1
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Liu J, McRae EKS, Zhang M, Geary C, Andersen ES, Ren G. Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography. Nat Commun 2024; 15:9084. [PMID: 39433544 PMCID: PMC11494099 DOI: 10.1038/s41467-024-52914-1] [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: 12/22/2023] [Accepted: 09/23/2024] [Indexed: 10/23/2024] Open
Abstract
Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e-Å-2, achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions.
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Affiliation(s)
- Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ewan K S McRae
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000, Aarhus, Denmark
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Cody Geary
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000, Aarhus, Denmark
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, 69120, Heidelberg, Germany
| | - Ebbe Sloth Andersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000, Aarhus, Denmark.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, 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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Wańczura P, Aebisher D, Iwański MA, Myśliwiec A, Dynarowicz K, Bartusik-Aebisher D. The Essence of Lipoproteins in Cardiovascular Health and Diseases Treated by Photodynamic Therapy. Biomedicines 2024; 12:961. [PMID: 38790923 PMCID: PMC11117957 DOI: 10.3390/biomedicines12050961] [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: 03/10/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Lipids, together with lipoprotein particles, are the cause of atherosclerosis, which is a pathology of the cardiovascular system. In addition, it affects inflammatory processes and affects the vessels and heart. In pharmaceutical answer to this, statins are considered a first-stage treatment method to block cholesterol synthesis. Many times, additional drugs are also used with this method to lower lipid concentrations in order to achieve certain values of low-density lipoprotein (LDL) cholesterol. Recent advances in photodynamic therapy (PDT) as a new cancer treatment have gained the therapy much attention as a minimally invasive and highly selective method. Photodynamic therapy has been proven more effective than chemotherapy, radiotherapy, and immunotherapy alone in numerous studies. Consequently, photodynamic therapy research has expanded in many fields of medicine due to its increased therapeutic effects and reduced side effects. Currently, PDT is the most commonly used therapy for treating age-related macular degeneration, as well as inflammatory diseases, and skin infections. The effectiveness of photodynamic therapy against a number of pathogens has also been demonstrated in various studies. Also, PDT has been used in the treatment of cardiovascular diseases, such as atherosclerosis and hyperplasia of the arterial intima. This review evaluates the effectiveness and usefulness of photodynamic therapy in cardiovascular diseases. According to the analysis, photodynamic therapy is a promising approach for treating cardiovascular diseases and may lead to new clinical trials and management standards. Our review addresses the used therapeutic strategies and also describes new therapeutic strategies to reduce the cardiovascular burden that is induced by lipids.
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Affiliation(s)
- Piotr Wańczura
- Department of Cardiology, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
| | - David Aebisher
- Department of Photomedicine and Physical Chemistry, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
| | - Mateusz A Iwański
- English Division Science Club, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
| | - Angelika Myśliwiec
- Center for Innovative Research in Medical and Natural Sciences, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
| | - Klaudia Dynarowicz
- Center for Innovative Research in Medical and Natural Sciences, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
| | - Dorota Bartusik-Aebisher
- Department of Biochemistry and General Chemistry, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
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4
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Xu Y, Jia H, Gao P, Galvez-Aranda DE, Beltran SP, Cao X, Le PML, Liu J, Engelhard MH, Li S, Ren G, Seminario JM, Balbuena PB, Zhang JG, Xu W, Wang C. Direct in situ measurements of electrical properties of solid-electrolyte interphase on lithium metal anodes. NATURE ENERGY 2023; 8:1345-1354. [PMID: 38249622 PMCID: PMC10798234 DOI: 10.1038/s41560-023-01361-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/22/2023] [Indexed: 01/23/2024]
Abstract
The solid-electrolyte interphase (SEI) critically governs the performance of rechargeable batteries. An ideal SEI is expected to be electrically insulative to prevent persistently parasitic reactions between the electrode and the electrolyte and ionically conductive to facilitate Faradaic reactions of the electrode. However, the true nature of the electrical properties of the SEI remains hitherto unclear due to the lack of a direct characterization method. Here we use in situ bias transmission electron microscopy to directly measure the electrical properties of SEIs formed on copper and lithium substrates. We reveal that SEIs show a voltage-dependent differential conductance. A higher rate of differential conductance induces a thicker SEI with an intricate topographic feature, leading to an inferior Coulombic efficiency and cycling stability in Li∣∣Cu and Li∣∣LiNi0.8Mn0.1Co0.1O2 cells. Our work provides insight into the targeted design of the SEI with desired characteristics towards better battery performance.
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Affiliation(s)
- Yaobin Xu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
- These authors contributed equally: Yaobin Xu, Hao Jia
| | - Hao Jia
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- These authors contributed equally: Yaobin Xu, Hao Jia
| | - Peiyuan Gao
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Diego E. Galvez-Aranda
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Saul Perez Beltran
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Xia Cao
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Phung M. L. Le
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mark H. Engelhard
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Shuang Li
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jorge M. Seminario
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Perla B. Balbuena
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, USA
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Ji-Guang Zhang
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wu Xu
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chongmin Wang
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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5
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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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6
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McRae EKS, Rasmussen HØ, Liu J, Bøggild A, Nguyen MTA, Sampedro Vallina N, Boesen T, Pedersen JS, Ren G, Geary C, Andersen ES. Structure, folding and flexibility of co-transcriptional RNA origami. NATURE NANOTECHNOLOGY 2023; 18:808-817. [PMID: 36849548 PMCID: PMC10566746 DOI: 10.1038/s41565-023-01321-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic biology. However, to advance the method further, an improved understanding of RNA structural properties and folding principles is required. Here we use cryogenic electron microscopy to study RNA origami sheets and bundles at sub-nanometre resolution revealing structural parameters of kissing-loop and crossover motifs, which are used to improve designs. In RNA bundle designs, we discover a kinetic folding trap that forms during folding and is only released after 10 h. Exploration of the conformational landscape of several RNA designs reveal the flexibility of helices and structural motifs. Finally, sheets and bundles are combined to construct a multidomain satellite shape, which is characterized by individual-particle cryo-electron tomography to reveal the domain flexibility. Together, the study provides a structural basis for future improvements to the design cycle of genetically encoded RNA nanodevices.
