LL-37. ACS Infect Dis 2019; 5:1214-1222. [PMID: 31083918 DOI: 10.1021/acsinfecdis.9b00066] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gram-negative bacteria are protected from their environment by an outer membrane that is primarily composed of lipopolysaccharides (LPSs). Under stress, pathogenic serotypes of Salmonella enterica remodel their LPSs through the PhoPQ two-component regulatory system that increases resistance to both conventional antibiotics and antimicrobial peptides (AMPs). Acquired resistance to AMPs is contrary to the established narrative that AMPs circumvent bacterial resistance by targeting the general chemical properties of membrane lipids. However, the specific mechanisms underlying AMP resistance remain elusive. Here we report a 2-fold increase in bacteriostatic concentrations of human AMP LL-37 for S. enterica with modified LPSs. LPSs with and without chemical modifications were isolated and investigated by Langmuir films coupled with grazing-incidence X-ray diffraction (GIXD) and specular X-ray reflectivity (XR). The initial interactions between LL-37 and LPS bilayers were probed using all-atom molecular dynamics simulations. These simulations suggest that initial association is nonspecific to the type of LPS and governed by hydrogen bonding to the LPS outer carbohydrates. GIXD experiments indicate that the interactions of the peptide with monolayers reduce the number of crystalline domains but greatly increase the typical domain size in both LPS isoforms. Electron densities derived from XR experiments corroborate the bacteriostatic values found in vitro and indicate that peptide intercalation is reduced by LPS modification. We hypothesize that defects at the liquid-ordered boundary facilitate LL-37 intercalation into the outer membrane, whereas PhoPQ-mediated LPS modification protects against this process by having innately increased crystallinity. Since induced ordering has been observed with other AMPs and drugs, LPS modification may represent a general mechanism by which Gram-negative bacteria protect against host innate immunity.
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Affiliation(s)
- Michael W. Martynowycz
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, 10 West 35th Street, Chicago, Illinois 60616, United States
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Building 401, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Amy Rice
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, 10 West 35th Street, Chicago, Illinois 60616, United States
| | - Konstantin Andreev
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, 10 West 35th Street, Chicago, Illinois 60616, United States
| | - Thatyane M. Nobre
- Departamento de Fisica e Ciecias dos Materiais, Instituto de Fisica de São Carlos, 400 Parque Arnold Schimidt, 13566-590 São Carlos-SP, Brazil
| | - Ivan Kuzmenko
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Building 401, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Jeff Wereszczynski
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, 10 West 35th Street, Chicago, Illinois 60616, United States
| | - David Gidalevitz
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, 10 West 35th Street, Chicago, Illinois 60616, United States
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31
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Andreev K, Martynowycz MW, Gidalevitz D. Peptoid drug discovery and optimization via surface X-ray scattering. Biopolymers 2019; 110:e23274. [PMID: 30892696 PMCID: PMC6661014 DOI: 10.1002/bip.23274] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 12/31/2022]
Abstract
Synthetic polymers mimicking antimicrobial peptides have drawn considerable interest as potential therapeutics. N-substituted glycines, or peptoids, are recognized by their in vivo stability and ease of synthesis. Peptoids are thought to act primarily on the negatively charged lipids that are abundant in bacterial cell membranes. A mechanistic understanding of lipid-peptoid interaction at the molecular level will provide insights for rational design and optimization of peptoids. Here, we highlight recent studies that utilize synchrotron liquid surface X-ray scattering to characterize the underlying peptoid interactions with bacterial and eukaryotic membranes. Cellular membranes are highly complex, and difficult to characterize at the molecular level. Model systems including Langmuir monolayers, are used in these studies to reduce system complexity. The general workflow of these systems and the corresponding data analysis techniques are presented alongside recent findings. These studies investigate the role of peptoid physicochemical characteristics on membrane activity. Specifically, the roles of cationic charge, conformational constraint via macrocyclization, and hydrophobicity are shown to correlate their membrane interactions to biological activities in vitro. These structure-activity relationships have led to new insights into the mechanism of action by peptoid antimicrobials, and suggest optimization strategies for future therapeutics based on peptoids.
