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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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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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A New Structural Model of Apolipoprotein B100 Based on Computational Modeling and Cross Linking. Int J Mol Sci 2022; 23:ijms231911480. [PMID: 36232786 PMCID: PMC9569473 DOI: 10.3390/ijms231911480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/17/2022] [Accepted: 09/18/2022] [Indexed: 12/02/2022] Open
Abstract
ApoB-100 is a member of a large lipid transfer protein superfamily and is one of the main apolipoproteins found on low-density lipoprotein (LDL) and very low-density lipoprotein (VLDL) particles. Despite its clinical significance for the development of cardiovascular disease, there is limited information on apoB-100 structure. We have developed a novel method based on the “divide and conquer” algorithm, using PSIPRED software, by dividing apoB-100 into five subunits and 11 domains. Models of each domain were prepared using I-TASSER, DEMO, RoseTTAFold, Phyre2, and MODELLER. Subsequently, we used disuccinimidyl sulfoxide (DSSO), a new mass spectrometry cleavable cross-linker, and the known position of disulfide bonds to experimentally validate each model. We obtained 65 unique DSSO cross-links, of which 87.5% were within a 26 Å threshold in the final model. We also evaluated the positions of cysteine residues involved in the eight known disulfide bonds in apoB-100, and each pair was measured within the expected 5.6 Å constraint. Finally, multiple domains were combined by applying constraints based on detected long-range DSSO cross-links to generate five subunits, which were subsequently merged to achieve an uninterrupted architecture for apoB-100 around a lipoprotein particle. Moreover, the dynamics of apoB-100 during particle size transitions was examined by comparing VLDL and LDL computational models and using experimental cross-linking data. In addition, the proposed model of receptor ligand binding of apoB-100 provides new insights into some of its functions.
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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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5
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Małys MS, Aigner C, Schulz SM, Schachner H, Rees AJ, Kain R. Isolation of Small Extracellular Vesicles from Human Sera. Int J Mol Sci 2021; 22:ijms22094653. [PMID: 33925027 PMCID: PMC8124960 DOI: 10.3390/ijms22094653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/17/2022] Open
Abstract
Robust, well-characterized methods for purifying small extracellular vesicles (sEV) from blood are needed before their potential as disease biomarkers can be realized. Here, we compared isolation of sEV from serum by differential ultracentrifugation (DUC) and by exclusion chromatography using commercially available Exo-spin™ columns. We show that sEV can be purified by both methods but Exo-spin™ columns contain copious additional particles recorded by nanoparticle tracking analysis, invalidating its use for quantifying yields. DUC samples contained higher concentrations of exosome specific proteins CD9, CD63 and CD81 and electron microscopy confirmed that most particles in DUC preparations were sEV, whereas Exo-spin™ samples also contained copious co-purified plasma lipids. MACSPlex bead analysis identified multiple exosome surface proteins, with stronger signals in DUC samples, enabling detection of 21 of 37, compared to only 10 in Exo-spin™ samples. Nevertheless, the pattern of expression was consistent in both preparations, indicating that lipids do not interfere with bead-based technologies. Thus, both DUC and Exo-spin™ can be used to isolate sEV from human serum and what is most appropriate depends on the subsequent use of sEV. In summary, Exo-spin™ enables isolation of sEV from blood with vesicle populations similar to the ones recovered by DUC, but with lower concentrations.
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Affiliation(s)
- Małgorzata S. Małys
- Department of Pathology, Medical University Vienna, 1090 Vienna, Austria; (M.S.M.); (C.A.); (S.M.S.); (H.S.); (A.J.R.)
| | - Christof Aigner
- Department of Pathology, Medical University Vienna, 1090 Vienna, Austria; (M.S.M.); (C.A.); (S.M.S.); (H.S.); (A.J.R.)
