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Giesecke Y, Soete S, MacKinnon K, Tsiaras T, Ward M, Althobaiti M, Suveges T, Lucocq JE, McKenna SJ, Lucocq JM. Developing Electron Microscopy Tools for Profiling Plasma Lipoproteins Using Methyl Cellulose Embedment, Machine Learning and Immunodetection of Apolipoprotein B and Apolipoprotein(a). Int J Mol Sci 2020; 21:ijms21176373. [PMID: 32887372 PMCID: PMC7503711 DOI: 10.3390/ijms21176373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/26/2020] [Accepted: 08/06/2020] [Indexed: 01/17/2023] Open
Abstract
Plasma lipoproteins are important carriers of cholesterol and have been linked strongly to cardiovascular disease (CVD). Our study aimed to achieve fine-grained measurements of lipoprotein subpopulations such as low-density lipoprotein (LDL), lipoprotein(a) (Lp(a), or remnant lipoproteins (RLP) using electron microscopy combined with machine learning tools from microliter samples of human plasma. In the reported method, lipoproteins were absorbed onto electron microscopy (EM) support films from diluted plasma and embedded in thin films of methyl cellulose (MC) containing mixed metal stains, providing intense edge contrast. The results show that LPs have a continuous frequency distribution of sizes, extending from LDL (> 15 nm) to intermediate density lipoprotein (IDL) and very low-density lipoproteins (VLDL). Furthermore, mixed metal staining produces striking “positive” contrast of specific antibodies attached to lipoproteins providing quantitative data on apolipoprotein(a)-positive Lp(a) or apolipoprotein B (ApoB)-positive particles. To enable automatic particle characterization, we also demonstrated efficient segmentation of lipoprotein particles using deep learning software characterized by a Mask Region-based Convolutional Neural Networks (R-CNN) architecture with transfer learning. In future, EM and machine learning could be combined with microarray deposition and automated imaging for higher throughput quantitation of lipoproteins associated with CVD risk.
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Affiliation(s)
- Yvonne Giesecke
- Structural Cell Biology Group, School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK; (Y.G.); (S.S.); (M.W.); (M.A.)
| | - Samuel Soete
- Structural Cell Biology Group, School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK; (Y.G.); (S.S.); (M.W.); (M.A.)
| | - Katarzyna MacKinnon
- CVIP, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK; (K.M.); (T.T.); (T.S.); (S.J.M.)
| | - Thanasis Tsiaras
- CVIP, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK; (K.M.); (T.T.); (T.S.); (S.J.M.)
| | - Madeline Ward
- Structural Cell Biology Group, School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK; (Y.G.); (S.S.); (M.W.); (M.A.)
| | - Mohammed Althobaiti
- Structural Cell Biology Group, School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK; (Y.G.); (S.S.); (M.W.); (M.A.)
| | - Tamas Suveges
- CVIP, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK; (K.M.); (T.T.); (T.S.); (S.J.M.)
| | - James E. Lucocq
- Department of Orthopaedics, Ninewells Hospital, James Arrott Drive, Dundee DD1 9SY, UK;
| | - Stephen J. McKenna
- CVIP, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK; (K.M.); (T.T.); (T.S.); (S.J.M.)
| | - John M. Lucocq
- Structural Cell Biology Group, School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK; (Y.G.); (S.S.); (M.W.); (M.A.)
- Correspondence:
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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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3
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Jeeawoody S, Yamauchi KA, Su A, Herr AE. Laterally Aggregated Polyacrylamide Gels for Immunoprobed Isoelectric Focusing. Anal Chem 2020; 92:3180-3188. [PMID: 31985208 PMCID: PMC7861876 DOI: 10.1021/acs.analchem.9b04913] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Immunoprobed isoelectric focusing (IEF) resolves proteins based on differences in isoelectric point (pI) and then identifies protein targets through immunoprobing of IEF-separated proteins that have been immobilized onto a gel scaffold. During the IEF stage, the gel functions as an anti-convective medium and not as a molecular sieving matrix. During the immunoprobing stage, the gel acts as an immobilization scaffold for IEF-focused proteins via photoactive moieties. Here, we characterized the effect of gel pore size on IEF separation and in-gel immunoassay performance. We modulated polyacrylamide (PA) gel pore size via lateral chain aggregation initiated by PEG monomers. During IEF, the 2% PEG highly porous PA gel formulation offered higher resolution (minimum pI difference ∼0.07 ± 0.02) than unmodified 6%T, 3.3%C (benchmark) and 6%T, 8%C (negative control) PA gels. The highly porous gels supported a pH gradient with slope and linearity comparable to benchmark gels. The partition coefficient for antibodies into the highly porous gels (K = 0.35 ± 0.02) was greater than the benchmark (3×) and negative control (1.75×) gels. The highly porous gels also had lower immunoassay background signal than the benchmark (2×) and negative control (3×) gels. Taken together, lateral aggregation creates PA gels that are suitable for both IEF and subsequent in-gel immunoprobing by mitigating immunoprobe exclusion from the gels while facilitating removal of unbound immunoprobe.