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Affiliation(s)
- Ewan K S McRae
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Helena Østergaard Rasmussen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andreas Bøggild
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Michael T A Nguyen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | | | - Thomas Boesen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cody Geary
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Ebbe Sloth Andersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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7
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Xia Y, Liu J, Kancharla R, Li J, Hatamlee SM, Ren G, Semeykina V, Hamed A, Kane JJ. Insights into the 3D permeable pore structure within novel monodisperse mesoporous silica nanoparticles by cryogenic electron tomography. NANOSCALE ADVANCES 2023; 5:2879-2886. [PMID: 37260494 PMCID: PMC10228490 DOI: 10.1039/d3na00145h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/14/2023] [Indexed: 06/02/2023]
Abstract
Sintered agglomerate of synthetic mesoporous silica nanoparticles (MSNs) is an architected geomaterial that provides confinement-mediated flow and transport properties of fluids needed for environmental research such as geological subsurface energy storage or carbon capture. The design of those properties can be guided by numerical simulations but is hindered by the lack of method to characterize the permeable pores within MSNs due to pore size. This work uses the advances of an Individual Particle cryogenic transmission Electron Tomography (IPET) technique to obtain detailed 3D morphology of monodispersed MSNs with diameters below 50 nm. The 3D reconstructed density-maps show the diameters of those MSNs vary from 35-46 nm, containing connected intraparticle pores in diameter of 2-20 nm with a mean of 9.2 ± 3 nm, which is comparable to the mean interparticle pore diameters in sintered agglomerate. The characterization of the pore shape and dimensions provides key information for estimating the flow and transport properties of fluids within the sintered agglomerate of those MSNs and for modeling the atomic MSN structures needed for pore-fluid simulations.
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Affiliation(s)
- Yidong Xia
- Energy and Environment Science & Technology, Idaho National Laboratory Idaho Falls 83415 ID USA +01 208 526 7490
| | - Jianfang Liu
- Molecular Foundry, Lawrence Berkeley National Laboratory Berkeley 94720 CA USA
| | - Rahul Kancharla
- Materials & Fuels Complex, Idaho National Laboratory Idaho Falls 83415 ID USA
| | - Jiaoyan Li
- Department of Mechanical and Aerospace Engineering, University at Buffalo Buffalo 14260 NY USA
| | - Seyed M Hatamlee
- Department of Mechanical and Aerospace Engineering, University at Buffalo Buffalo 14260 NY USA
| | - Gang Ren
- Molecular Foundry, Lawrence Berkeley National Laboratory Berkeley 94720 CA USA
| | | | - Ahmed Hamed
- Energy and Environment Science & Technology, Idaho National Laboratory Idaho Falls 83415 ID USA +01 208 526 7490
| | - Joshua J Kane
- Materials & Fuels Complex, Idaho National Laboratory Idaho Falls 83415 ID USA
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8
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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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9
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Xue H, Zhang M, Liu J, Wang J, Ren G. Structure-based mechanism and inhibition of cholesteryl ester transfer protein. Curr Atheroscler Rep 2023; 25:155-166. [PMID: 36881278 PMCID: PMC10027838 DOI: 10.1007/s11883-023-01087-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
PURPOSE OF REVIEW Cholesteryl ester transfer proteins (CETP) regulate plasma cholesterol levels by transferring cholesteryl esters (CEs) among lipoproteins. Lipoprotein cholesterol levels correlate with the risk factors for atherosclerotic cardiovascular disease (ASCVD). This article reviews recent research on CETP structure, lipid transfer mechanism, and its inhibition. RECENT FINDINGS Genetic deficiency in CETP is associated with a low plasma level of low-density lipoprotein cholesterol (LDL-C) and a profoundly elevated plasma level of high-density lipoprotein cholesterol (HDL-C), which correlates with a lower risk of atherosclerotic cardiovascular disease (ASCVD). However, a very high concentration of HDL-C also correlates with increased ASCVD mortality. Considering that the elevated CETP activity is a major determinant of the atherogenic dyslipidemia, i.e., pro-atherogenic reductions in HDL and LDL particle size, inhibition of CETP emerged as a promising pharmacological target during the past two decades. CETP inhibitors, including torcetrapib, dalcetrapib, evacetrapib, anacetrapib and obicetrapib, were designed and evaluated in phase III clinical trials for the treatment of ASCVD or dyslipidemia. Although these inhibitors increase in plasma HDL-C levels and/or reduce LDL-C levels, the poor efficacy against ASCVD ended interest in CETP as an anti-ASCVD target. Nevertheless, interest in CETP and the molecular mechanism by which it inhibits CE transfer among lipoproteins persisted. Insights into the structural-based CETP-lipoprotein interactions can unravel CETP inhibition machinery, which can hopefully guide the design of more effective CETP inhibitors that combat ASCVD. Individual-molecule 3D structures of CETP bound to lipoproteins provide a model for understanding the mechanism by which CETP mediates lipid transfer and which in turn, guide the rational design of new anti-ASCVD therapeutics.
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Affiliation(s)
- Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- 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, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - 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, USA.