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Affiliation(s)
- Konstantin Andreev
- Howard Hughes Medical Institute, Northwestern University, Evanston, Illinois
| | | | - David Gidalevitz
- Center for the Molecular Study of Condensed Soft Matter and Department of Physics, Illinois Institute of Technology, Chicago, Illinois
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32
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Abstract
The cryoEM method Microcrystal Electron Diffraction (MicroED) involves transmission electron microscope (TEM) and electron detector working in synchrony to collect electron diffraction data by continuous rotation. We previously reported several protein, peptide, and small molecule structures by MicroED using manual control of the microscope and detector to collect data. Here we present a procedure to automate this process using a script developed for the popular open-source software package SerialEM. With this approach, SerialEM coordinates stage rotation, microscope operation, and camera functions for automated continuous-rotation MicroED data collection. Depending on crystal and substrate geometry, more than 300 datasets can be collected overnight in this way, facilitating high-throughput MicroED data collection for large-scale data analyses.
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Affiliation(s)
- M Jason de la Cruz
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA; Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| | - Michael W Martynowycz
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA; Howard Hughes Medical Institute and Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA; Howard Hughes Medical Institute and Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA; Howard Hughes Medical Institute and Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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33
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Andreev K, Martynowycz MW, Lingaraju M, Bianchi C, Mor A, Gidalevitz D. Antimicrobial Peptidomimetics with Activity Towards Cancer Cells. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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34
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Jones C, Martynowycz MW, Hattne J, Fulton TJ, Stoltz BM, Rodriguez JA, Nelson HM, Gonen T. The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination. ACS Cent Sci 2018; 4:1587-1592. [PMID: 30555912 PMCID: PMC6276044 DOI: 10.1021/acscentsci.8b00760] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 05/20/2023]
Abstract
In the many scientific endeavors that are driven by organic chemistry, unambiguous identification of small molecules is of paramount importance. Over the past 50 years, NMR and other powerful spectroscopic techniques have been developed to address this challenge. While almost all of these techniques rely on inference of connectivity, the unambiguous determination of a small molecule's structure requires X-ray and/or neutron diffraction studies. In practice, however, X-ray crystallography is rarely applied in routine organic chemistry due to intrinsic limitations of both the analytes and the technique. Here we report the use of the electron cryo-microscopy (cryoEM) method microcrystal electron diffraction (MicroED) to provide routine and unambiguous structural determination of small organic molecules. From simple powders, with minimal sample preparation, we could collect high-quality MicroED data from nanocrystals (∼100 nm, ∼10-15 g) resulting in atomic resolution (<1 Å) crystal structures in minutes.
