1
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Janus BM, Wang R, Cleveland TE, Metcalf MC, Lemmer AC, van Dyk N, Jeong S, Astavans A, Class K, Fuerst TR, Ofek G. Macaque antibodies targeting Marburg virus glycoprotein induced by multivalent immunization. J Virol 2024:e0015524. [PMID: 38832790 DOI: 10.1128/jvi.00155-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
Marburg virus infection in humans is associated with case fatality rates that can reach up to 90%, but to date, there are no approved vaccines or monoclonal antibody (mAb) countermeasures. Here, we immunized Rhesus macaques with multivalent combinations of filovirus glycoprotein (GP) antigens belonging to Marburg, Sudan, and Ebola viruses to generate monospecific and cross-reactive antibody responses against them. From the animal that developed the highest titers of Marburg virus GP-specific neutralizing antibodies, we sorted single memory B cells using a heterologous Ravn virus GP probe and cloned and characterized a panel of 34 mAbs belonging to 28 unique lineages. Antibody specificities were assessed by overlapping pepscan and binding competition analyses, revealing that roughly a third of the lineages mapped to the conserved receptor binding region, including potent neutralizing lineages that were confirmed by negative stain electron microscopy to target this region. Additional lineages targeted a protective region on GP2, while others were found to possess cross-filovirus reactivity. Our study advances the understanding of orthomarburgvirus glycoprotein antigenicity and furthers efforts to develop candidate antibody countermeasures against these lethal viruses. IMPORTANCE Marburg viruses were the first filoviruses characterized to emerge in humans in 1967 and cause severe hemorrhagic fever with average case fatality rates of ~50%. Although mAb countermeasures have been approved for clinical use against the related Ebola viruses, there are currently no approved countermeasures against Marburg viruses. We successfully isolated a panel of orthomarburgvirus GP-specific mAbs from a macaque immunized with a multivalent combination of filovirus antigens. Our analyses revealed that roughly half of the antibodies in the panel mapped to regions on the glycoprotein shown to protect from infection, including the host cell receptor binding domain and a protective region on the membrane-anchoring subunit. Other antibodies in the panel exhibited broad filovirus GP recognition. Our study describes the discovery of a diverse panel of cross-reactive macaque antibodies targeting orthomarburgvirus and other filovirus GPs and provides candidate immunotherapeutics for further study and development.
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Affiliation(s)
- Benjamin M Janus
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Ruixue Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Thomas E Cleveland
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Matthew C Metcalf
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Aaron C Lemmer
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Nydia van Dyk
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Sarah Jeong
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Anagh Astavans
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Kenneth Class
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Thomas R Fuerst
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Gilad Ofek
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
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2
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Zhang M, Díaz-Celis C, Liu J, Tao J, Ashby PD, Bustamante C, Ren G. Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography. Nat Commun 2024; 15:4395. [PMID: 38782894 PMCID: PMC11116431 DOI: 10.1038/s41467-024-48305-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo-ET), we determine the three-dimensional (3D) structures of individual mononucleosomes and arrays comprising di-, tri-, and tetranucleosomes. By slowing the rate of condensation through a reduction in ionic strength, we probe the intra-array structural transitions that precede inter-array interactions and liquid droplet formation. Under these conditions, the arrays exhibite irregular zig-zag conformations with loose packing. Increasing the ionic strength promoted intra-array compaction, yet we do not observe the previously reported regular 30-nanometer fibers. Interestingly, the presence of H1 do not induce array compaction; instead, one-third of the arrays display nucleosomes invaded by foreign DNA, suggesting an alternative role for H1 in chromatin network construction. We also find that the crucial parameter determining the structure adopted by chromatin arrays is the angle between the entry and exit of the DNA and the corresponding tangents to the nucleosomal disc. Our results provide insights into the initial stages of intra-array compaction, a critical precursor to condensation in the regulation of chromatin organization.
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Affiliation(s)
- Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Applied Science and Technology Graduate Group, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - César Díaz-Celis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jinhui Tao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Ashby
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carlos Bustamante
- Applied Science and Technology Graduate Group, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Department of Physics, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Kavli Energy Nanoscience Institute, University of California, Berkeley, CA, USA.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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3
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Zhdanov DD, Ivin YY, Shishparenok AN, Kraevskiy SV, Kanashenko SL, Agafonova LE, Shumyantseva VV, Gnedenko OV, Pinyaeva AN, Kovpak AA, Ishmukhametov AA, Archakov AI. Perspectives for the creation of a new type of vaccine preparations based on pseudovirus particles using polio vaccine as an example. BIOMEDITSINSKAIA KHIMIIA 2023; 69:253-280. [PMID: 37937429 DOI: 10.18097/pbmc20236905253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Traditional antiviral vaccines are currently created by inactivating the virus chemically, most often using formaldehyde or β-propiolactone. These approaches are not optimal since they negatively affect the safety of the antigenic determinants of the inactivated particles and require additional purification stages. The most promising platforms for creating vaccines are based on pseudoviruses, i.e., viruses that have completely preserved the outer shell (capsid), while losing the ability to reproduce owing to the destruction of the genome. The irradiation of viruses with electron beam is the optimal way to create pseudoviral particles. In this review, with the example of the poliovirus, the main algorithms that can be applied to characterize pseudoviral particles functionally and structurally in the process of creating a vaccine preparation are presented. These algorithms are, namely, the analysis of the degree of genome destruction and coimmunogenicity. The structure of the poliovirus and methods of its inactivation are considered. Methods for assessing residual infectivity and immunogenicity are proposed for the functional characterization of pseudoviruses. Genome integrity analysis approaches, atomic force and electron microscopy, surface plasmon resonance, and bioelectrochemical methods are crucial to structural characterization of the pseudovirus particles.
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Affiliation(s)
- D D Zhdanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - Yu Yu Ivin
- Institute of Biomedical Chemistry, Moscow, Russia; Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | - V V Shumyantseva
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - O V Gnedenko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A N Pinyaeva
- Institute of Biomedical Chemistry, Moscow, Russia; Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - A A Kovpak
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A A Ishmukhametov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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4
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Kong L, Liu J, Zhang M, Lu Z, Xue H, Ren A, Liu J, Li J, Ling WL, Ren G. Facile hermetic TEM grid preparation for molecular imaging of hydrated biological samples at room temperature. Nat Commun 2023; 14:5641. [PMID: 37704637 PMCID: PMC10499825 DOI: 10.1038/s41467-023-41266-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023] Open
Abstract
Although structures of vitrified supramolecular complexes have been determined at near-atomic resolution, elucidating in situ molecular structure in living cells remains a challenge. Here, we report a straightforward liquid cell technique, originally developed for real-time visualization of dynamics at a liquid-gas interface using transmission electron microscopy, to image wet biological samples. Due to the scattering effects from the liquid phase, the micrographs display an amplitude contrast comparable to that observed in negatively stained samples. We succeed in resolving subunits within the protein complex GroEL imaged in a buffer solution at room temperature. Additionally, we capture various stages of virus cell entry, a process for which only sparse structural data exists due to their transient nature. To scrutinize the morphological details further, we used individual particle electron tomography for 3D reconstruction of each virus. These findings showcase this approach potential as an efficient, cost-effective complement to other microscopy technique in addressing biological questions at the molecular level.
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Affiliation(s)
- Lingli Kong
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Zhuoyang Lu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Amy Ren
- Department of Physics, University of California, Santa Barbara, CA, 93106, USA
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, Shandong, 266071, China
| | - Jinping Li
- Department of Biochemistry & Molecular Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Wai Li Ling
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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5
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Liu J, McRae EKS, Zhang M, Geary C, Andersen ES, Ren G. Tertiary structure of single-instant RNA molecule reveals folding landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541511. [PMID: 37292713 PMCID: PMC10245749 DOI: 10.1101/2023.05.19.541511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The folding of RNA and protein molecules during their synthesis is a crucial self-assembly process that nature employs to convert genetic information into the complex molecular machinery that supports life. Misfolding events are the cause of several diseases, and the folding pathway of central biomolecules, such as the ribosome, is strictly regulated by programmed maturation processes and folding chaperones. However, the dynamic folding processes are challenging to study because current structure determination methods heavily rely on averaging, and existing computational methods do not efficiently simulate non-equilibrium dynamics. Here we utilize individual-particle cryo-electron tomography (IPET) to investigate the folding landscape of a rationally designed RNA origami 6-helix bundle that undergoes slow maturation from a "young" to "mature" conformation. By optimizing the IPET imaging and electron dose conditions, we obtain 3D reconstructions of 120 individual particles at resolutions ranging from 23-35 Å, enabling us first-time to observe individual RNA helices and tertiary structures without averaging. Statistical analysis of 120 tertiary structures confirms the two main conformations and suggests a possible folding pathway driven by helix-helix compaction. Studies of the full conformational landscape reveal both trapped states, misfolded states, intermediate states, and fully compacted states. The study provides novel insight into RNA folding pathways and paves the way for future studies of the energy landscape of molecular machines and self-assembly processes.
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6
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Kong L, Liu J, Zhang M, Lu Z, Xue H, Ren A, Liu J, Li J, Li Ling W, Ren G. Facile hermetic TEM grid preparation for molecular imaging of hydrated biological samples at room temperature. RESEARCH SQUARE 2023:rs.3.rs-2464569. [PMID: 36824820 PMCID: PMC9949181 DOI: 10.21203/rs.3.rs-2464569/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Although structures of vitrified supramolecular complexes have been determined at near-atomic resolution, elucidating in situ molecular structure in living cells remains a major challenge. Here, we apply a novel but simple liquid-cell technique, developed previously for real-time imaging of the dynamics at a liquid-gas interface, to image wet biological samples. With extra scattering from the liquid phase, the transmission electron micrographs show amplitude contrast comparable to that in negatively stained samples. Single-molecule domains are resolved in the protein complex GroEL imaged in buffer solution at room temperature. Moreover, various stages of virus cell entry, which are transient events with very few structural information to date, are also captured. Morphological details are reconstructed using the technique of individual particle electron tomography. These results demonstrate that this approach can be a valuable yet cost-effective technique complementary to other microscopy techniques for addressing important biological questions at the molecular level.