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10
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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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11
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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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12
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Ling WL, Kimura Y, Han Y, Li Y. Editorial: Recent advances and challenges in electron microscopy characterizations of radiation-sensitive nanoparticles. Front Chem 2023; 11:1171240. [PMID: 36936524 PMCID: PMC10018536 DOI: 10.3389/fchem.2023.1171240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Affiliation(s)
- Wai Li Ling
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- *Correspondence: Wai Li Ling,
| | | | - Yu Han
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Yanbin Li
- Stanford University, Stanford, CA, United States
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13
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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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14
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Zhang M, Díaz-Celis C, Onoa B, Cañari-Chumpitaz C, Requejo KI, Liu J, Vien M, Nogales E, Ren G, Bustamante C. Molecular organization of the early stages of nucleosome phase separation visualized by cryo-electron tomography. Mol Cell 2022; 82:3000-3014.e9. [PMID: 35907400 DOI: 10.1016/j.molcel.2022.06.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/09/2022] [Accepted: 06/28/2022] [Indexed: 12/16/2022]
Abstract
It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, understanding nucleosomal LLPS has been hindered by the challenge to characterize the structure of the resulting heterogeneous condensates. We used cryo-electron tomography and deep-learning-based 3D reconstruction/segmentation to determine the molecular organization of condensates at various stages of LLPS. We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates, followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion of spinodal materials or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure of nucleosome hydrophobic surfaces causing modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures.
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Affiliation(s)
- Meng Zhang
- Applied Science and Technology Graduate Group, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; The Molecular Foundry, Lawrence Berkeley National Laboratory, 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
| | - Bibiana Onoa
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | | | - Katherinne I Requejo
- 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
| | - Michael Vien
- Department of Physics, University of California, Berkeley, CA, USA
| | - Eva Nogales
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, 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
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Carlos Bustamante
- 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.
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15
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Cryo-electron tomography provides topological insights into mutant huntingtin exon 1 and polyQ aggregates. Commun Biol 2021; 4:849. [PMID: 34239038 PMCID: PMC8266869 DOI: 10.1038/s42003-021-02360-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/15/2021] [Indexed: 01/27/2023] Open
Abstract
Huntington disease (HD) is a neurodegenerative trinucleotide repeat disorder caused by an expanded poly-glutamine (polyQ) tract in the mutant huntingtin (mHTT) protein. The formation and topology of filamentous mHTT inclusions in the brain (hallmarks of HD implicated in neurotoxicity) remain elusive. Using cryo-electron tomography and subtomogram averaging, here we show that mHTT exon 1 and polyQ-only aggregates in vitro are structurally heterogenous and filamentous, similar to prior observations with other methods. Yet, we find filaments in both types of aggregates under ~2 nm in width, thinner than previously reported, and regions forming large sheets. In addition, our data show a prevalent subpopulation of filaments exhibiting a lumpy slab morphology in both aggregates, supportive of the polyQ core model. This provides a basis for future cryoET studies of various aggregated mHTT and polyQ constructs to improve their structure-based modeling as well as their identification in cells without fusion tags.
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16
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Wang ST, Minevich B, Liu J, Zhang H, Nykypanchuk D, Byrnes J, Liu W, Bershadsky L, Liu Q, Wang T, Ren G, Gang O. Designed and biologically active protein lattices. Nat Commun 2021; 12:3702. [PMID: 34140491 PMCID: PMC8211860 DOI: 10.1038/s41467-021-23966-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/13/2021] [Indexed: 01/13/2023] Open
Abstract
Versatile methods to organize proteins in space are required to enable complex biomaterials, engineered biomolecular scaffolds, cell-free biology, and hybrid nanoscale systems. Here, we demonstrate how the tailored encapsulation of proteins in DNA-based voxels can be combined with programmable assembly that directs these voxels into biologically functional protein arrays with prescribed and ordered two-dimensional (2D) and three-dimensional (3D) organizations. We apply the presented concept to ferritin, an iron storage protein, and its iron-free analog, apoferritin, in order to form single-layers, double-layers, as well as several types of 3D protein lattices. Our study demonstrates that internal voxel design and inter-voxel encoding can be effectively employed to create protein lattices with designed organization, as confirmed by in situ X-ray scattering and cryo-electron microscopy 3D imaging. The assembled protein arrays maintain structural stability and biological activity in environments relevant for protein functionality. The framework design of the arrays then allows small molecules to access the ferritins and their iron cores and convert them into apoferritin arrays through the release of iron ions. The presented study introduces a platform approach for creating bio-active protein-containing ordered nanomaterials with desired 2D and 3D organizations.
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Affiliation(s)
- Shih-Ting Wang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York City, NY, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Honghu Zhang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Dmytro Nykypanchuk
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - James Byrnes
- Energy Sciences Directorate/Photon Science Division, NSLS II, Brookhaven National Laboratory, Upton, NY, USA
| | - Wu Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Lev Bershadsky
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Tong Wang
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York City, NY, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA.
- Department of Chemical Engineering, Columbia University, New York City, NY, USA.
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA.
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17
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Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells. Nat Methods 2021; 18:186-193. [PMID: 33542511 PMCID: PMC7611018 DOI: 10.1038/s41592-020-01054-7] [Citation(s) in RCA: 237] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and three-dimensional deformation during exposures are crucial for achieving high-resolution reconstructions. Here we describe M, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and couples a comprehensive spatial deformation model to in silico correction of electron-optical aberrations. M provides a unified optimization framework for both frame-series and tomographic tilt-series data. We show that tilt-series data can provide the same resolution as frame-series data on a purified protein specimen, indicating that the alignment step no longer limits the resolution obtainable from tomographic data. In combination with Warp and RELION, M resolves to residue level a 70S ribosome bound to an antibiotic inside intact bacterial cells. Our work provides a computational tool that facilitates structural biology in cells.