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, 1090 Vienna, Austria
| | - Stefan M. Schulz
- Department of Pathology, Medical University Vienna, 1090 Vienna, Austria; (M.S.M.); (C.A.); (S.M.S.); (H.S.); (A.J.R.)
| | - Helga Schachner
- Department of Pathology, Medical University Vienna, 1090 Vienna, Austria; (M.S.M.); (C.A.); (S.M.S.); (H.S.); (A.J.R.)
| | - Andrew J. Rees
- Department of Pathology, Medical University Vienna, 1090 Vienna, Austria; (M.S.M.); (C.A.); (S.M.S.); (H.S.); (A.J.R.)
| | - Renate Kain
- Department of Pathology, Medical University Vienna, 1090 Vienna, Austria; (M.S.M.); (C.A.); (S.M.S.); (H.S.); (A.J.R.)
- Correspondence:
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Polyhedral liquid droplets: Recent advances in elucidation and application. Curr Opin Colloid Interface Sci 2020. [DOI: 10.1016/j.cocis.2020.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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7
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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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Jamme F, Cinquin B, Gohon Y, Pereiro E, Réfrégiers M, Froissard M. Synchrotron multimodal imaging in a whole cell reveals lipid droplet core organization. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:772-778. [PMID: 32381780 PMCID: PMC7206545 DOI: 10.1107/s1600577520003847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
A lipid droplet (LD) core of a cell consists mainly of neutral lipids, triacylglycerols and/or steryl esters (SEs). The structuration of these lipids inside the core is still under debate. Lipid segregation inside LDs has been observed but is sometimes suggested to be an artefact of LD isolation and chemical fixation. LD imaging in their native state and in unaltered cellular environments appears essential to overcome these possible technical pitfalls. Here, imaging techniques for ultrastructural study of native LDs in cellulo are provided and it is shown that LDs are organized structures. Cryo soft X-ray tomography and deep-ultraviolet (DUV) transmittance imaging are showing a partitioning of SEs at the periphery of the LD core. Furthermore, DUV transmittance and tryptophan/tyrosine auto-fluorescence imaging on living cells are combined to obtain complementary information on cell chemical contents. This multimodal approach paves the way for a new label-free organelle imaging technique in living cells.
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Affiliation(s)
- Frédéric Jamme
- DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Bertrand Cinquin
- DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Yann Gohon
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | - Eva Pereiro
- MISTRAL Beamline, ALBA Synchrotron, Cerdanyola del Vallès, Barcelona 08290, Spain
| | | | - Marine Froissard
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
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Liber SR, Marin O, Butenko AV, Ron R, Shool L, Salomon A, Deutsch M, Sloutskin E. Polyhedral Water Droplets: Shape Transitions and Mechanism. J Am Chem Soc 2020; 142:8672-8678. [DOI: 10.1021/jacs.0c00184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Shir R. Liber
- Physics Department & Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Orlando Marin
- Physics Department & Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Alexander V. Butenko
- Physics Department & Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Racheli Ron
- Chemistry Department & Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Lee Shool
- Physics Department & Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Adi Salomon
- Chemistry Department & Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Moshe Deutsch
- Physics Department & Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Eli Sloutskin
- Physics Department & Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
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10
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Kataoka-Hamai C, Kawakami K. Interaction Mechanisms of Giant Unilamellar Vesicles with Hydrophobic Glass Surfaces and Silicone Oil-Water Interfaces: Adsorption, Deformation, Rupture, Dynamic Shape Changes, Internal Vesicle Formation, and Desorption. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:16136-16145. [PMID: 31697503 DOI: 10.1021/acs.langmuir.9b02472] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phospholipid monolayers at oil-water interfaces are often obtained via vesicle adsorption. However, the interaction mechanisms of vesicles with these oil-water interfaces remain unclear. Herein, we studied the adsorption of giant unilamellar vesicles (GUVs) of approximately 2-5 μm diameter onto silicone oil-water interfaces and glass surfaces modified with hexamethyldisilazane (HMDS) and octadecyltrimethoxysilane (ODTMS) using fluorescence microscopy. The GUVs exhibited various modes of interaction, adsorbing on the silanized glass surfaces without sizable deformation, whereas GUVs bound to the silicone oil-water interface exhibited large deformation. After adsorption, GUV rupture occurred within 350, 110, and 3 ms on HMDS-modified glass, ODTMS-modified glass, and silicone oil-water interface, respectively. On glass surfaces, GUV rupture was often initiated and proceeded with pore formation near the surface. The monolayer patches formed by GUV rupture on HMDS-modified glass remained for at least 1 h over an area approximately twice of that estimated from the original GUV. On the ODTMS-modified glass and silicone oil surfaces, the monolayer patch structures disappeared in milliseconds owing to lipid diffusion across the interface. When adsorbed on the oil-water interface, the GUVs spontaneously underwent dynamic shape changes, internal vesicle formation, and desorption without rupture. Thus, it can be concluded that these different pathways arose from different lipid-surface affinities.