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Affiliation(s)
- Lingli Kong
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Zhuoyang Lu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- School of Life Science and Technology, and Frontier Institute of Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Amy Ren
- Department of Physics, University of California, Santa Barba, CA 93106
| | - Jiankang Liu
- School of Life Science and Technology, and Frontier Institute of Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Jinping Li
- Department of Biochemistry & Molecular Biology, Mayo Clinic, Jacksonville, FL 32224
| | - Wai Li Ling
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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7
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Zhang M, Celis CD, Liu J, Bustamante C, Ren G. Conformational Change of Nucleosome Arrays prior to Phase Separation. RESEARCH SQUARE 2023:rs.3.rs-2460504. [PMID: 36711774 PMCID: PMC9882673 DOI: 10.21203/rs.3.rs-2460504/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Chromatin phase transition serves as a regulatory mechanism for eukaryotic transcription. Understanding this process requires the characterization of the nucleosome array structure in response to external stimuli prior to phase separation. However, the intrinsic flexibility and heterogeneity hinders the arrays' structure determination. Here we exploit advances in cryogenic electron tomography (cryo-ET) to determine the three-dimensional (3D) structure of each individual particle of mono-, di-, tri-, and tetranucleosome arrays. Statistical analysis reveals the ionic strength changes the angle between the DNA linker and nucleosome core particle (NCP), which regulate the overall morphology of nucleosome arrays. The finding that one-third of the arrays in the presence of H1 contain an NCP invaded by foreign DNA suggests an alternative function of H1 in constructing nucleosomal networks. The new insights into the nucleosome conformational changes prior to the intermolecular interaction stage extends our understanding of chromatin phase separation regulation.
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Affiliation(s)
- Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, USA
- Applied Science and Technology Graduate Group, University of California, Berkeley, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, USA
| | - César-Díaz Celis
- California Institute for Quantitative Biosciences, University of California, Berkeley, USA
- Howard Hughes Medical Institute, University of California, Berkeley, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Carlos Bustamante
- Applied Science and Technology Graduate Group, University of California, Berkeley, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, USA
- Howard Hughes Medical Institute, University of California, Berkeley, USA
- Department of Chemistry, University of California, Berkeley, USA
- Department of Physics, University of California, Berkeley, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, USA
- Kavli Energy Nanoscience Institute, University of California, Berkeley, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, USA
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8
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Xue H, Zhang M, Liu J, Wang J, Ren G. Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination. Front Chem 2022; 10:889203. [PMID: 36110139 PMCID: PMC9468540 DOI: 10.3389/fchem.2022.889203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/13/2022] [Indexed: 11/28/2022] Open
Abstract
To understand the dynamic structure-function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.
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Affiliation(s)
- Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianjun Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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9
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Lin M, Wang M, Liu D, Zuckermann RN, Sun J. Nanoscale Polyelectrolyte Complex Vesicles from Bioinspired Peptidomimetic Homopolymers with Zwitterionic Property and Extreme Stability. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Min Lin
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Meiyao Wang
- College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China
| | - Dandan Liu
- College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China
| | - Ronald N. Zuckermann
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jing Sun
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
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10
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He Q, Lin X, Chavez BL, Agrawal S, Lusk BL, Lim CJ. Structures of the human CST-Polα-primase complex bound to telomere templates. Nature 2022; 608:826-832. [PMID: 35830881 DOI: 10.1038/s41586-022-05040-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/29/2022] [Indexed: 01/26/2023]
Abstract
The mammalian DNA polymerase-α-primase (Polα-primase) complex is essential for DNA metabolism, providing the de novo RNA-DNA primer for several DNA replication pathways1-4 such as lagging-strand synthesis and telomere C-strand fill-in. The physical mechanism underlying how Polα-primase, alone or in partnership with accessory proteins, performs its complicated multistep primer synthesis function is unknown. Here we show that CST, a single-stranded DNA-binding accessory protein complex for Polα-primase, physically organizes the enzyme for efficient primer synthesis. Cryogenic electron microscopy structures of the CST-Polα-primase preinitiation complex (PIC) bound to various types of telomere overhang reveal that template-bound CST partitions the DNA and RNA catalytic centres of Polα-primase into two separate domains and effectively arranges them in RNA-DNA synthesis order. The architecture of the PIC provides a single solution for the multiple structural requirements for the synthesis of RNA-DNA primers by Polα-primase. Several insights into the template-binding specificity of CST, template requirement for assembly of the CST-Polα-primase PIC and activation are also revealed in this study.
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Affiliation(s)
- Qixiang He
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Xiuhua Lin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Bianca L Chavez
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Sourav Agrawal
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Benjamin L Lusk
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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11
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A Robust Assay to Monitor Ataxin-3 Amyloid Fibril Assembly. Cells 2022; 11:cells11121969. [PMID: 35741099 PMCID: PMC9222203 DOI: 10.3390/cells11121969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 02/05/2023] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3) is caused by the expansion of a glutamine repeat in the protein ataxin-3, which is deposited as intracellular aggregates in affected brain regions. Despite the controversial role of ataxin-3 amyloid structures in SCA3 pathology, the identification of molecules with the capacity to prevent aberrant self-assembly and stabilize functional conformation(s) of ataxin-3 is a key to the development of therapeutic solutions. Amyloid-specific kinetic assays are routinely used to measure rates of protein self-assembly in vitro and are employed during screening for fibrillation inhibitors. The high tendency of ataxin-3 to assemble into oligomeric structures implies that minor changes in experimental conditions can modify ataxin-3 amyloid assembly kinetics. Here, we determine the self-association rates of ataxin-3 and present a detailed study of the aggregation of normal and pathogenic ataxin-3, highlighting the experimental conditions that should be considered when implementing and validating ataxin-3 amyloid progress curves in different settings and in the presence of ataxin-3 interactors. This assay provides a unique and robust platform to screen for modulators of the first steps of ataxin-3 aggregation—a starting point for further studies with cell and animal models of SCA3.
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12
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Vadla GP, Daghat B, Patterson N, Ahmad V, Perez G, Garcia A, Manjunath Y, Kaifi JT, Li G, Chabu CY. Combining plasma extracellular vesicle Let-7b-5p, miR-184 and circulating miR-22-3p levels for NSCLC diagnosis and drug resistance prediction. Sci Rep 2022; 12:6693. [PMID: 35461372 PMCID: PMC9035169 DOI: 10.1038/s41598-022-10598-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 04/05/2022] [Indexed: 01/04/2023] Open
Abstract
Low-dose computed tomography (LDCT) Non-Small Cell Lung (NSCLC) screening is associated with high false-positive rates, leading to unnecessary expensive and invasive follow ups. There is a need for minimally invasive approaches to improve the accuracy of NSCLC diagnosis. In addition, NSCLC patients harboring sensitizing mutations in epidermal growth factor receptor EGFR (T790M, L578R) are treated with Osimertinib, a potent tyrosine kinase inhibitor (TKI). However, nearly all patients develop TKI resistance. The underlying mechanisms are not fully understood. Plasma extracellular vesicle (EV) and circulating microRNA (miRNA) have been proposed as biomarkers for cancer screening and to inform treatment decisions. However, the identification of highly sensitive and broadly predictive core miRNA signatures remains a challenge. Also, how these systemic and diverse miRNAs impact cancer drug response is not well understood. Using an integrative approach, we examined plasma EV and circulating miRNA isolated from NSCLC patients versus screening controls with a similar risk profile. We found that combining EV (Hsa-miR-184, Let-7b-5p) and circulating (Hsa-miR-22-3p) miRNAs abundance robustly discriminates between NSCLC patients and high-risk cancer-free controls. Further, we found that Hsa-miR-22-3p, Hsa-miR-184, and Let-7b-5p functionally converge on WNT/βcatenin and mTOR/AKT signaling axes, known cancer therapy resistance signals. Targeting Hsa-miR-22-3p and Hsa-miR-184 desensitized EGFR-mutated (T790M, L578R) NSCLC cells to Osimertinib. These findings suggest that the expression levels of circulating hsa-miR-22-3p combined with EV hsa-miR-184 and Let-7b-5p levels potentially define a core biomarker signature for improving the accuracy of NSCLC diagnosis. Importantly, these biomarkers have the potential to enable prospective identification of patients who are at risk of responding poorly to Osimertinib alone but likely to benefit from Osimertinib/AKT blockade combination treatments.
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Affiliation(s)
- G P Vadla
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - B Daghat
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - N Patterson
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - V Ahmad
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - G Perez
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - A Garcia
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Y Manjunath
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, 65212, USA
| | - J T Kaifi
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, 65212, USA
- Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - G Li
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, 65212, USA
- Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - C Y Chabu
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.
- Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA.
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13
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Seo PW, Hofmann A, Kim JH, Hwangbo SA, Kim JH, Kim JW, Huynh TYL, Choy HE, Kim SJ, Lee J, Lee JO, Jin KS, Park SY, Kim JS. Structural features of a minimal intact methyltransferase of a type I restriction-modification system. Int J Biol Macromol 2022; 208:381-389. [PMID: 35337914 DOI: 10.1016/j.ijbiomac.2022.03.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/05/2022]
Abstract
Type I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (M2S1 MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S1/2-domain of a TRD and a CR α-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (M1S1/2)2 structure reveals a symmetric (S1/2)2 assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal M1S1/2 MTase dimer indicates a particular state resembling the structure of M2S1 MTases.