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18
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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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19
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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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20
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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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21
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Wu H, Zhai X, Lei D, Liu J, Yu Y, Bie R, Ren G. An Algorithm for Enhancing the Image Contrast of Electron Tomography. Sci Rep 2018; 8:16711. [PMID: 30420636 PMCID: PMC6232092 DOI: 10.1038/s41598-018-34652-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/02/2018] [Indexed: 12/14/2022] Open
Abstract
Three-dimensional (3D) reconstruction of a single protein molecule is essential for understanding the relationship between the structural dynamics and functions of the protein. Electron tomography (ET) provides a tool for imaging an individual particle of protein from a series of tilted angles. Individual-particle electron tomography (IPET) provides an approach for reconstructing a 3D density map from a single targeted protein particle (without averaging from different particles of this type of protein), in which the target particle was imaged from a series of tilting angles. However, owing to radiation damage limitations, low-dose images (high noise, and low image contrast) are often challenging to be aligned for 3D reconstruction at intermediate resolution (1-3 nm). Here, we propose a computational method to enhance the image contrast, without increasing any experimental dose, for IPET 3D reconstruction. Using an edge-preserving smoothing-based multi-scale image decomposition algorithm, this method can detect the object against a high-noise background and enhance the object image contrast without increasing the noise level or significantly decreasing the image resolution. The method was validated by using both negative staining (NS) ET and cryo-ET images. The successful 3D reconstruction of a small molecule (<100 kDa) indicated that this method can be used as a supporting tool to current ET 3D reconstruction methods for studying protein dynamics via structure determination from each individual particle of the same type of protein.
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Affiliation(s)
- Hao Wu
- College of Information Science and Technology, Beijing Normal University, Beijing, China.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Xiaobo Zhai
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - 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
| | - Yadong Yu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Rongfang Bie
- College of Information Science and Technology, Beijing Normal University, Beijing, China.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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22
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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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23
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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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24
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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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25
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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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26
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Fernandez JJ, Li S, Bharat TAM, Agard DA. Cryo-tomography tilt-series alignment with consideration of the beam-induced sample motion. J Struct Biol 2018; 202:200-209. [PMID: 29410148 PMCID: PMC5949096 DOI: 10.1016/j.jsb.2018.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/18/2022]
Abstract
Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series alignment and tomographic reconstruction that considers the beam-induced sample motion through the tilt-series. It extends the standard fiducial-based alignment approach in cryoET by introducing quadratic polynomials to model the sample motion. The model can be used during reconstruction to yield a motion-compensated tomogram. We evaluated our method on various datasets with different sample sizes. The results demonstrate that our method could be a useful tool to improve the quality of tomograms and the resolution in cryoET.
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Affiliation(s)
| | - Sam Li
- Dept. Biochemistry and Biophysics, University of California, San Francisco, USA
| | - Tanmay A M Bharat
- MRC Laboratory of Molecular Biology, Francis Crick Avenue Cambridge CB2 0QH, UK; Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David A Agard
- Dept. Biochemistry and Biophysics, University of California, San Francisco, USA
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27
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Zhu L, Petrlova J, Gysbers P, Hebert H, Wallin S, Jegerschöld C, Lagerstedt JO. Structures of apolipoprotein A-I in high density lipoprotein generated by electron microscopy and biased simulations. Biochim Biophys Acta Gen Subj 2017; 1861:2726-2738. [DOI: 10.1016/j.bbagen.2017.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/18/2017] [Accepted: 07/24/2017] [Indexed: 10/19/2022]
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28
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Turoňová B, Schur FKM, Wan W, Briggs JAG. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. J Struct Biol 2017; 199:187-195. [PMID: 28743638 PMCID: PMC5614107 DOI: 10.1016/j.jsb.2017.07.007] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/07/2017] [Accepted: 07/21/2017] [Indexed: 11/17/2022]
Abstract
Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments. Cryo-electron tomograms are reconstructed from projection images taken at defined tilt-angles. In order to recover high-resolution information from cryo-electron tomograms, it is necessary to measure and correct for the contrast transfer function (CTF) of the microscope. Most commonly, this is performed using protocols that approximate the sample as a two-dimensional (2D) plane. This approximation accounts for differences in defocus and therefore CTF across the tilted sample. It does not account for differences in defocus of objects at different heights within the sample; instead, a 3D approach is required. Currently available approaches for 3D-CTF correction are computationally expensive and have not been widely implemented. Here we simulate the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF, that is compatible with standard tomogram reconstruction workflows in IMOD. We validate the approach on synthetic data and test it using subtomogram averaging of real data. Consistent with our simulations, we find that 3D-CTF correction allows high-resolution structures to be obtained with much smaller subtomogram averaging datasets than are required using 2D-CTF. We also show that using equivalent dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures. We present a 3.4 Å resolution structure determined by subtomogram averaging.
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Affiliation(s)
- Beata Turoňová
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
| | - Florian K M Schur
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
| | - William Wan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany; Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
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29
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Galaz-Montoya JG, Ludtke SJ. The advent of structural biology in situ by single particle cryo-electron tomography. BIOPHYSICS REPORTS 2017; 3:17-35. [PMID: 28781998 PMCID: PMC5516000 DOI: 10.1007/s41048-017-0040-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/30/2017] [Indexed: 01/06/2023] Open
Abstract
Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.
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Affiliation(s)
- Jesús G Galaz-Montoya
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
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30
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Lu Z, Reddy MVVVS, Liu J, Kalichava A, Liu J, Zhang L, Chen F, Wang Y, Holthauzen LMF, White MA, Seshadrinathan S, Zhong X, Ren G, Rudenko G. Molecular Architecture of Contactin-associated Protein-like 2 (CNTNAP2) and Its Interaction with Contactin 2 (CNTN2). J Biol Chem 2016; 291:24133-24147. [PMID: 27621318 DOI: 10.1074/jbc.m116.748236] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/02/2016] [Indexed: 11/06/2022] Open
Abstract
Contactin-associated protein-like 2 (CNTNAP2) is a large multidomain neuronal adhesion molecule implicated in a number of neurological disorders, including epilepsy, schizophrenia, autism spectrum disorder, intellectual disability, and language delay. We reveal here by electron microscopy that the architecture of CNTNAP2 is composed of a large, medium, and small lobe that flex with respect to each other. Using epitope labeling and fragments, we assign the F58C, L1, and L2 domains to the large lobe, the FBG and L3 domains to the middle lobe, and the L4 domain to the small lobe of the CNTNAP2 molecular envelope. Our data reveal that CNTNAP2 has a very different architecture compared with neurexin 1α, a fellow member of the neurexin superfamily and a prototype, suggesting that CNTNAP2 uses a different strategy to integrate into the synaptic protein network. We show that the ectodomains of CNTNAP2 and contactin 2 (CNTN2) bind directly and specifically, with low nanomolar affinity. We show further that mutations in CNTNAP2 implicated in autism spectrum disorder are not segregated but are distributed over the whole ectodomain. The molecular shape and dimensions of CNTNAP2 place constraints on how CNTNAP2 integrates in the cleft of axo-glial and neuronal contact sites and how it functions as an organizing and adhesive molecule.