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Affiliation(s)
- Christopher
G. Jones
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute,
David Geffen School of Medicine, Departments of Biological Chemistry
and Physiology, and UCLA-DOE Institute, University of California, Los Angeles, California 90095, United States
| | - Michael W. Martynowycz
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute,
David Geffen School of Medicine, Departments of Biological Chemistry
and Physiology, and UCLA-DOE Institute, University of California, Los Angeles, California 90095, United States
| | - Johan Hattne
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute,
David Geffen School of Medicine, Departments of Biological Chemistry
and Physiology, and UCLA-DOE Institute, University of California, Los Angeles, California 90095, United States
| | - Tyler J. Fulton
- The
Warren and Katharine Schlinger Laboratory of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Brian M. Stoltz
- The
Warren and Katharine Schlinger Laboratory of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
- (B.M.S.) E-mail:
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute,
David Geffen School of Medicine, Departments of Biological Chemistry
and Physiology, and UCLA-DOE Institute, University of California, Los Angeles, California 90095, United States
- (J.A.R.) E-mail:
| | - Hosea M. Nelson
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute,
David Geffen School of Medicine, Departments of Biological Chemistry
and Physiology, and UCLA-DOE Institute, University of California, Los Angeles, California 90095, United States
- (H.M.N.) E-mail:
| | - Tamir Gonen
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute,
David Geffen School of Medicine, Departments of Biological Chemistry
and Physiology, and UCLA-DOE Institute, University of California, Los Angeles, California 90095, United States
- (T.G.) E-mail:
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35
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Sowah-Kuma D, Fransishyn KM, Cayabyab C, Martynowycz MW, Kuzmenko I, Paige MF. Molecular-Level Structure and Packing in Phase-Separated Arachidic Acid-Perfluorotetradecanoic Acid Monolayer Films. Langmuir 2018; 34:10673-10683. [PMID: 30102043 DOI: 10.1021/acs.langmuir.8b02291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Synchrotron-based X-ray scattering measurements of phase-separated surfactant monolayers at the air-water interface provide molecular-level structural information about the packing and ordering of film components. In this work, grazing incidence X-ray diffraction (GIXD) and X-ray reflectivity (XR) measurements were used to collect crystallographic structural information for binary mixed monolayers of arachidic acid (AA, C19H39COOH) with perfluorotetradecanoic acid (PA, C13F27COOH), a system that has previously been investigated using a variety of thermodynamic and micron-scale structural characterization methods. GIXD measurements at surface pressures of π = 5, 15, and 30 mN/m indicated that AA in pure and mixed films forms a rectangular lattice at π = 5 and 15 mN/m but a hexagonal lattice at π = 30 mN/m. PA formed hexagonal lattices under all conditions, with films being highly ordered and crystalline (as determined by Bragg peak width) at even the lowest surface pressures investigated. Phase separation occurred for all mixed monolayer film compositions and surface pressures, manifesting as diffraction peaks characteristic of the individual components appearing at different in-plane scattering vector qxy. For both pure and mixed films, the molecular tilt angle of the AA hydrocarbon chain toward the nearest-neighbor was substantial at low pressures but decreased with increasing pressure. The PA fluorocarbon chain showed negligible molecular tilt under all conditions, and was oriented normal to the subphase surface regardless of surface pressure or the presence of AA in the films. In all cases, the two components in the mixed film behaved entirely independently of film composition, which is exactly the expected result for a fully phase-separated, immiscible system. XR measurements of film thickness at the air-water interface supported these results; overall film thickness approached the calculated ideal surfactant tail lengths with increasing surface pressure, indicating nearly normal oriented surfactants. The overall surfactant packing and crystallographic features of the mixed monolayers are discussed in terms of the lipophobic nature of the perfluorinated surfactant as well as in context of thermodynamic miscibility and domain structure formation reported elsewhere in the literature for these mixed monolayer systems.
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Affiliation(s)
- David Sowah-Kuma
- Department of Chemistry , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5A2 , Canada
| | - Kyle M Fransishyn
- Department of Chemistry , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5A2 , Canada
| | - Chelsea Cayabyab
- Department of Chemistry , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5A2 , Canada
| | - Michael W Martynowycz
- Advanced Photon Source , Argonne National Lab , Lemont , Illinois 60439 , United States
| | - Ivan Kuzmenko
- Advanced Photon Source , Argonne National Lab , Lemont , Illinois 60439 , United States
| | - Matthew F Paige
- Department of Chemistry , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5A2 , Canada
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36
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Hattne J, Shi D, Glynn C, Zee CT, Gallagher-Jones M, Martynowycz MW, Rodriguez JA, Gonen T. Analysis of Global and Site-Specific Radiation Damage in Cryo-EM. Structure 2018; 26:759-766.e4. [PMID: 29706530 DOI: 10.1016/j.str.2018.03.021] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/01/2018] [Accepted: 03/30/2018] [Indexed: 11/20/2022]
Abstract
Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data.