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Affiliation(s)
- Chiho Kataoka-Hamai
- International Center for Materials Nanoarchitectonics (WPI-MANA) , National Institute for Materials Science , 1-1 Namiki , Tsukuba , Ibaraki 305-0044 , Japan
| | - Kohsaku Kawakami
- International Center for Materials Nanoarchitectonics (WPI-MANA) , National Institute for Materials Science , 1-1 Namiki , Tsukuba , Ibaraki 305-0044 , Japan
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11
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Liber SR, Butenko AV, Caspi M, Guttman S, Schultz M, Schofield AB, Deutsch M, Sloutskin E. Precise Self-Positioning of Colloidal Particles on Liquid Emulsion Droplets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:13053-13061. [PMID: 31502850 DOI: 10.1021/acs.langmuir.9b01833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Decorating emulsion droplets by particles stabilizes foodstuff and pharmaceuticals. Interfacial particles also influence aerosol formation, thus impacting atmospheric CO2 exchange. While studies of particles at disordered droplet interfaces abound in the literature, such studies for ubiquitous ordered interfaces are not available. Here, we report such an experimental study, showing that particles residing at crystalline interfaces of liquid droplets spontaneously self-position to specific surface locations, identified as structural topological defects in the crystalline surface monolayer. This monolayer forms at temperature T = Ts, leaving the droplet liquid and driving at Td < Ts a spontaneous shape-change transition of the droplet from spherical to icosahedral. The particle's surface position remains unchanged in the transition, demonstrating these positions to coincide with the vertices of the sphere-inscribed icosahedron. Upon further cooling, droplet shape-changes to other polyhedra occur, with the particles remaining invariably at the polyhedra's vertices. At still lower temperatures, the particles are spontaneously expelled from the droplets. Our results probe the molecular-scale elasticity of quasi-two-dimensional curved crystals, impacting also other fields, such as protein positioning on cell membranes, controlling essential biological functions. Using ligand-decorated particles, and the precise temperature-tunable surface position control found here, may also allow using these droplets for directed supra-droplet self-assembly into larger structures, with a possible post-assembly structure fixation by UV polymerization of the droplet's liquid.
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Affiliation(s)
- Shir R Liber
- Physics Department and Institute of Nanotechnology & Advanced Materials , Bar-Ilan University , Ramat-Gan 5290002 , Israel
| | - Alexander V Butenko
- Physics Department and Institute of Nanotechnology & Advanced Materials , Bar-Ilan University , Ramat-Gan 5290002 , Israel
| | - Moshe Caspi
- Physics Department and Institute of Nanotechnology & Advanced Materials , Bar-Ilan University , Ramat-Gan 5290002 , Israel
| | - Shani Guttman
- Physics Department and Institute of Nanotechnology & Advanced Materials , Bar-Ilan University , Ramat-Gan 5290002 , Israel
| | - Moty Schultz
- Physics Department and Institute of Nanotechnology & Advanced Materials , Bar-Ilan University , Ramat-Gan 5290002 , Israel
| | - Andrew B Schofield
- The School of Physics and Astronomy , University of Edinburgh , Edinburgh EH9 3FD , U.K
| | - Moshe Deutsch
- Physics Department and Institute of Nanotechnology & Advanced Materials , Bar-Ilan University , Ramat-Gan 5290002 , Israel
| | - Eli Sloutskin
- Physics Department and Institute of Nanotechnology & Advanced Materials , Bar-Ilan University , Ramat-Gan 5290002 , Israel
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12
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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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