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Affiliation(s)
- Zhuoyang Lu
- From the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720.,the Center for Mitochondrial Biology and Medicine, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - M V V V Sekhar Reddy
- the Department of Pharmacology and Toxicology.,the Sealy Center for Structural Biology and Molecular Biophysics and
| | - Jianfang Liu
- From the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Ana Kalichava
- the Department of Pharmacology and Toxicology.,the Sealy Center for Structural Biology and Molecular Biophysics and
| | - Jiankang Liu
- the Center for Mitochondrial Biology and Medicine, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lei Zhang
- From the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Fang Chen
- the University of Michigan, Ann Arbor, Michigan 48109
| | - Yun Wang
- the University of Michigan, Ann Arbor, Michigan 48109
| | | | - Mark A White
- the Sealy Center for Structural Biology and Molecular Biophysics and.,the Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555, and
| | - Suchithra Seshadrinathan
- the Department of Pharmacology and Toxicology.,the Sealy Center for Structural Biology and Molecular Biophysics and
| | - Xiaoying Zhong
- the Department of Pharmacology and Toxicology.,the Sealy Center for Structural Biology and Molecular Biophysics and
| | - Gang Ren
- From the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720,
| | - Gabby Rudenko
- the Department of Pharmacology and Toxicology, .,the Sealy Center for Structural Biology and Molecular Biophysics and
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31
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Hou X, Rivers J, León P, McQuinn RP, Pogson BJ. Synthesis and Function of Apocarotenoid Signals in Plants. TRENDS IN PLANT SCIENCE 2016; 21:792-803. [PMID: 27344539 DOI: 10.1016/j.tplants.2016.06.001] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 05/17/2023]
Abstract
In plants, carotenoids are essential for photosynthesis and photoprotection. However, carotenoids are not the end products of the pathway; apocarotenoids are produced by carotenoid cleavage dioxygenases (CCDs) or non-enzymatic processes. Apocarotenoids are more soluble or volatile than carotenoids but they are not simply breakdown products, as there can be modifications post-cleavage and their functions include hormones, volatiles, and signals. Evidence is emerging for a class of apocarotenoids, here referred to as apocarotenoid signals (ACSs), that have regulatory roles throughout plant development beyond those ascribed to abscisic acid (ABA) and strigolactone (SL). In this context we review studies of carotenoid feedback regulation, chloroplast biogenesis, stress signaling, and leaf and root development providing evidence that apocarotenoids may fine-tune plant development and responses to environmental stimuli.
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Affiliation(s)
- Xin Hou
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - John Rivers
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Patricia León
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Ryan P McQuinn
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia.
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32
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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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33
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Liu J, Li H, Zhang L, Rames M, Zhang M, Yu Y, Peng B, Celis CD, Xu A, Zou Q, Yang X, Chen X, Ren G. Fully Mechanically Controlled Automated Electron Microscopic Tomography. Sci Rep 2016; 6:29231. [PMID: 27403922 PMCID: PMC4941525 DOI: 10.1038/srep29231] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 06/16/2016] [Indexed: 11/23/2022] Open
Abstract
Knowledge of three-dimensional (3D) structures of each individual particles of asymmetric and flexible proteins is essential in understanding those proteins’ functions; but their structures are difficult to determine. Electron tomography (ET) provides a tool for imaging a single and unique biological object from a series of tilted angles, but it is challenging to image a single protein for three-dimensional (3D) reconstruction due to the imperfect mechanical control capability of the specimen goniometer under both a medium to high magnification (approximately 50,000–160,000×) and an optimized beam coherence condition. Here, we report a fully mechanical control method for automating ET data acquisition without using beam tilt/shift processes. This method could reduce the accumulation of beam tilt/shift that used to compensate the error from the mechanical control, but downgraded the beam coherence. Our method was developed by minimizing the error of the target object center during the tilting process through a closed-loop proportional-integral (PI) control algorithm. The validations by both negative staining (NS) and cryo-electron microscopy (cryo-EM) suggest that this method has a comparable capability to other ET methods in tracking target proteins while maintaining optimized beam coherence conditions for imaging.
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Affiliation(s)
- Jinxin Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,State Key Laboratory for Manufacturing System Engineering, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Hongchang Li
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,School of Electrical Engineering, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Lei Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew Rames
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yadong Yu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bo Peng
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - César Díaz Celis
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, USA
| | - April Xu
- Pfizer BioTherapeutics Pharmaceutical Sciences, 401 N Middletown Rd, Pear River, NY 10956, USA
| | - Qin Zou
- Pfizer BioTherapeutics Pharmaceutical Sciences, 700 Chesterfield Parkway West, St Louis, MO 63017, USA
| | - Xu Yang
- School of Electrical Engineering, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Xuefeng Chen
- State Key Laboratory for Manufacturing System Engineering, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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34
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Abstract
Cryo-electron tomography (cryo-ET) allows 3D volumes to be reconstructed from a set of 2D projection images of a tilted biological sample. It allows densities to be resolved in 3D that would otherwise overlap in 2D projection images. Cryo-ET can be applied to resolve structural features in complex native environments, such as within the cell. Analogous to single-particle reconstruction in cryo-electron microscopy, structures present in multiple copies within tomograms can be extracted, aligned, and averaged, thus increasing the signal-to-noise ratio and resolution. This reconstruction approach, termed subtomogram averaging, can be used to determine protein structures in situ. It can also be applied to facilitate more conventional 2D image analysis approaches. In this chapter, we provide an introduction to cryo-ET and subtomogram averaging. We describe the overall workflow, including tomographic data collection, preprocessing, tomogram reconstruction, subtomogram alignment and averaging, classification, and postprocessing. We consider theoretical issues and practical considerations for each step in the workflow, along with descriptions of recent methodological advances and remaining limitations.