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Affiliation(s)
- Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles CA 90095, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Calina Glynn
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chih-Te Zee
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marcus Gallagher-Jones
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael W Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles CA 90095, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jose A Rodriguez
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles CA 90095, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Departments of Physiology and Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles CA 90095, USA.
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37
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Andreev K, Martynowycz MW, Huang ML, Kuzmenko I, Bu W, Kirshenbaum K, Gidalevitz D. Hydrophobic interactions modulate antimicrobial peptoid selectivity towards anionic lipid membranes. Biochim Biophys Acta Biomembr 2018; 1860:1414-1423. [PMID: 29621496 DOI: 10.1016/j.bbamem.2018.03.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/15/2018] [Accepted: 03/26/2018] [Indexed: 12/21/2022]
Abstract
Hydrophobic interactions govern specificity for natural antimicrobial peptides. No such relationship has been established for synthetic peptoids that mimic antimicrobial peptides. Peptoid macrocycles synthesized with five different aromatic groups are investigated by minimum inhibitory and hemolytic concentration assays, epifluorescence microscopy, atomic force microscopy, and X-ray reflectivity. Peptoid hydrophobicity is determined using high performance liquid chromatography. Disruption of bacterial but not eukaryotic lipid membranes is demonstrated on the solid supported lipid bilayers and Langmuir monolayers. X-ray reflectivity studies demonstrate that intercalation of peptoids with zwitterionic or negatively charged lipid membranes is found to be regulated by hydrophobicity. Critical levels of peptoid selectivity are demonstrated and found to be modulated by their hydrophobic groups. It is suggested that peptoids may follow different optimization schemes as compared to their natural analogues.
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Affiliation(s)
- Konstantin Andreev
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, 3440 South Dearborn Street, Chicago, IL 60616, United States
| | - Michael W Martynowycz
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, 3440 South Dearborn Street, Chicago, IL 60616, United States; Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, United States
| | - Mia L Huang
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, United States
| | - Ivan Kuzmenko
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, United States
| | - Wei Bu
- The Center for Advanced Radiation Sources (CARS), University of Chicago, Chicago, IL 60637, United States
| | - Kent Kirshenbaum
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, United States
| | - David Gidalevitz
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, 3440 South Dearborn Street, Chicago, IL 60616, United States.
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38
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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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39
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Vergara S, Lukes DA, Martynowycz MW, Santiago U, Plascencia-Villa G, Weiss SC, de la Cruz MJ, Black DM, Alvarez MM, Lopez-Lozano X, Barnes CO, Lin G, Weissker HC, Whetten RL, Gonen T, Jose-Yacaman M, Calero G. MicroED Structure of Au 146(p-MBA) 57 at Subatomic Resolution Reveals a Twinned FCC Cluster. J Phys Chem Lett 2017; 8:5523-5530. [PMID: 29072840 PMCID: PMC5769702 DOI: 10.1021/acs.jpclett.7b02621] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au146(p-MBA)57 (p-MBA: para-mercaptobenzoic acid), solved by electron micro-diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure, whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.
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Affiliation(s)
- Sandra Vergara
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Dylan A. Lukes
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Ulises Santiago
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - German Plascencia-Villa
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Simon C. Weiss
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - David M. Black
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Marcos M. Alvarez
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Xochitl Lopez-Lozano
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | | | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Robert L. Whetten
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Howard Hughes Medical Institute, Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Miguel Jose-Yacaman
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
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Andreev K, Martynowycz MW, Ivankin A, Huang ML, Kuzmenko I, Meron M, Lin B, Kirshenbaum K, Gidalevitz D. Cyclization Improves Membrane Permeation by Antimicrobial Peptoids. Langmuir 2016; 32:12905-12913. [PMID: 27793068 PMCID: PMC9647730 DOI: 10.1021/acs.langmuir.6b03477] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The peptidomimetic approach has emerged as a powerful tool for overcoming the inherent limitations of natural antimicrobial peptides, where the therapeutic potential can be improved by increasing the selectivity and bioavailability. Restraining the conformational flexibility of a molecule may reduce the entropy loss upon its binding to the membrane. Experimental findings demonstrate that the cyclization of linear antimicrobial peptoids increases their bactericidal activity against Staphylococcus aureus while maintaining high hemolytic concentrations. Surface X-ray scattering shows that macrocyclic peptoids intercalate into Langmuir monolayers of anionic lipids with greater efficacy than for their linear analogues. It is suggested that cyclization may increase peptoid activity by allowing the macrocycle to better penetrate the bacterial cell membrane.