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Affiliation(s)
- Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 95326 Kulmbach, Germany
| | - Jun-Ha Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Kumoh National Institute of Technology, 61, Daehak-ro, Gumi, Gyeongbuk 39177, Republic of Korea
| | - Seung-A Hwangbo
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jun-Hong Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji-Won Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Thi Yen Ly Huynh
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Basic Medical Research Building, Chonnam National University Medical College, Hwasun, Jeonnam 58128, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jimin Lee
- Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jie-Oh Lee
- Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Suk-Youl Park
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
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14
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Li D, Chu W, Sheng X, Li W. Optimization of Membrane Protein TmrA Purification Procedure Guided by Analytical Ultracentrifugation. MEMBRANES 2021; 11:membranes11100780. [PMID: 34677546 PMCID: PMC8537081 DOI: 10.3390/membranes11100780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 12/02/2022]
Abstract
Membrane proteins are involved in various cellular processes. However, purification of membrane proteins has long been a challenging task, as membrane protein stability in detergent is the bottleneck for purification and subsequent analyses. Therefore, the optimization of detergent conditions is critical for the preparation of membrane proteins. Here, we utilize analytical ultracentrifugation (AUC) to examine the effects of different detergents (OG, Triton X-100, DDM), detergent concentrations, and detergent supplementation on the behavior of membrane protein TmrA. Our results suggest that DDM is more suitable for the purification of TmrA compared with OG and TritonX-100; a high concentration of DDM yields a more homogeneous protein aggregation state; supplementing TmrA purified with a low DDM concentration with DDM maintains the protein homogeneity and aggregation state, and may serve as a practical and cost-effective strategy for membrane protein purification.
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Affiliation(s)
- Dongdong Li
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Wendan Chu
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Xinlei Sheng
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Correspondence: (X.S.); (W.L.); Tel.: +86-1062782031 (W.L.)
| | - Wenqi Li
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
- Correspondence: (X.S.); (W.L.); Tel.: +86-1062782031 (W.L.)
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15
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Melchior JT, Street SE, Vaisar T, Hart R, Jerome J, Kuklenyik Z, Clouet-Foraison N, Thornock C, Bedi S, Shah AS, Segrest JP, Heinecke JW, Davidson WS. Apolipoprotein A-I modulates HDL particle size in the absence of apolipoprotein A-II. J Lipid Res 2021; 62:100099. [PMID: 34324889 PMCID: PMC8385444 DOI: 10.1016/j.jlr.2021.100099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/01/2021] [Accepted: 07/15/2021] [Indexed: 11/30/2022] Open
Abstract
Human high-density lipoproteins (HDL) are a complex mixture of structurally-related nanoparticles that perform distinct physiological functions. We previously showed human HDL containing apolipoprotein A-I (APOA1) but not apolipoprotein A-II (APOA2), designated LpA-I, is composed primarily of two discretely sized populations. Here, we isolated these particles directly from human plasma by antibody affinity chromatography, separated them by high-resolution size exclusion chromatography and performed a deep molecular characterization of each species. The large and small LpA-I populations were spherical with mean diameters of 109 Å and 91 Å, respectively. Unexpectedly, isotope dilution MS/MS with [15N]-APOA1 in concert with quantitation of particle concentration by calibrated ion mobility analysis demonstrated that the large particles contained fewer APOA1 molecules than the small particles; the stoichiometries were 3.0 and 3.7 molecules of APOA1 per particle, respectively. MS/MS experiments showed that the protein cargo of large LpA-I particles was more diverse. Human HDL and isolated particles containing both APOA1 and APOA2 exhibit a much wider range and variation of particle sizes than LpA-I, indicating that APOA2 is likely the major contributor to HDL size heterogeneity. We propose a ratchet model based on the trefoil structure of APOA1 whereby the helical cage maintaining particle structure has two 'settings' - large and small - that accounts for these findings. This understanding of the determinants of HDL particle size and protein cargo distribution serves as a basis for determining the roles of HDL subpopulations in metabolism and disease states.
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Affiliation(s)
- John T Melchior
- Center for Lipid and Arteriosclerosis Science, Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio 45237; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99354
| | - Scott E Street
- Center for Lipid and Arteriosclerosis Science, Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio 45237
| | - Tomas Vaisar
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109
| | - Rachel Hart
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Jay Jerome
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Zsuzsanna Kuklenyik
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA 30341
| | - Noemie Clouet-Foraison
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109
| | - Carissa Thornock
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109
| | - Shimpi Bedi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99354
| | - Amy S Shah
- Division of Endocrinology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio 45229
| | - Jere P Segrest
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Jay W Heinecke
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109
| | - W Sean Davidson
- Center for Lipid and Arteriosclerosis Science, Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio 45237.
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16
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Abstract
The cholesterol-dependent cytolysins’ pore-forming mechanism relies on the ability to sense the completion of the oligomeric prepore structure and initiate the insertion of the β-barrel pore from the assembled prepore structure. These studies show that a conserved motif is an important component of the sensor that triggers the prepore-to-pore transition and that it is conserved in a large family of previously unidentified CDC-like proteins, the genes for which are present in a vast array of microbial species that span most terrestrial environments, as well as most animal and human microbiomes. These studies establish the foundation for future investigations that will probe the contribution of this large family of CDC-like proteins to microbial survival and human disease. The cholesterol-dependent cytolysins (CDCs) are bacterial, β-barrel, pore-forming toxins. A central enigma of the pore-forming mechanism is how completion of the prepore is sensed to initiate its conversion to the pore. We identified a motif that is conserved between the CDCs and a diverse family of nearly 300 uncharacterized proteins present in over 220 species that span at least 10 bacterial and 2 eukaryotic phyla. Except for this motif, these proteins exhibit little similarity to the CDCs at the primary structure level. Studies herein show this motif is a critical component of the sensor that initiates the prepore-to-pore transition in the CDCs. We further show by crystallography, single particle analysis, and biochemical studies of one of these CDC-like (CDCL) proteins from Elizabethkingia anophelis, a commensal of the malarial mosquito midgut, that a high degree of structural similarity exists between the CDC and CDCL monomer structures and both form large oligomeric pore complexes. Furthermore, the conserved motif in the E. anophelis CDCL crystal structure occupies a nearly identical position and makes similar contacts to those observed in the structure of the archetype CDC, perfringolysin O (PFO). This suggests a common function in the CDCs and CDCLs and may explain why only this motif is conserved in the CDCLs. Hence, these studies identify a critical component of the sensor involved in initiating the prepore-to-pore transition in the CDCs, which is conserved in a large and diverse group of distant relatives of the CDCs.
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17
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Wyatt JW, Korasick DA, Qureshi IA, Campbell AC, Gates KS, Tanner JJ. Inhibition, crystal structures, and in-solution oligomeric structure of aldehyde dehydrogenase 9A1. Arch Biochem Biophys 2020; 691:108477. [PMID: 32717224 DOI: 10.1016/j.abb.2020.108477] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 10/23/2022]
Abstract
Aldehyde dehydrogenase 9A1 (ALDH9A1) is a human enzyme that catalyzes the NAD+-dependent oxidation of the carnitine precursor 4-trimethylaminobutyraldehyde to 4-N-trimethylaminobutyrate. Here we show that the broad-spectrum ALDH inhibitor diethylaminobenzaldehyde (DEAB) reversibly inhibits ALDH9A1 in a time-dependent manner. Possible mechanisms of inhibition include covalent reversible inactivation involving the thiohemiacetal intermediate and slow, tight-binding inhibition. Two crystal structures of ALDH9A1 are reported, including the first of the enzyme complexed with NAD+. One of the structures reveals the active conformation of the enzyme, in which the Rossmann dinucleotide-binding domain is fully ordered and the inter-domain linker adopts the canonical β-hairpin observed in other ALDH structures. The oligomeric structure of ALDH9A1 was investigated using analytical ultracentrifugation, small-angle X-ray scattering, and negative stain electron microscopy. These data show that ALDH9A1 forms the classic ALDH superfamily dimer-of-dimers tetramer in solution. Our results suggest that the presence of an aldehyde substrate and NAD+ promotes isomerization of the enzyme into the active conformation.
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Affiliation(s)
- Jesse W Wyatt
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States
| | - David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Insaf A Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad, 500046, India
| | - Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - John J Tanner
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States.
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18
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Kroeck KG, Qiu W, Catalano C, Trinh TKH, Guo Y. Native Cell Membrane Nanoparticles System for Membrane Protein-Protein Interaction Analysis. J Vis Exp 2020. [PMID: 32744521 DOI: 10.3791/61298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Protein-protein interactions in cell membrane systems play crucial roles in a wide range of biological processes- from cell-to-cell interactions to signal transduction; from sensing environmental signals to biological response; from metabolic regulation to developmental control. Accurate structural information of protein-protein interactions is crucial for understanding the molecular mechanisms of membrane protein complexes and for the design of highly specific molecules to modulate these proteins. Many in vivo and in vitro approaches have been developed for the detection and analysis of protein-protein interactions. Among them the structural biology approach is unique in that it can provide direct structural information of protein-protein interactions at the atomic level. However, current membrane protein structural biology is still largely limited to detergent-based methods. The major drawback of detergent-based methods is that they often dissociate or denature membrane protein complexes once their native lipid bilayer environment is removed by detergent molecules. We have been developing a native cell membrane nanoparticle system for membrane protein structural biology. Here, we demonstrate the use of this system in the analysis of protein-protein interactions on the cell membrane with a case study of the oligomeric state of AcrB.
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Affiliation(s)
- Kyle G Kroeck
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Weihua Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Claudio Catalano
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Thi Kim Hoang Trinh
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University;
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19
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LoTToR: An Algorithm for Missing-Wedge Correction of the Low-Tilt Tomographic 3D Reconstruction of a Single-Molecule Structure. Sci Rep 2020; 10:10489. [PMID: 32591588 PMCID: PMC7320192 DOI: 10.1038/s41598-020-66793-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 05/27/2020] [Indexed: 01/01/2023] Open
Abstract
A single-molecule three-dimensional (3D) structure is essential for understanding the thermal vibrations and dynamics as well as the conformational changes during the chemical reaction of macromolecules. Individual-particle electron tomography (IPET) is an approach for obtaining a snap-shot 3D structure of an individual macromolecule particle by aligning the tilt series of electron tomographic (ET) images of a targeted particle through a focused iterative 3D reconstruction method. The method can reduce the influence on the 3D reconstruction from large-scale image distortion and deformation. Due to the mechanical tilt limitation, 3D reconstruction often contains missing-wedge artifacts, presented as elongation and an anisotropic resolution. Here, we report a post-processing method to correct the missing-wedge artifact. This low-tilt tomographic reconstruction (LoTToR) method contains a model-free iteration process under a set of constraints in real and reciprocal spaces. A proof of concept is conducted by using the LoTToR on a phantom, i.e., a simulated 3D reconstruction from a low-tilt series of images, including that within a tilt range of ±15°. The method is validated by using both negative-staining (NS) and cryo-electron tomography (cryo-ET) experimental data. A significantly reduced missing-wedge artifact verifies the capability of LoTToR, suggesting a new tool to support the future study of macromolecular dynamics, fluctuation and chemical activity from the viewpoint of single-molecule 3D structure determination.