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Affiliation(s)
- W Wan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - J A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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35
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Goh BC, Hadden JA, Bernardi RC, Singharoy A, McGreevy R, Rudack T, Cassidy CK, Schulten K. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes. Annu Rev Biophys 2016; 45:253-78. [PMID: 27145875 DOI: 10.1146/annurev-biophys-062215-011113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed.
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Affiliation(s)
- Boon Chong Goh
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Jodi A Hadden
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Rafael C Bernardi
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Abhishek Singharoy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Ryan McGreevy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Till Rudack
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - C Keith Cassidy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Klaus Schulten
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801;
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36
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Turoňová B, Marsalek L, Slusallek P. On geometric artifacts in cryo electron tomography. Ultramicroscopy 2016; 163:48-61. [DOI: 10.1016/j.ultramic.2016.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 12/29/2015] [Accepted: 01/23/2016] [Indexed: 11/26/2022]
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37
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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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Galaz-Montoya JG, Hecksel CW, Baldwin PR, Wang E, Weaver SC, Schmid MF, Ludtke SJ, Chiu W. Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography. J Struct Biol 2016; 194:383-94. [PMID: 27016284 DOI: 10.1016/j.jsb.2016.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 10/22/2022]
Abstract
Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen, the cryo-electron microscopy (cryoEM) grid and/or the carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions.
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Affiliation(s)
- Jesús G Galaz-Montoya
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Corey W Hecksel
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Philip R Baldwin
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Eryu Wang
- Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael F Schmid
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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39
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Gogonea V. Structural Insights into High Density Lipoprotein: Old Models and New Facts. Front Pharmacol 2016; 6:318. [PMID: 26793109 PMCID: PMC4709926 DOI: 10.3389/fphar.2015.00318] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/22/2015] [Indexed: 11/13/2022] Open
Abstract
The physiological link between circulating high density lipoprotein (HDL) levels and cardiovascular disease is well-documented, albeit its intricacies are not well-understood. An improved appreciation of HDL function and overall role in vascular health and disease requires at its foundation a better understanding of the lipoprotein's molecular structure, its formation, and its process of maturation through interactions with various plasma enzymes and cell receptors that intervene along the pathway of reverse cholesterol transport. This review focuses on summarizing recent developments in the field of lipid free apoA-I and HDL structure, with emphasis on new insights revealed by newly published nascent and spherical HDL models constructed by combining low resolution structures obtained from small angle neutron scattering (SANS) with contrast variation and geometrical constraints derived from hydrogen-deuterium exchange (HDX), crosslinking mass spectrometry, electron microscopy, Förster resonance energy transfer, and electron spin resonance. Recently published low resolution structures of nascent and spherical HDL obtained from SANS with contrast variation and isotopic labeling of apolipoprotein A-I (apoA-I) will be critically reviewed and discussed in terms of how they accommodate existing biophysical structural data from alternative approaches. The new low resolution structures revealed and also provided some answers to long standing questions concerning lipid organization and particle maturation of lipoproteins. The review will discuss the merits of newly proposed SANS based all atom models for nascent and spherical HDL, and compare them with accepted models. Finally, naturally occurring and bioengineered mutations in apoA-I, and their impact on HDL phenotype, are reviewed and discuss together with new therapeutics employed for restoring HDL function.
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Affiliation(s)
- Valentin Gogonea
- Department of Chemistry, Cleveland State UniversityCleveland, OH, USA; Departments of Cellular and Molecular Medicine and the Center for Cardiovascular Diagnostics and Prevention, Cleveland ClinicCleveland, OH, USA
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40
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Abstract
Cup-shaped secretory portals at the cell plasma membrane called porosomes mediate the precision release of intravesicular material from cells. Membrane-bound secretory vesicles transiently dock and fuse at the base of porosomes facing the cytosol to expel pressurized intravesicular contents from the cell during secretion. The structure, isolation, composition, and functional reconstitution of the neuronal porosome complex have greatly progressed, providing a molecular understanding of its function in health and disease. Neuronal porosomes are 15 nm cup-shaped lipoprotein structures composed of nearly 40 proteins, compared to the 120 nm nuclear pore complex composed of >500 protein molecules. Membrane proteins compose the porosome complex, making it practically impossible to solve its atomic structure. However, atomic force microscopy and small-angle X-ray solution scattering studies have provided three-dimensional structural details of the native neuronal porosome at sub-nanometer resolution, providing insights into the molecular mechanism of its function. The participation of several porosome proteins previously implicated in neurotransmission and neurological disorders, further attest to the crosstalk between porosome proteins and their coordinated involvement in release of neurotransmitter at the synapse.
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Affiliation(s)
- Akshata R Naik
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Kenneth T Lewis
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Bhanu P Jena
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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41
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Shan H, Wang Z, Zhang F, Xiong Y, Yin CC, Sun F. A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules. Protein Cell 2015; 7:46-62. [PMID: 26678751 PMCID: PMC4707152 DOI: 10.1007/s13238-015-0229-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 10/11/2015] [Indexed: 11/25/2022] Open
Abstract
Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macromolecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate alignments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orientations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimensional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large (60S/50S) and the small (40S/30S) subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolution single particle analysis of macromolecular complexes with dynamic conformations.