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Affiliation(s)
- Konstantin Andreev
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, 3440 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Michael W. Martynowycz
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, 3440 South Dearborn Street, Chicago, Illinois 60616, United States
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Andrey Ivankin
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, 3440 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Mia L. Huang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Ivan Kuzmenko
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Mati Meron
- The Center for Advanced Radiation Sources (CARS), University of Chicago, Chicago, Illinois 60637, United States
| | - Binhua Lin
- The Center for Advanced Radiation Sources (CARS), University of Chicago, Chicago, Illinois 60637, United States
| | - Kent Kirshenbaum
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - David Gidalevitz
- Department of Physics, Center for Molecular Study of Condensed Soft Matter (μCoSM), Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, 3440 South Dearborn Street, Chicago, Illinois 60616, United States
- Corresponding Author: Fax: (+1) 312-567-8856.
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41
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Nobre TM, Martynowycz MW, Andreev K, Kuzmenko I, Nikaido H, Gidalevitz D. Modification of Salmonella Lipopolysaccharides Prevents the Outer Membrane Penetration of Novobiocin. Biophys J 2016; 109:2537-2545. [PMID: 26682812 DOI: 10.1016/j.bpj.2015.10.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/23/2015] [Accepted: 10/08/2015] [Indexed: 11/29/2022] Open
Abstract
Small hydrophilic antibiotics traverse the outer membrane of Gram-negative bacteria through porin channels. Large lipophilic agents traverse the outer membrane through its bilayer, containing a majority of lipopolysaccharides in its outer leaflet. Genes controlled by the two-component regulatory system PhoPQ modify lipopolysaccharides. We isolate lipopolysaccharides from isogenic mutants of Salmonella sp., one lacking the modification, the other fully modified. These lipopolysaccharides were reconstituted as monolayers at the air-water interface, and their properties, as well as their interaction with a large lipophilic drug, novobiocin, was studied. X-ray reflectivity showed that the drug penetrated the monolayer of the unmodified lipopolysaccharides reaching the hydrophobic region, but was prevented from this penetration into the modified lipopolysaccharides. Results correlate with behavior of bacterial cells, which become resistant to antibiotics after PhoPQ-regulated modifications. Grazing incidence x-ray diffraction showed that novobiocin produced a striking increase in crystalline coherence length, and the size of the near-crystalline domains.
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Affiliation(s)
- Thatyane M Nobre
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California.
| | - Michael W Martynowycz
- Center for Molecular Study of Condensed Soft Matter and Department of Physics, Illinois Institute of Technology, Chicago, Illinois; X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois
| | - Konstantin Andreev
- Center for Molecular Study of Condensed Soft Matter and Department of Physics, Illinois Institute of Technology, Chicago, Illinois
| | - Ivan Kuzmenko
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California
| | - David Gidalevitz
- Center for Molecular Study of Condensed Soft Matter and Department of Physics, Illinois Institute of Technology, Chicago, Illinois.