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20
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Lim CJ, Barbour AT, Zaug AJ, Goodrich KJ, McKay AE, Wuttke DS, Cech TR. The structure of human CST reveals a decameric assembly bound to telomeric DNA. Science 2020; 368:1081-1085. [PMID: 32499435 DOI: 10.1126/science.aaz9649] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/10/2020] [Indexed: 12/26/2022]
Abstract
The CTC1-STN1-TEN1 (CST) complex is essential for telomere maintenance and resolution of stalled replication forks genome-wide. Here, we report the 3.0-angstrom cryo-electron microscopy structure of human CST bound to telomeric single-stranded DNA (ssDNA), which assembles as a decameric supercomplex. The atomic model of the 134-kilodalton CTC1 subunit, built almost entirely de novo, reveals the overall architecture of CST and the DNA-binding anchor site. The carboxyl-terminal domain of STN1 interacts with CTC1 at two separate docking sites, allowing allosteric mediation of CST decamer assembly. Furthermore, ssDNA appears to staple two monomers to nucleate decamer assembly. CTC1 has stronger structural similarity to Replication Protein A than the expected similarity to yeast Cdc13. The decameric structure suggests that CST can organize ssDNA analogously to the nucleosome's organization of double-stranded DNA.
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Affiliation(s)
- Ci Ji Lim
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Alexandra T Barbour
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Arthur J Zaug
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Karen J Goodrich
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Allison E McKay
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA.
| | - Thomas R Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA. .,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
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21
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Abstract
Immunoelectron microscopy is a powerful technique for identifying viral antigens and determining their structural localization and organization within vaccines and viruses. While traditional negative staining transmission electron microscopy provides structural information, identity of components within a sample may be confounding. Immunoelectron microscopy allows for identification and visualization of antigens and their relative positions within a particulate sample. This allows for simple qualitative analysis of samples including whole virus, viral components, and viral‐like particles. This article describes methods for immunogold labeling of viral antigens in a liquid suspension, with examples of immunogold‐labeled influenza virus glycoproteins, and also discusses the important considerations for sample preparation and determination of morphologies. Together, these methods allow for understanding the antigenic makeup of viral particulate samples, which have important implications for molecular virology and vaccine development. © 2019 The Authors. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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Affiliation(s)
- Neetu M Gulati
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Udana Torian
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - John R Gallagher
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Audray K Harris
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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22
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Kim JH, Kim SC, Kline MA, Grzincic EM, Tresca BW, Cardiel J, Karbaschi M, Dehigaspitiya DC, Chen Y, Udumula V, Jian T, Murray DJ, Yun L, Connolly MD, Liu J, Ren G, Chen CL, Kirshenbaum K, Abate AR, Zuckermann RN. Discovery of Stable and Selective Antibody Mimetics from Combinatorial Libraries of Polyvalent, Loop-Functionalized Peptoid Nanosheets. ACS NANO 2020; 14:185-195. [PMID: 31789500 PMCID: PMC9506602 DOI: 10.1021/acsnano.9b07498] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The ability of antibodies to bind a wide variety of analytes with high specificity and high affinity makes them ideal candidates for therapeutic and diagnostic applications. However, the poor stability and high production cost of antibodies have prompted exploration of a variety of synthetic materials capable of specific molecular recognition. Unfortunately, it remains a fundamental challenge to create a chemically diverse population of protein-like, folded synthetic nanostructures with defined molecular conformations in water. Here we report the synthesis and screening of combinatorial libraries of sequence-defined peptoid polymers engineered to fold into ordered, supramolecular nanosheets displaying a high spatial density of diverse, conformationally constrained peptoid loops on their surface. These polyvalent, loop-functionalized nanosheets were screened using a homogeneous Förster resonance energy transfer (FRET) assay for binding to a variety of protein targets. Peptoid sequences were identified that bound to the heptameric protein, anthrax protective antigen, with high avidity and selectivity. These nanosheets were shown to be resistant to proteolytic degradation, and the binding was shown to be dependent on the loop display density. This work demonstrates that key aspects of antibody structure and function-the creation of multivalent, combinatorial chemical diversity within a well-defined folded structure-can be realized with completely synthetic materials. This approach enables the rapid discovery of biomimetic affinity reagents that combine the durability of synthetic materials with the specificity of biomolecular materials.
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Affiliation(s)
- Jae Hong Kim
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Samuel C. Kim
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Mark A. Kline
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Elissa M. Grzincic
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Blakely W. Tresca
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Joshua Cardiel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Mohsen Karbaschi
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
| | | | - Yulin Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Venkatareddy Udumula
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Tengyue Jian
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Daniel J. Murray
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lisa Yun
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Michael D. Connolly
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kent Kirshenbaum
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Adam R. Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
- Corresponding Authors: .
| | - Ronald N. Zuckermann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Corresponding Authors: .
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23
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Korasick DA, Campbell AC, Christgen SL, Chakravarthy S, White TA, Becker DF, Tanner JJ. Redox Modulation of Oligomeric State in Proline Utilization A. Biophys J 2019; 114:2833-2843. [PMID: 29925020 DOI: 10.1016/j.bpj.2018.04.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 10/28/2022] Open
Abstract
Homooligomerization of proline utilization A (PutA) bifunctional flavoenzymes is intimately tied to catalytic function and substrate channeling. PutA from Bradyrhizobium japonicum (BjPutA) is unique among PutAs in that it forms a tetramer in solution. Curiously, a dimeric BjPutA hot spot mutant was previously shown to display wild-type catalytic activity despite lacking the tetrameric structure. These observations raised the question of what is the active oligomeric state of BjPutA. Herein, we investigate the factors that contribute to tetramerization of BjPutA in vitro. Negative-stain electron microscopy indicates that BjPutA is primarily dimeric at nanomolar concentrations, suggesting concentration-dependent tetramerization. Further, sedimentation-velocity analysis of BjPutA at high (micromolar) concentration reveals that although the binding of active-site ligands does not alter oligomeric state, reduction of the flavin adenine dinucleotide cofactor results in dimeric protein. Size-exclusion chromatography coupled with multiangle light scattering and small-angle x-ray scattering analysis also reveals that reduced BjPutA is dimeric. Taken together, these results suggest that the BjPutA oligomeric state is dependent upon both enzyme concentration and the redox state of the flavin cofactor. This is the first report, to our knowledge, of redox-linked oligomerization in the PutA family.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Shelbi L Christgen
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois
| | - Tommi A White
- Department of Biochemistry, University of Missouri, Columbia, Missouri; Electron Microscopy Core Facility, University of Missouri, Columbia, Missouri
| | - Donald F Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri; Department of Chemistry, University of Missouri, Columbia, Missouri.
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Sharma IM, Rappé MC, Addepalli B, Grabow WW, Zhuang Z, Abeysirigunawardena SC, Limbach PA, Jaeger L, Woodson SA. A metastable rRNA junction essential for bacterial 30S biogenesis. Nucleic Acids Res 2019; 46:5182-5194. [PMID: 29850893 PMCID: PMC6007441 DOI: 10.1093/nar/gky120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/13/2018] [Indexed: 12/26/2022] Open
Abstract
Tertiary sequence motifs encode interactions between RNA helices that create the three-dimensional structures of ribosomal subunits. A Right Angle motif at the junction between 16S helices 5 and 6 (J5/6) is universally conserved amongst small subunit rRNAs and forms a stable right angle in minimal RNAs. J5/6 does not form a right angle in the mature ribosome, suggesting that this motif encodes a metastable structure needed for ribosome biogenesis. In this study, J5/6 mutations block 30S ribosome assembly and 16S maturation in Escherichia coli. Folding assays and in-cell X-ray footprinting showed that J5/6 mutations favor an assembly intermediate of the 16S 5' domain and prevent formation of the central pseudoknot. Quantitative mass spectrometry revealed that mutant pre-30S ribosomes lack protein uS12 and are depleted in proteins uS5 and uS2. Together, these results show that impaired folding of the J5/6 right angle prevents the establishment of inter-domain interactions, resulting in global collapse of the 30S structure observed in electron micrographs of mutant pre-30S ribosomes. We propose that the J5/6 motif is part of a spine of RNA helices that switch conformation at distinct stages of assembly, linking peripheral domains with the 30S active site to ensure the integrity of 30S biogenesis.
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Affiliation(s)
- Indra Mani Sharma
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Mollie C Rappé
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Balasubrahmanyam Addepalli
- Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Wade W Grabow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | - Zhuoyun Zhuang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | | | - Patrick A Limbach
- Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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25
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Lei D, Liu J, Liu H, Cleveland TE, Marino JP, Lei M, Ren G. Single-Molecule 3D Images of "Hole-Hole" IgG1 Homodimers by Individual-Particle Electron Tomography. Sci Rep 2019; 9:8864. [PMID: 31221961 PMCID: PMC6586654 DOI: 10.1038/s41598-019-44978-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/30/2019] [Indexed: 12/20/2022] Open
Abstract
The engineering of immunoglobulin-G molecules (IgGs) is of wide interest for improving therapeutics, for example by modulating the activity or multiplexing the specificity of IgGs to recognize more than one antigen. Optimization of engineered IgG requires knowledge of three-dimensional (3D) structure of synthetic IgG. However, due to flexible nature of the molecules, their structural characterization is challenging. Here, we use our reported individual-particle electron tomography (IPET) method with optimized negative-staining (OpNS) for direct 3D reconstruction of individual IgG hole-hole homodimer molecules. The hole-hole homodimer is an undesired variant generated during the production of a bispecific antibody using the knob-into-hole heterodimer technology. A total of 64 IPET 3D density maps at ~15 Å resolutions were reconstructed from 64 individual molecules, revealing 64 unique conformations. In addition to the known Y-shaped conformation, we also observed an unusual X-shaped conformation. The 3D structure of the X-shaped conformation contributes to our understanding of the structural details of the interaction between two heavy chains in the Fc domain. The IPET approach, as an orthogonal technique to characterize the 3D structure of therapeutic antibodies, provides insight into the 3D structural variety and dynamics of heterogeneous IgG molecules.