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Affiliation(s)
- Hong Shan
- Department of Biophysics, College of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Zihao Wang
- Key Lab of Intelligent Information Processing and Advanced Computing Research Lab, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fa Zhang
- Key Lab of Intelligent Information Processing and Advanced Computing Research Lab, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA
| | - Chang-Cheng Yin
- Department of Biophysics, College of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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42
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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: 98] [Impact Index Per Article: 10.9] [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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43
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Bharat TAM, Russo CJ, Löwe J, Passmore LA, Scheres SHW. Advances in Single-Particle Electron Cryomicroscopy Structure Determination applied to Sub-tomogram Averaging. Structure 2015; 23:1743-1753. [PMID: 26256537 PMCID: PMC4559595 DOI: 10.1016/j.str.2015.06.026] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/11/2015] [Accepted: 06/21/2015] [Indexed: 01/03/2023]
Abstract
Recent innovations in specimen preparation, data collection, and image processing have led to improved structure determination using single-particle electron cryomicroscopy (cryo-EM). Here we explore some of these advances to improve structures determined using electron cryotomography (cryo-ET) and sub-tomogram averaging. We implement a new three-dimensional model for the contrast transfer function, and use this in a regularized likelihood optimization algorithm as implemented in the RELION program. Using direct electron detector data, we apply both single-particle analysis and sub-tomogram averaging to analyze radiation-induced movements of the specimen. As in single-particle cryo-EM, we find that significant sample movements occur during tomographic data acquisition, and that these movements are substantially reduced through the use of ultrastable gold substrates. We obtain a sub-nanometer resolution structure of the hepatitis B capsid, and show that reducing radiation-induced specimen movement may be central to attempts at further improving tomogram quality and resolution. The Bayesian approach in RELION is extended to sub-tomogram averaging A new 3D CTF and missing-wedge model for sub-tomogram averaging is proposed Ultrastable gold supports reduce radiation-induced motion in tomography tilt series Using the above, an 8 Å structure of hepatitis B capsid from cryo-ET is presented
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Affiliation(s)
- Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Christopher J Russo
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Lori A Passmore
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sjors H W Scheres
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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44
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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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45
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Single particle tomography in EMAN2. J Struct Biol 2015; 190:279-90. [PMID: 25956334 DOI: 10.1016/j.jsb.2015.04.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/24/2015] [Accepted: 04/29/2015] [Indexed: 11/22/2022]
Abstract
Single particle tomography (SPT or subtomogram averaging) offers a powerful alternative to traditional 2-D single particle reconstruction for studying conformationally or compositionally heterogeneous macromolecules. It can also provide direct observation (without labeling or staining) of complexes inside cells at nanometer resolution. The development of computational methods and tools for SPT remains an area of active research. Here we present the EMAN2.1 SPT toolbox, which offers a full SPT processing pipeline, from particle picking to post-alignment analysis of subtomogram averages, automating most steps. Different algorithm combinations can be applied at each step, providing versatility and allowing for procedural cross-testing and specimen-specific strategies. Alignment methods include all-vs-all, binary tree, iterative single-model refinement, multiple-model refinement, and self-symmetry alignment. An efficient angular search, Graphic Processing Unit (GPU) acceleration and both threaded and distributed parallelism are provided to speed up processing. Finally, automated simulations, per particle reconstruction of subtiltseries, and per-particle Contrast Transfer Function (CTF) correction have been implemented. Processing examples using both real and simulated data are shown for several structures.
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46
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Zhang M, Charles R, Tong H, Zhang L, Patel M, Wang F, Rames MJ, Ren A, Rye KA, Qiu X, Johns DG, Charles MA, Ren G. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation. Sci Rep 2015; 5:8741. [PMID: 25737239 PMCID: PMC4348656 DOI: 10.1038/srep08741] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/29/2015] [Indexed: 02/07/2023] Open
Abstract
Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.
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Affiliation(s)
- Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - River Charles
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Huimin Tong
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Lei Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Mili Patel
- Centre for Vascular Research, University of New South Wales, Kensington, Sydney, NSW 2052, Australia
| | - Francis Wang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Matthew J Rames
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Amy Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Kerry-Anne Rye
- Centre for Vascular Research, University of New South Wales, Kensington, Sydney, NSW 2052, Australia
| | | | | | - M Arthur Charles
- School of Medicine, University of California, San Francisco, California 94115, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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47
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Rajagopal A, Kulkarni S, Lewis KT, Chen X, Maarouf A, Kelly CV, Taatjes DJ, Jena BP. Proteome of the insulin-secreting Min6 cell porosome complex: involvement of Hsp90 in its assembly and function. J Proteomics 2014; 114:83-92. [PMID: 25464371 DOI: 10.1016/j.jprot.2014.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/19/2014] [Accepted: 11/03/2014] [Indexed: 11/15/2022]
Abstract
UNLABELLED Porosomes are secretory portals located at the cell plasma membrane involved in the regulated release of intravesicular contents from cells. Porosomes have been immunoisolated from a number of cells including the exocrine pancreas and neurons, biochemically characterized, and functionally reconstituted into an artificial lipid membrane. In the current study, the proteome of the porosome complex in mouse insulinoma Min6 cells was determined, demonstrating among other proteins, the presence of 30 core proteins including the heat shock protein Hsp90. Half maximal inhibition of Hsp90 using the specific inhibitor 17-demethoxy-17-(2-prophenylamino) geldanamycin, results in the loss of proteins, including the calcium-transporting ATPase type 2C and the potassium channel subfamily K member 2 from the Min6 porosome. This loss of porosome proteins is reflected in the observed inhibition of glucose stimulated insulin release from Min6 cells exposed to the Hsp90 specific inhibitor. Results from the study implicate Hsp90 in the assembly and function of the porosome complex. BIOLOGICAL SIGNIFICANCE In the present study, the porosome proteome in the insulin-secreting mouse β-cell line Min6 has been determined. Nearly 30 core proteins including the heat shock protein Hsp90 are found to compose the Min6 porosome complex. Results from the study implicate Hsp90 in the assembly of the Min6 porosome. These new findings will facilitate understanding of the porosome assembly and its function in insulin secretion.