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42
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Martynowycz MW, Hu B, Kuzmenko I, Bu W, Hock A, Gidalevitz D. Monomolecular Siloxane Film as a Model of Single Site Catalysts. J Am Chem Soc 2016; 138:12432-9. [DOI: 10.1021/jacs.6b05711] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Ivan Kuzmenko
- Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Wei Bu
- Center
for Advanced Radiation Sources, University of Chicago, Chicago, Illinois 60637, United States
| | - Adam Hock
- Argonne National Laboratory, Lemont, Illinois 60439, United States
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43
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Feinstein DL, Akpa BS, Ayee MA, Boullerne AI, Braun D, Brodsky SV, Gidalevitz D, Hauck Z, Kalinin S, Kowal K, Kuzmenko I, Lis K, Marangoni N, Martynowycz MW, Rubinstein I, van Breemen R, Ware K, Weinberg G. The emerging threat of superwarfarins: history, detection, mechanisms, and countermeasures. Ann N Y Acad Sci 2016; 1374:111-22. [PMID: 27244102 DOI: 10.1111/nyas.13085] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/04/2016] [Accepted: 04/08/2016] [Indexed: 12/11/2022]
Abstract
Superwarfarins were developed following the emergence of warfarin resistance in rodents. Compared to warfarin, superwarfarins have much longer half-lives and stronger affinity to vitamin K epoxide reductase and therefore can cause death in warfarin-resistant rodents. By the mid-1970s, the superwarfarins brodifacoum and difenacoum were the most widely used rodenticides throughout the world. Unfortunately, increased use was accompanied by a rise in accidental poisonings, reaching >16,000 per year in the United States. Risk of exposure has become a concern since large quantities, up to hundreds of kilograms of rodent bait, are applied by aerial dispersion over regions with rodent infestations. Reports of intentional use of superwarfarins in civilian and military scenarios raise the specter of larger incidents or mass casualties. Unlike warfarin overdose, for which 1-2 days of treatment with vitamin K is effective, treatment of superwarfarin poisoning with vitamin K is limited by extremely high cost and can require daily treatment for a year or longer. Furthermore, superwarfarins have actions that are independent of their anticoagulant effects, including both vitamin K-dependent and -independent effects, which are not mitigated by vitamin K therapy. In this review, we summarize superwarfarin development, biology and pathophysiology, their threat as weapons, and possible therapeutic approaches.
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Affiliation(s)
- Douglas L Feinstein
- Department of Anesthesiology, University of Illinois, Chicago, Illinois.,Jesse Brown VA Medical Center, Chicago, Illinois
| | - Belinda S Akpa
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina
| | - Manuela A Ayee
- Department of Medicine, University of Illinois, Chicago, Illinois
| | - Anne I Boullerne
- Department of Anesthesiology, University of Illinois, Chicago, Illinois.,Jesse Brown VA Medical Center, Chicago, Illinois
| | - David Braun
- Department of Anesthesiology, University of Illinois, Chicago, Illinois
| | - Sergey V Brodsky
- Department of Pathology, the Ohio State University, Columbus, Ohio
| | - David Gidalevitz
- Department of Physics and the Center for the Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Zane Hauck
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago, Illinois
| | - Sergey Kalinin
- Department of Anesthesiology, University of Illinois, Chicago, Illinois
| | - Kathy Kowal
- Department of Anesthesiology, University of Illinois, Chicago, Illinois
| | - Ivan Kuzmenko
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois
| | - Kinga Lis
- Department of Anesthesiology, University of Illinois, Chicago, Illinois
| | - Natalia Marangoni
- Department of Anesthesiology, University of Illinois, Chicago, Illinois
| | - Michael W Martynowycz
- Department of Physics and the Center for the Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois.,X-ray Science Division, Argonne National Laboratory, Lemont, Illinois
| | - Israel Rubinstein
- Department of Anesthesiology, University of Illinois, Chicago, Illinois.,Department of Medicine, University of Illinois, Chicago, Illinois
| | | | - Kyle Ware
- Department of Pathology, the Ohio State University, Columbus, Ohio
| | - Guy Weinberg
- Department of Anesthesiology, University of Illinois, Chicago, Illinois.,Jesse Brown VA Medical Center, Chicago, Illinois
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44
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Martynowycz MW, Morimoto Nobre T, Nikaido H, Gidalevitz D. The Structural Role of Lipid Domain Modifications in Antimicrobial Resistance for Salmonella Enterica Serovar Typhimurium. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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