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Affiliation(s)
- Dongsheng Lei
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hongbin Liu
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Thomas E Cleveland
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - Ming Lei
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, 94080, USA.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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26
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Liu J, Wu H, Huang C, Lei D, Zhang M, Xie W, Li J, Ren G. Optimized Negative-Staining Protocol for Lipid-Protein Interactions Investigated by Electron Microscopy. Methods Mol Biol 2019; 2003:163-173. [PMID: 31218618 PMCID: PMC6817366 DOI: 10.1007/978-1-4939-9512-7_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A large number of proteins are capable of inserting themselves into lipids, and interacting with membranes, such as transmembrane proteins and apolipoproteins. Insights into the lipid-protein interactions are important in understanding biological processes, and the structure of proteins at the lipid binding stage can help identify their roles and critical functions. Previously, such structural determination was challenging to obtain because the traditional methods, such as X-ray crystallography, are unable to capture the conformational and compositional heterogeneity of protein-lipid complexes. Electron microscopy (EM) is an alternative approach to determining protein structures and visualizing lipid-protein interactions directly, and negative-staining (OpNS), a subset of EM techniques, is a rapid, frequently used qualitative approach. The concern, however, is that current NS protocols often generate artifacts with lipid-related proteins, such as rouleaux formation from lipoproteins. To overcome this artifact formation, Ren and his colleagues have refined early NS protocols, and developed an optimized NS protocol that validated by comparing images of lipoproteins from cryo-electron microscopy (cryo-EM). This optimized NS protocol produces "near native-state" particle images and high contrast images of the protein in its native lipid-binding state, which can be used to create higher-quality three-dimensional (3D) reconstruction by single-particle analysis and electron tomography (e.g. IPET). This optimized protocol is thus a promising hands-on approach for examining the structure of proteins at their lipid-binding status.
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Affiliation(s)
- Jianfang Liu
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hao Wu
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Computer Science, College of Information Science and Technology, Beijing Normal University, Beijing, China
| | - Changyu Huang
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dongsheng Lei
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Meng Zhang
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Wei Xie
- State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Cellular and Structural Biology, The Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jinping Li
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, GA, USA
| | - Gang Ren
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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27
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Liu J, Misra A, Reddy MVVVS, White MA, Ren G, Rudenko G. Structural Plasticity of Neurexin 1α: Implications for its Role as Synaptic Organizer. J Mol Biol 2018; 430:4325-4343. [PMID: 30193986 PMCID: PMC6223652 DOI: 10.1016/j.jmb.2018.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 11/24/2022]
Abstract
α-Neurexins are synaptic organizing molecules implicated in neuropsychiatric disorders. They bind and arrange an array of different partners in the synaptic cleft. The extracellular region of neurexin 1α (n1α) contains six LNS domains (L1-L6) interspersed by three Egf-like repeats. N1α must encode highly evolved structure-function relationships in order to fit into the narrow confines of the synaptic cleft, and also recruit its large, membrane-bound partners. Internal molecular flexibility could provide a solution; however, it is challenging to delineate because currently no structural methods permit high-resolution structure determination of large, flexible, multi-domain protein molecules. To investigate the structural plasticity of n1α, in particular the conformation of domains that carry validated binding sites for different protein partners, we used a panel of structural techniques. Individual particle electron tomography revealed that the N-terminally and C-terminally tethered domains, L1 and L6, have a surprisingly limited range of conformational freedom with respect to the linear central core containing L2 through L5. A 2.8-Å crystal structure revealed an unexpected arrangement of the L2 and L3 domains. Small-angle X-ray scattering and electron tomography indicated that incorporation of the alternative splice insert SS6 relieves the restricted conformational freedom between L5 and L6, suggesting that SS6 may work as a molecular toggle. The architecture of n1α thus encodes a combination of rigid and flexibly tethered domains that are uniquely poised to work together to promote its organizing function in the synaptic cleft, and may permit allosterically regulated and/or concerted protein partner binding.
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Affiliation(s)
- Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Anurag Misra
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - M V V V Sekhar Reddy
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mark Andrew White
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Gabby Rudenko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
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28
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Korasick DA, White TA, Chakravarthy S, Tanner JJ. NAD + promotes assembly of the active tetramer of aldehyde dehydrogenase 7A1. FEBS Lett 2018; 592:3229-3238. [PMID: 30184263 PMCID: PMC6188814 DOI: 10.1002/1873-3468.13238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/24/2018] [Accepted: 08/28/2018] [Indexed: 02/04/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) is the redox cofactor of many enzymes, including the vast aldehyde dehydrogenase (ALDH) superfamily. Although the function of NAD(H) in hydride transfer is established, its influence on protein structure is less understood. Herein, we show that NAD+ -binding promotes assembly of the ALDH7A1 tetramer. Multiangle light scattering, small-angle X-ray scattering, and sedimentation velocity all show a pronounced shift of the dimer-tetramer equilibrium toward the tetramer when NAD+ is present. Furthermore, electron microscopy shows that cofactor binding enhances tetramer formation even at the low enzyme concentration used in activity assays, suggesting the tetramer is the active species. Altogether, our results suggest that the catalytically active oligomer of ALDH7A1 is assembled on demand in response to cofactor availability.
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Affiliation(s)
- David A. Korasick
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Tommi A. White
- Department of Biochemistry, University of Missouri, Columbia, Missouri
- Electron Microscopy Core Facility, University of Missouri, Columbia, Missouri
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois
| | - John J. Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri
- Department of Chemistry, University of Missouri, Columbia, Missouri
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29
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Zhang M, Zhai X, Li J, Albers JJ, Vuletic S, Ren G. Structural basis of the lipid transfer mechanism of phospholipid transfer protein (PLTP). Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:1082-1094. [PMID: 29883800 PMCID: PMC6114099 DOI: 10.1016/j.bbalip.2018.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/10/2018] [Accepted: 06/01/2018] [Indexed: 12/14/2022]
Abstract
Human phospholipid transfer protein (PLTP) mediates the transfer of phospholipids among atheroprotective high-density lipoproteins (HDL) and atherogenic low-density lipoproteins (LDL) by an unknown mechanism. Delineating this mechanism would represent the first step towards understanding PLTP-mediated lipid transfers, which may be important for treating lipoprotein abnormalities and cardiovascular disease. Here, using various electron microscopy techniques, PLTP is revealed to have a banana-shaped structure similar to cholesteryl ester transfer protein (CETP). We provide evidence that PLTP penetrates into the HDL and LDL surfaces, respectively, and then forms a ternary complex with HDL and LDL. Insights into the interaction of PLTP with lipoproteins at the molecular level provide a basis to understand the PLTP-dependent lipid transfer mechanisms for dyslipidemia treatment.
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Affiliation(s)
- Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Xiaobo Zhai
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jinping Li
- Department of Biomedical Science, Mercer University School of Medicine, Savannah, GA 31404, United States
| | - John J Albers
- Northwest Lipid Metabolism and Diabetes Research Laboratories, Seattle, WA 98109, United States
| | - Simona Vuletic
- Northwest Lipid Metabolism and Diabetes Research Laboratories, Seattle, WA 98109, United States.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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30
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Pre-Analytical Handling Conditions and Small RNA Recovery from Urine for miRNA Profiling. J Mol Diagn 2018; 20:565-571. [PMID: 29936254 DOI: 10.1016/j.jmoldx.2018.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/19/2018] [Accepted: 04/30/2018] [Indexed: 12/24/2022] Open
Abstract
There are currently no standardized protocols for pre-analytical handling of urine to best preserve small RNA for miRNA profiling studies. miRNA is an attractive candidate as a potential biomarker because of the high level of stability in body fluids and its ability to be quantified on multiple high-throughput platforms. We present a comparison of small RNA recovery and stability in urine under alternate pre-analytical handling conditions and extend recommendations on what conditions optimize yield of miRNA from cell-free urine and urine extracellular vesicles (EVs). Using an affinity slurry for isolation of small RNA from urine, we found that urine samples held at room temperature (20°C) for up to 8 hours before processing yield the highest amounts of intact small RNAs from EVs. Some miRNA is lost from urine samples when held 2°C to 4°C and/or frozen before EV isolation, likely because of EV entrapment in uromodulin precipitates. However, we found that a simple 5-minute incubation of urine containing cold-induced precipitate at 37°C resolubilizes much of this precipitate and results in an increased recovery of EVs and miRNAs. Finally, small RNA integrity can be compromised when whole urine is held at 37°C for as little as 4 hours and is not conducive to efficient miRNA profiling.
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31
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Gallagher JR, McCraw DM, Torian U, Gulati NM, Myers ML, Conlon MT, Harris AK. Characterization of Hemagglutinin Antigens on Influenza Virus and within Vaccines Using Electron Microscopy. Vaccines (Basel) 2018; 6:E31. [PMID: 29799445 PMCID: PMC6027289 DOI: 10.3390/vaccines6020031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/11/2018] [Accepted: 05/21/2018] [Indexed: 01/08/2023] Open
Abstract
Influenza viruses affect millions of people worldwide on an annual basis. Although vaccines are available, influenza still causes significant human mortality and morbidity. Vaccines target the major influenza surface glycoprotein hemagglutinin (HA). However, circulating HA subtypes undergo continual variation in their dominant epitopes, requiring vaccines to be updated annually. A goal of next-generation influenza vaccine research is to produce broader protective immunity against the different types, subtypes, and strains of influenza viruses. One emerging strategy is to focus the immune response away from variable epitopes, and instead target the conserved stem region of HA. To increase the display and immunogenicity of the HA stem, nanoparticles are being developed to display epitopes in a controlled spatial arrangement to improve immunogenicity and elicit protective immune responses. Engineering of these nanoparticles requires structure-guided design to optimize the fidelity and valency of antigen presentation. Here, we review electron microscopy applied to study the 3D structures of influenza viruses and different vaccine antigens. Structure-guided information from electron microscopy should be integrated into pipelines for the development of both more efficacious seasonal and universal influenza vaccine antigens. The lessons learned from influenza vaccine electron microscopic research could aid in the development of novel vaccines for other pathogens.