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Affiliation(s)
- Amulya Rajagopal
- Wayne State University School of Medicine, Department of Physiology, Detroit, MI, USA
| | - Sanjana Kulkarni
- Wayne State University School of Medicine, Department of Physiology, Detroit, MI, USA
| | - Kenneth T Lewis
- Wayne State University School of Medicine, Department of Physiology, Detroit, MI, USA
| | - Xuequn Chen
- Wayne State University School of Medicine, Department of Physiology, Detroit, MI, USA
| | - Abir Maarouf
- Wayne State University, Department of Physics and Astronomy, Detroit, MI, USA
| | - Christopher V Kelly
- Wayne State University, Department of Physics and Astronomy, Detroit, MI, USA
| | - Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Microscopy Imaging Center, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Bhanu P Jena
- Wayne State University School of Medicine, Department of Physiology, Detroit, MI, USA; Wayne State University, Department of Physics and Astronomy, Detroit, MI, USA.
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48
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Szőnyi A, Mayer MI, Cserép C, Takács VT, Watanabe M, Freund TF, Nyiri G. The ascending median raphe projections are mainly glutamatergic in the mouse forebrain. Brain Struct Funct 2014; 221:735-51. [PMID: 25381463 DOI: 10.1007/s00429-014-0935-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 10/28/2014] [Indexed: 12/26/2022]
Abstract
The median raphe region (MRR) is thought to be serotonergic and plays an important role in the regulation of many cognitive functions. In the hippocampus (HIPP), the MRR exerts a fast excitatory control, partially through glutamatergic transmission, on a subpopulation of GABAergic interneurons that are key regulators of local network activity. However, not all receptors of this connection in the HIPP and in synapses established by MRR in other brain areas are known. Using combined anterograde tracing and immunogold methods, we show that the GluN2A subunit of the NMDA receptor is present in the synapses established by MRR not only in the HIPP, but also in the medial septum (MS) and in the medial prefrontal cortex (mPFC) of the mouse. We estimated similar amounts of NMDA receptors in these synapses established by the MRR and in local adjacent excitatory synapses. Using retrograde tracing and confocal laser scanning microscopy, we found that the majority of the projecting cells of the mouse MRR contain the vesicular glutamate transporter type 3 (vGluT3). Furthermore, using double retrograde tracing, we found that single cells of the MRR can innervate the HIPP and mPFC or the MS and mPFC simultaneously, and these double-projecting cells are also predominantly vGluT3-positive. Our results indicate that the majority of the output of the MRR is glutamatergic and acts through NMDA receptor-containing synapses. This suggests that key forebrain areas receive precisely targeted excitatory input from the MRR, which is able to synchronously modify activity in those regions via individual MRR cells with dual projections.
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Affiliation(s)
- András Szőnyi
- Laboratory of Cerebral Cortex Research, Institute of Experimental Medicine Hungarian Academy of Sciences, Budapest, 1083, Hungary.,János Szentágothai Doctoral School of Neurosciences, Semmelweis University, Budapest, 1085, Hungary
| | - Márton I Mayer
- Laboratory of Cerebral Cortex Research, Institute of Experimental Medicine Hungarian Academy of Sciences, Budapest, 1083, Hungary
| | - Csaba Cserép
- Laboratory of Cerebral Cortex Research, Institute of Experimental Medicine Hungarian Academy of Sciences, Budapest, 1083, Hungary
| | - Virág T Takács
- Laboratory of Cerebral Cortex Research, Institute of Experimental Medicine Hungarian Academy of Sciences, Budapest, 1083, Hungary
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University School of Medicine, Sapporo, 060-8638, Japan
| | - Tamás F Freund
- Laboratory of Cerebral Cortex Research, Institute of Experimental Medicine Hungarian Academy of Sciences, Budapest, 1083, Hungary
| | - Gábor Nyiri
- Laboratory of Cerebral Cortex Research, Institute of Experimental Medicine Hungarian Academy of Sciences, Budapest, 1083, Hungary.
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49
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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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50
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Jena BP. Neuronal Porosome-The Secretory Portal at the Nerve Terminal: It's Structure-Function, Composition, and Reconstitution. J Mol Struct 2014; 1073:187-195. [PMID: 26412873 PMCID: PMC4580341 DOI: 10.1016/j.molstruc.2014.04.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cup-shaped secretory portals at the cell plasma membrane called porosomes mediate secretion from cells. Membrane bound secretory vesicles transiently dock and fuse at the cytosolic compartment of the porosome base to expel intravesicular contents to the outside during cell secretion. In the past decade, the structure, isolation, composition, and functional reconstitution of the neuronal porosome complex has been accomplished providing a molecular understanding of its structure-function. Neuronal porosomes are 15 nm cup-shaped lipoprotein structures composed of nearly 40 proteins. Being a membrane-associated supramolecular complex has precluded determination of the atomic structure of the porosome. However recent studies using small-angle X-ray solution scattering (SAXS), provide at sub-nanometer resolution, the native 3D structure of the neuronal porosome complex associated with docked synaptic vesicle at the nerve terminal. Additionally, results from the SAXS study and earlier studies using atomic force microscopy, provide the possible molecular mechanism involved in porosome-mediated neurotransmitter release at the nerve terminal.
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Affiliation(s)
- Bhanu P. Jena
- Wayne State University School of Medicine, Department of Physiology, Detroit, MI, USA
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