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Affiliation(s)
- John R Gallagher
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Dustin M McCraw
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Udana Torian
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Neetu M Gulati
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Mallory L Myers
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Michael T Conlon
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Audray K Harris
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
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32
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Xiao K, Zhao Y, Choi M, Liu H, Blanc A, Qian J, Cahill TJ, Li X, Xiao Y, Clark LJ, Li S. Revealing the architecture of protein complexes by an orthogonal approach combining HDXMS, CXMS, and disulfide trapping. Nat Protoc 2018; 13:1403-1428. [PMID: 29844522 DOI: 10.1038/nprot.2018.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many cellular functions necessitate structural assemblies of two or more associated proteins. The structural characterization of protein complexes using standard methods, such as X-ray crystallography, is challenging. Herein, we describe an orthogonal approach using hydrogen-deuterium-exchange mass spectrometry (HDXMS), cross-linking mass spectrometry (CXMS), and disulfide trapping to map interactions within protein complexes. HDXMS measures changes in solvent accessibility and hydrogen bonding upon complex formation; a decrease in HDX rate could account for newly formed intermolecular or intramolecular interactions. To distinguish between inter- and intramolecular interactions, we use a CXMS method to determine the position of direct interface regions by trapping intermolecular residues in close proximity to various cross-linkers (e.g., disuccinimidyl adipate (DSA)) of different lengths and reactive groups. Both MS-based experiments are performed on high-resolution mass spectrometers (e.g., an Orbitrap Elite hybrid mass spectrometer). The physiological relevance of the interactions identified through HDXMS and CXMS is investigated by transiently co-expressing cysteine mutant pairs, one mutant on each protein at the discovered interfaces, in an appropriate cell line, such as HEK293. Disulfide-trapped protein complexes are formed within cells spontaneously or are facilitated by addition of oxidation reagents such as H2O2 or diamide. Western blotting analysis, in the presence and absence of reducing reagents, is used to determine whether the disulfide bonds are formed in the proposed complex interface in physiologically relevant milieus. The procedure described here requires 1-2 months. We demonstrate this approach using the β2-adrenergic receptor-β-arrestin1 complex as the model system.
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Affiliation(s)
- Kunhong Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Vascular Medicine Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Biomedical Mass Spectrometry Center, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yang Zhao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Minjung Choi
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Hongda Liu
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adi Blanc
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Jiang Qian
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Thomas J Cahill
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Xue Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Yunfang Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lisa J Clark
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sheng Li
- Department of Chemistry, University of California at San Diego, La Jolla, California, USA
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33
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IgG Antibody 3D Structures and Dynamics. Antibodies (Basel) 2018; 7:antib7020018. [PMID: 31544870 PMCID: PMC6698877 DOI: 10.3390/antib7020018] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/19/2022] Open
Abstract
Antibodies are vital for human health because of their ability to function as nature's drugs by protecting the body from infection. In recent decades, antibodies have been used as pharmaceutics for targeted therapy in patients with cancer, autoimmune diseases, and cardiovascular diseases. Capturing the dynamic structure of antibodies and characterizing antibody fluctuation is critical for gaining a deeper understanding of their structural characteristics and for improving drug development. Current techniques for studying three-dimensional (3D) structural heterogeneity and variability of proteins have limitations in ascertaining the dynamic structural behavior of antibodies and antibody-antigen complexes. Here, we review current techniques used to study antibody structures with a focus on the recently developed individual-particle electron tomography (IPET) technique. IPET, as a particle-by-particle methodology for 3D structural characterization, has shown advantages in studying structural variety and conformational changes of antibodies, providing direct imaging data for biomolecular engineering to improve development and clinical application of synthetic antibodies.
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34
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Image Processing and Cryo-Transmission Electron Microscopy; Example of Human Proteasome. Appl Microsc 2018. [DOI: 10.9729/am.2018.48.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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35
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Lei D, Marras AE, Liu J, Huang CM, Zhou L, Castro CE, Su HJ, Ren G. Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography. Nat Commun 2018; 9:592. [PMID: 29426880 PMCID: PMC5807444 DOI: 10.1038/s41467-018-03018-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/11/2018] [Indexed: 01/25/2023] Open
Abstract
Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. Here we use the individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~ 6-14 nm resolution. The statistical analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides experimental verification of a theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences and routing.
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Affiliation(s)
- Dongsheng Lei
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alexander E Marras
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Lifeng Zhou
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Hai-Jun Su
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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36
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Krishnamoorthy A, Tavoosi N, Chan GKL, Liu J, Ren G, Cavigiolio G, Ryan RO. Effect of curcumin on amyloid-like aggregates generated from methionine-oxidized apolipoprotein A-I. FEBS Open Bio 2018; 8:302-310. [PMID: 29435420 PMCID: PMC5794470 DOI: 10.1002/2211-5463.12372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/06/2017] [Accepted: 12/12/2017] [Indexed: 12/13/2022] Open
Abstract
Curcumin is a polyphenolic phytonutrient that has antineurodegenerative properties. In this study, we investigated the anti‐amyloidogenic properties of curcumin. Following incubation with curcumin, intrinsic tryptophan fluorescence emission of apolipoprotein (apo) A‐I was strongly quenched. At the same time, curcumin fluorescence emission was enhanced. The fluorescence emission spectra of curcumin in the presence of amyloid‐like aggregates formed by methionine‐oxidized (ox) apoA‐I varied, depending on whether curcumin was added before, or after, aggregate formation. The impact of curcumin on the structure of the aggregating material was revealed by the lower amount of β‐structure in ox‐apoA‐I amyloid‐like aggregates formed in the presence of curcumin, compared to aggregates formed without curcumin. However, the kinetics of ox‐apoA‐I amyloid‐like aggregate formation was not altered by the presence of curcumin. Moreover, electron microscopy analysis detected no discernable differences in amyloid morphology when ox‐apoA‐I amyloid‐like aggregates were formed in the presence or absence of curcumin. In conclusion, curcumin interacts with apoA‐I and alters the structure of ox‐apoA‐I amyloid‐like aggregates yet does not diminish the propensity of ox‐apoA‐I to form aggregates.
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Affiliation(s)
- Aparna Krishnamoorthy
- Department of Nutritional Sciences and Toxicology University of California Berkeley CA USA
| | - Narjes Tavoosi
- Children's Hospital Oakland Research Institute CA USA.,Present address: Department of Biotechnology College of Science University of Tehran Iran
| | - Gary K L Chan
- Children's Hospital Oakland Research Institute CA USA
| | - Jianfang Liu
- Lawrence Berkeley National Laboratory The Molecular Foundry Berkeley CA USA
| | - Gang Ren
- Lawrence Berkeley National Laboratory The Molecular Foundry Berkeley CA USA
| | | | - Robert O Ryan
- Department of Nutritional Sciences and Toxicology University of California Berkeley CA USA.,Children's Hospital Oakland Research Institute CA USA.,Department of Biochemistry and Molecular Biology University of Nevada Reno NV USA
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37
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Peng Z, Parker AS, Peralta MDR, Ravikumar KM, Cox DL, Toney MD. High Tensile Strength of Engineered β-Solenoid Fibrils via Sonication and Pulling. Biophys J 2017; 113:1945-1955. [PMID: 29117519 DOI: 10.1016/j.bpj.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/17/2017] [Accepted: 09/06/2017] [Indexed: 01/17/2023] Open
Abstract
We present estimates of ultimate tensile strength (UTS) for two engineered β-solenoid protein mutant fibril structures (spruce budworm and Rhagium inquisitor antifreeze proteins) derived from sonication-based measurements and from force pulling molecular dynamics simulations, both in water. Sonication experiments generate limiting scissioned fibrils with a well-defined length-to-width correlation for the mutant spruce budworm protein and the resultant UTS estimate is 0.66 ± 0.08 GPa. For fibrils formed from engineered R. inquisitor antifreeze protein, depending upon geometry, we estimate UTSs of 3.5 ± 3.2-5.5 ± 5.1 GPa for proteins with interfacial disulfide bonds, and 1.6 ± 1.5-2.5 ± 2.3 GPa for the reduced form. The large error bars for the R. inquisitor structures are intrinsic to the broad distribution of limiting scission lengths. Simulations provide pulling velocity-dependent UTSs increasing from 0.2 to 1 GPa in the available speed range, and 1.5 GPa extrapolated to the speeds expected in the sonication experiments. Simulations yield low-velocity values for the Young's modulus of 6.0 GPa. Without protein optimization, these mechanical parameters are similar to those of spider silk and Kevlar, but in contrast to spider silk, these proteins have a precisely known sequence-structure relationship.
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Affiliation(s)
- Zeyu Peng
- Department of Chemistry, University of California, Davis, Davis, California
| | - Amanda S Parker
- Department of Physics, University of California, Davis, Davis, California
| | - Maria D R Peralta
- Department of Chemistry, University of California, Davis, Davis, California
| | | | - Daniel L Cox
- Department of Physics, University of California, Davis, Davis, California.
| | - Michael D Toney
- Department of Chemistry, University of California, Davis, Davis, California
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38
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Peng Z, Peralta MDR, Toney MD. Extraordinarily Stable Amyloid Fibrils Engineered from Structurally Defined β-Solenoid Proteins. Biochemistry 2017; 56:6041-6050. [DOI: 10.1021/acs.biochem.7b00364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zeyu Peng
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Maria D. R. Peralta
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Michael D. Toney
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
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39
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Zhang M, Lei D, Peng B, Yang M, Zhang L, Charles MA, Rye KA, Krauss RM, Johns DG, Ren G. Assessing the mechanisms of cholesteryl ester transfer protein inhibitors. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:1606-1617. [PMID: 28911944 PMCID: PMC6239860 DOI: 10.1016/j.bbalip.2017.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/11/2017] [Accepted: 09/08/2017] [Indexed: 12/30/2022]
Abstract
Cholesteryl ester transfer protein (CETP) inhibitors are a new class of therapeutics for dyslipidemia that simultaneously improve two major cardiovascular disease (CVD) risk factors: elevated low-density lipoprotein (LDL) cholesterol and decreased high-density lipoprotein (HDL) cholesterol. However, the detailed molecular mechanisms underlying their efficacy are poorly understood, as are any potential mechanistic differences among the drugs in this class. Herein, we used electron microscopy (EM) to investigate the effects of three of these agents (Torcetrapib, Dalcetrapib and Anacetrapib) on CETP structure, CETP-lipoprotein complex formation and CETP-mediated cholesteryl ester (CE) transfer. We found that although none of these inhibitors altered the structure of CETP or the conformation of CETP-lipoprotein binary complexes, all inhibitors, especially Torcetrapib and Anacetrapib, increased the binding ratios of the binary complexes (e.g., HDL-CETP and LDLCETP) and decreased the binding ratios of the HDL-CETP-LDL ternary complexes. The findings of more binary complexes and fewer ternary complexes reflect a new mechanism of inhibition: one distal end of CETP bound to the first lipoprotein would trigger a conformational change at the other distal end, thus resulting in a decreased binding ratio to the second lipoprotein and a degraded CE transfer rate among lipoproteins. Thus, we suggest a new inhibitor design that should decrease the formation of both binary and ternary complexes. Decreased concentrations of the binary complex may prevent the inhibitor was induced into cell by the tight binding of binary complexes during lipoprotein metabolism in the treatment of CVD.
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Affiliation(s)
- Meng Zhang
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Applied Science & Technology, University of California, Berkeley, CA 94720, USA
| | - Dongsheng Lei
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bo Peng
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mickey Yang
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lei Zhang
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - M Art Charles
- School of Medicine, University of California-San Francisco, San Francisco, CA 94110, USA
| | - Kerry-Anne Rye
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ronald M Krauss
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | | | - Gang Ren
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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40
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Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex. Proc Natl Acad Sci U S A 2017; 114:E5122-E5128. [PMID: 28611213 DOI: 10.1073/pnas.1618421114] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
CRISPR-Cas adaptive immune systems capture DNA fragments from invading bacteriophages and plasmids and integrate them as spacers into bacterial CRISPR arrays. In type I-E and II-A CRISPR-Cas systems, this adaptation process is driven by Cas1-Cas2 complexes. Type I-F systems, however, contain a unique fusion of Cas2, with the type I effector helicase and nuclease for invader destruction, Cas3. By using biochemical, structural, and biophysical methods, we present a structural model of the 400-kDa Cas14-Cas2-32 complex from Pectobacterium atrosepticum with bound protospacer substrate DNA. Two Cas1 dimers assemble on a Cas2 domain dimeric core, which is flanked by two Cas3 domains forming a groove where the protospacer binds to Cas1-Cas2. We developed a sensitive in vitro assay and demonstrated that Cas1-Cas2-3 catalyzed spacer integration into CRISPR arrays. The integrase domain of Cas1 was necessary, whereas integration was independent of the helicase or nuclease activities of Cas3. Integration required at least partially duplex protospacers with free 3'-OH groups, and leader-proximal integration was stimulated by integration host factor. In a coupled capture and integration assay, Cas1-Cas2-3 processed and integrated protospacers independent of Cas3 activity. These results provide insight into the structure of protospacer-bound type I Cas1-Cas2-3 adaptation complexes and their integration mechanism.
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41
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Asadi J, Ferguson S, Raja H, Hacker C, Marius P, Ward R, Pliotas C, Naismith J, Lucocq J. Enhanced imaging of lipid rich nanoparticles embedded in methylcellulose films for transmission electron microscopy using mixtures of heavy metals. Micron 2017; 99:40-48. [PMID: 28419915 PMCID: PMC5465805 DOI: 10.1016/j.micron.2017.03.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 02/01/2023]
Abstract
Uranyl acetate/tungsten double stains are proposed for imaging lipid rich nanoparticle in TEM. Combined with methylcellulose embedment, the technique enhances membrane contrast. The technique works for liposomes, nanodiscs and bicelles. The double staining should improve quantification of lipid rich nanoparticles.
Synthetic and naturally occurring lipid-rich nanoparticles are of wide ranging importance in biomedicine. They include liposomes, bicelles, nanodiscs, exosomes and virus particles. The quantitative study of these particles requires methods for high-resolution visualization of the whole population. One powerful imaging method is cryo-EM of vitrified samples, but this is technically demanding, requires specialized equipment, provides low contrast and does not reveal all particles present in a population. Another approach is classical negative stain-EM, which is more accessible but is difficult to standardize for larger lipidic structures, which are prone to artifacts of structure collapse and contrast variability. A third method uses embedment in methylcellulose films containing uranyl acetate as a contrasting agent. Methylcellulose embedment has been widely used for contrasting and supporting cryosections but only sporadically for visualizing lipid rich vesicular structures such as endosomes and exosomes. Here we present a simple methylcellulose-based method for routine and comprehensive visualization of synthetic lipid rich nanoparticles preparations, such as liposomes, bicelles and nanodiscs. It combines a novel double-staining mixture of uranyl acetate (UA) and tungsten-based electron stains (namely phosphotungstic acid (PTA) or sodium silicotungstate (STA)) with methylcellulose embedment. While the methylcellulose supports the delicate lipid structures during drying, the addition of PTA or STA to UA provides significant enhancement in lipid structure display and contrast as compared to UA alone. This double staining method should aid routine structural evaluation and quantification of lipid rich nanoparticles structures.
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Affiliation(s)
- Jalal Asadi
- School of Medicine, University of St Andrews, St. Andrews, Fife, KY16 9TF, UK
| | - Sophie Ferguson
- School of Medicine, University of St Andrews, St. Andrews, Fife, KY16 9TF, UK
| | - Hussain Raja
- School of Medicine, University of St Andrews, St. Andrews, Fife, KY16 9TF, UK
| | - Christian Hacker
- School of Medicine, University of St Andrews, St. Andrews, Fife, KY16 9TF, UK
| | - Phedra Marius
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, St. Andrews, Scotland, UK
| | - Richard Ward
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, St. Andrews, Scotland, UK
| | - Christos Pliotas
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, St. Andrews, Scotland, UK
| | - James Naismith
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, St. Andrews, Scotland, UK
| | - John Lucocq
- School of Medicine, University of St Andrews, St. Andrews, Fife, KY16 9TF, UK.
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42
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Ikon N, Shearer J, Liu J, Tran JJ, Feng S, Kamei A, Beckstead JA, Kiss RS, Weers PM, Ren G, Ryan RO. A facile method for isolation of recombinant human apolipoprotein A-I from E. coli. Protein Expr Purif 2017; 134:18-24. [PMID: 28336201 DOI: 10.1016/j.pep.2017.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 12/14/2022]
Abstract
Apolipoprotein (apo) A-I is the major protein component of high-density lipoprotein (HDL) and plays key roles in the Reverse Cholesterol Transport pathway. In the past decade, reconstituted HDL (rHDL) has been employed as a therapeutic agent for treatment of atherosclerosis. The ability of rHDL to promote cholesterol efflux from peripheral cells has been documented to reduce the size of atherosclerotic plaque lesions. However, development of apoA-I rHDL-based therapeutics for human use requires a cost effective process to generate an apoA-I product that meets "Good Manufacturing Practice" standards. Methods available for production and isolation of unmodified recombinant human apoA-I at scale are cumbersome, laborious and complex. To overcome this obstacle, a streamlined two-step procedure has been devised for isolation of recombinant untagged human apoA-I from E. coli that takes advantage of its ability to re-fold to a native conformation following denaturation. Heat treatment of a sonicated E. coli supernatant fraction induced precipitation of a large proportion of host cell proteins (HCP), yielding apoA-I as the major soluble protein. Reversed-phase HPLC of this material permitted recovery of apoA-I largely free of HCP and endotoxin. Purified apoA-I possessed α-helix secondary structure, formed rHDL upon incubation with phospholipid and efficiently promoted cholesterol efflux from cholesterol loaded J774 macrophages.
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Affiliation(s)
- Nikita Ikon
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland CA 94609, USA
| | - Jennifer Shearer
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland CA 94609, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - Jesse J Tran
- Department of Chemistry and Biochemistry, California State University, Long Beach 1250, Bellflower Boulevard, Long Beach, CA 90840, USA
| | - ShiBo Feng
- Research Institute of the McGill University Health Centre, Glen Site, EM1.2220, 1001 Boul Decarie, Montreal, QCH4A 3J1 Canada
| | - Ayako Kamei
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland CA 94609, USA
| | - Jennifer A Beckstead
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland CA 94609, USA
| | - Robert S Kiss
- Research Institute of the McGill University Health Centre, Glen Site, EM1.2220, 1001 Boul Decarie, Montreal, QCH4A 3J1 Canada
| | - Paul M Weers
- Department of Chemistry and Biochemistry, California State University, Long Beach 1250, Bellflower Boulevard, Long Beach, CA 90840, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - Robert O Ryan
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland CA 94609, USA.
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43
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B Kumar R, Zhu L, Hebert H, Jegerschöld C. Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy. J Vis Exp 2017. [PMID: 28287545 DOI: 10.3791/55148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Monotopic proteins exert their function when attached to a membrane surface, and such interactions depend on the specific lipid composition and on the availability of enough area to perform the function. Nanodiscs are used to provide a membrane surface of controlled size and lipid content. In the absence of bound extrinsic proteins, sodium phosphotungstate-stained nanodiscs appear as stacks of coins when viewed from the side by transmission electron microscopy (TEM). This protocol is therefore designed to intentionally promote stacking; consequently, the prevention of stacking can be interpreted as the binding of the membrane-binding protein to the nanodisc. In a further step, the TEM images of the protein-nanodisc complexes can be processed with standard single-particle methods to yield low-resolution structures as a basis for higher resolution cryoEM work. Furthermore, the nanodiscs provide samples suitable for either TEM or non-denaturing gel electrophoresis. To illustrate the method, Ca2+-induced binding of 5-lipoxygenase on nanodiscs is presented.
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Affiliation(s)
| | - Lin Zhu
- School of Technology and Health, KTH Royal Institute of Technology
| | - Hans Hebert
- Department of Biosciences and Nutrition, Karolinska Institutet; School of Technology and Health, KTH Royal Institute of Technology
| | - Caroline Jegerschöld
- Department of Biosciences and Nutrition, Karolinska Institutet; School of Technology and Health, KTH Royal Institute of Technology; ;
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44
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Yu Y, Kuang YL, Lei D, Zhai X, Zhang M, Krauss RM, Ren G. Polyhedral 3D structure of human plasma very low density lipoproteins by individual particle cryo-electron tomography1. J Lipid Res 2016; 57:1879-1888. [PMID: 27538822 PMCID: PMC5036368 DOI: 10.1194/jlr.m070375] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Indexed: 12/21/2022] Open
Abstract
Human VLDLs assembled in the liver and secreted into the circulation supply energy to peripheral tissues. VLDL lipolysis yields atherogenic LDLs and VLDL remnants that strongly correlate with CVD. Although the composition of VLDL particles has been well-characterized, their 3D structure is elusive because of their variations in size, heterogeneity in composition, structural flexibility, and mobility in solution. Here, we employed cryo-electron microscopy and individual-particle electron tomography to study the 3D structure of individual VLDL particles (without averaging) at both below and above their lipid phase transition temperatures. The 3D reconstructions of VLDL and VLDL bound to antibodies revealed an unexpected polyhedral shape, in contrast to the generally accepted model of a spherical emulsion-like particle. The smaller curvature of surface lipids compared with HDL may also reduce surface hydrophobicity, resulting in lower binding affinity to the hydrophobic distal end of the N-terminal β-barrel domain of cholesteryl ester transfer protein (CETP) compared with HDL. The directional binding of CETP to HDL and VLDL may explain the function of CETP in transferring TGs and cholesteryl esters between these particles. This first visualization of the 3D structure of VLDL could improve our understanding of the role of VLDL in atherogenesis.
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Affiliation(s)
- Yadong Yu
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Yu-Lin Kuang
- Atherosclerosis Research, Children's Hospital Oakland Research Institute, Oakland, CA 94609
| | - Dongsheng Lei
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Xiaobo Zhai
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Meng Zhang
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Ronald M Krauss
- Atherosclerosis Research, Children's Hospital Oakland Research Institute, Oakland, CA 94609
| | - Gang Ren
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
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45
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Zhang L, Lei D, Smith JM, Zhang M, Tong H, Zhang X, Lu Z, Liu J, Alivisatos AP, Ren G. Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography. Nat Commun 2016; 7:11083. [PMID: 27025159 PMCID: PMC4820932 DOI: 10.1038/ncomms11083] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 02/19/2016] [Indexed: 12/13/2022] Open
Abstract
DNA base pairing has been used for many years to direct the arrangement of inorganic
nanocrystals into small groupings and arrays with tailored optical and electrical
properties. The control of DNA-mediated assembly depends crucially on a better
understanding of three-dimensional structure of DNA-nanocrystal-hybridized building
blocks. Existing techniques do not allow for structural determination of these
flexible and heterogeneous samples. Here we report cryo-electron microscopy and
negative-staining electron tomography approaches to image, and three-dimensionally
reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two
5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By
individual-particle electron tomography reconstruction, we obtain 14 density maps at
∼2-nm resolution. Using these maps as constraints, we derive 14
conformations of dsDNA by molecular dynamics simulations. The conformational
variation is consistent with that from liquid solution, suggesting that
individual-particle electron tomography could be an expected approach to study
DNA-assembling and flexible protein structure and dynamics. The control of DNA-mediated assembly depends on a precise
understanding of the three-dimensional structure of DNA-nanocrystal-hybridized building
blocks. Here, the authors use cryo-electron microscopy and negative-staining techniques
to investigate the morphology of DNA-nanogold conjugates.
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Affiliation(s)
- Lei Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Applied Physics, School of Science, Xi'an Jiaotong University, Xi'an 710049, China
| | - Dongsheng Lei
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jessica M Smith
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Chemistry, University of California, Berkeley, California 94720, USA.,Department of Materials Science, University of California, Berkeley, California 94720, USA
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Huimin Tong
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Xing Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Applied Physics, School of Science, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhuoyang Lu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China.,School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.,Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China.,School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.,Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - A Paul Alivisatos
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Chemistry, University of California, Berkeley, California 94720, USA.,Department of Materials Science, University of California, Berkeley, California 94720, USA.,Kavli Energy NanoScience Institute, University of California, Berkeley, California 94720, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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46
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Mukhitov N, Spear JM, Stagg SM, Roper MG. Interfacing Microfluidics with Negative Stain Transmission Electron Microscopy. Anal Chem 2016; 88:629-34. [PMID: 26642355 PMCID: PMC4730115 DOI: 10.1021/acs.analchem.5b03884] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A microfluidic platform is presented for preparing negatively stained grids for use in transmission electron microscopy (EM). The microfluidic device is composed of glass etched with readily fabricated features that facilitate the extraction of the grid poststaining and maintains the integrity of the sample. Utilization of this device simultaneously reduced environmental contamination on the grids and improved the homogeneity of the heavy metal stain needed to enhance visualization of biological specimens as compared to conventionally prepared EM grids. This easy-to-use EM grid preparation device provides the basis for future developments of systems with more integrated features, which will allow for high-throughput and dynamic structural biology studies.
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Affiliation(s)
- Nikita Mukhitov
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL USA 32306
| | - John M. Spear
- Institute of Molecular Biophysics, Florida State University, 91 Chieftain Way, Tallahassee, FL USA 32306
| | - Scott M. Stagg
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL USA 32306
- Institute of Molecular Biophysics, Florida State University, 91 Chieftain Way, Tallahassee, FL USA 32306
| | - Michael G. Roper
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL USA 32306
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47
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Berleman J, Zemla M, Remis J, Auer M. Preparation of Outer Membrane Vesicles from Myxococcus xanthus. Bio Protoc 2016. [DOI: 10.21769/bioprotoc.1716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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48
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Ercius P, Alaidi O, Rames MJ, Ren G. Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:5638-63. [PMID: 26087941 PMCID: PMC4710474 DOI: 10.1002/adma.201501015] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/22/2015] [Indexed: 05/23/2023]
Abstract
Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is a technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. This review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated.
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Affiliation(s)
- Peter Ercius
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Osama Alaidi
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Matthew J. Rames
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Gang Ren
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
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Zhang X, Zhang L, Tong H, Peng B, Rames MJ, Zhang S, Ren G. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography. Sci Rep 2015; 5:9803. [PMID: 25940394 PMCID: PMC4419541 DOI: 10.1038/srep09803] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/02/2015] [Indexed: 12/21/2022] Open
Abstract
Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1-3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.
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Affiliation(s)
- Xing Zhang
- 1] The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA [2] Department of Applied Physics, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Lei Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Huimin Tong
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bo Peng
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew J Rames
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shengli Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Lu Z, Wang Y, Chen F, Tong H, Reddy MVVVS, Luo L, Seshadrinathan S, Zhang L, Holthauzen LMF, Craig AM, Ren G, Rudenko G. Calsyntenin-3 molecular architecture and interaction with neurexin 1α. J Biol Chem 2014; 289:34530-42. [PMID: 25352602 DOI: 10.1074/jbc.m114.606806] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Calsyntenin 3 (Cstn3 or Clstn3), a recently identified synaptic organizer, promotes the development of synapses. Cstn3 localizes to the postsynaptic membrane and triggers presynaptic differentiation. Calsyntenin members play an evolutionarily conserved role in memory and learning. Cstn3 was recently shown in cell-based assays to interact with neurexin 1α (n1α), a synaptic organizer that is implicated in neuropsychiatric disease. Interaction would permit Cstn3 and n1α to form a trans-synaptic complex and promote synaptic differentiation. However, it is contentious whether Cstn3 binds n1α directly. To understand the structure and function of Cstn3, we determined its architecture by electron microscopy and delineated the interaction between Cstn3 and n1α biochemically and biophysically. We show that Cstn3 ectodomains form monomers as well as tetramers that are stabilized by disulfide bonds and Ca(2+), and both are probably flexible in solution. We show further that the extracellular domains of Cstn3 and n1α interact directly and that both Cstn3 monomers and tetramers bind n1α with nanomolar affinity. The interaction is promoted by Ca(2+) and requires minimally the LNS domain of Cstn3. Furthermore, Cstn3 uses a fundamentally different mechanism to bind n1α compared with other neurexin partners, such as the synaptic organizer neuroligin 2, because Cstn3 does not strictly require the sixth LNS domain of n1α. Our structural data suggest how Cstn3 as a synaptic organizer on the postsynaptic membrane, particularly in tetrameric form, may assemble radially symmetric trans-synaptic bridges with the presynaptic synaptic organizer n1α to recruit and spatially organize proteins into networks essential for synaptic function.
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Affiliation(s)
- Zhuoyang Lu
- the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, the School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yun Wang
- the University of Michigan, Ann Arbor, Michigan 48109
| | - Fang Chen
- the University of Michigan, Ann Arbor, Michigan 48109
| | - Huimin Tong
- the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | | | - Lin Luo
- the Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada, and
| | | | - Lei Zhang
- the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Luis Marcelo F Holthauzen
- the Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston Texas 77555
| | - Ann Marie Craig
- the Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada, and
| | - Gang Ren
- the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720,
| | - Gabby Rudenko
- From the Department of Pharmacology and Toxicology and the Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston Texas 77555,
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