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Affiliation(s)
- Shaheen Jeeawoody
- Department of Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
- The UC Berkeley/UCSF Graduate Program in Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
| | - Kevin A Yamauchi
- Department of Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
- The UC Berkeley/UCSF Graduate Program in Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
| | - Alison Su
- Department of Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
- The UC Berkeley/UCSF Graduate Program in Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
| | - Amy E Herr
- Department of Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
- The UC Berkeley/UCSF Graduate Program in Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
- Chan Zuckerberg Biohub , 499 Illinois Street , San Francisco , California 94158 , United States
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4
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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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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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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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7
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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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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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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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Zhang M, Lei D, Peng B, Yang M, Zhang L, Charles MA, Rye KA, Krauss RM, Johns DG, Ren G. Assessing the mechanisms of cholesteryl ester transfer protein inhibitors. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:1606-1617. [PMID: 28911944 PMCID: PMC6239860 DOI: 10.1016/j.bbalip.2017.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/11/2017] [Accepted: 09/08/2017] [Indexed: 12/30/2022]
Abstract
Cholesteryl ester transfer protein (CETP) inhibitors are a new class of therapeutics for dyslipidemia that simultaneously improve two major cardiovascular disease (CVD) risk factors: elevated low-density lipoprotein (LDL) cholesterol and decreased high-density lipoprotein (HDL) cholesterol. However, the detailed molecular mechanisms underlying their efficacy are poorly understood, as are any potential mechanistic differences among the drugs in this class. Herein, we used electron microscopy (EM) to investigate the effects of three of these agents (Torcetrapib, Dalcetrapib and Anacetrapib) on CETP structure, CETP-lipoprotein complex formation and CETP-mediated cholesteryl ester (CE) transfer. We found that although none of these inhibitors altered the structure of CETP or the conformation of CETP-lipoprotein binary complexes, all inhibitors, especially Torcetrapib and Anacetrapib, increased the binding ratios of the binary complexes (e.g., HDL-CETP and LDLCETP) and decreased the binding ratios of the HDL-CETP-LDL ternary complexes. The findings of more binary complexes and fewer ternary complexes reflect a new mechanism of inhibition: one distal end of CETP bound to the first lipoprotein would trigger a conformational change at the other distal end, thus resulting in a decreased binding ratio to the second lipoprotein and a degraded CE transfer rate among lipoproteins. Thus, we suggest a new inhibitor design that should decrease the formation of both binary and ternary complexes. Decreased concentrations of the binary complex may prevent the inhibitor was induced into cell by the tight binding of binary complexes during lipoprotein metabolism in the treatment of CVD.
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Affiliation(s)
- Meng Zhang
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Applied Science & Technology, University of California, Berkeley, CA 94720, USA
| | - Dongsheng Lei
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bo Peng
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mickey Yang
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lei Zhang
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - M Art Charles
- School of Medicine, University of California-San Francisco, San Francisco, CA 94110, USA
| | - Kerry-Anne Rye
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ronald M Krauss
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | | | - Gang Ren
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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The Effect of Physicochemical Modification on the Function of Antibodies Induced by Anti-Nicotine Vaccine in Mice. Vaccines (Basel) 2017; 5:vaccines5020011. [PMID: 28513561 PMCID: PMC5492008 DOI: 10.3390/vaccines5020011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/03/2017] [Accepted: 05/11/2017] [Indexed: 11/17/2022] Open
Abstract
Smoking remains one of the major causes of morbidity and mortality worldwide. One approach to assisting smoking cessation is via anti-nicotine vaccines, composed of nicotine-like haptens conjugated to a carrier protein plus adjuvant(s). We have previously shown that the carrier, hapten, linker, hapten load, degree of conjugate aggregation, and presence of adducts can each influence the function (nicotine-binding capacity) of the antibody (Ab) induced. Herein, we extend those findings and show that tertiary structure is also critical to the induction of functional immune responses and that this can be influenced by conjugation conditions. We evaluated immunogenicity in mice using six lots of NIC7-CRM, a conjugate of 5-aminoethoxy-nicotine (Hapten 7), and a single point (glycine 52 to glutamic acid) mutant nontoxic form of diphtheria toxin, cross-reactive material 197 (CRM197), which were synthesized under different reaction conditions resulting in conjugates with equivalent molecular characteristics (hapten load, aggregates, adducts), but a different tertiary structure. When tested in mice, better functional responses (reduced nicotine in the brain of immunized animals relative to non-immunized controls) were obtained with conjugates with a more closed structure than those with an open conformation. These studies highlight the need for a better understanding of the physicochemical properties of small molecule conjugate vaccines.
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Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages. PLoS One 2017; 12:e0175758. [PMID: 28406969 PMCID: PMC5391116 DOI: 10.1371/journal.pone.0175758] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/30/2017] [Indexed: 11/19/2022] Open
Abstract
Dynamics of three MET antibody constructs (IgG1, IgG2, and IgG4) and the IgG4-MET antigen complex was investigated by creating their atomic models with an integrative experimental and computational approach. In particular, we used two-dimensional (2D) Electron Microscopy (EM) images, image class averaging, homology modeling, Rapidly exploring Random Tree (RRT) structure sampling, and fitting of models to images, to find the relative orientations of antibody domains that are consistent with the EM images. We revealed that the conformational preferences of the constructs depend on the extent of the hinge flexibility. We also quantified how the MET antigen impacts on the conformational dynamics of IgG4. These observations allow to create testable hypothesis to investigate MET biology. Our protocol may also help describe structural diversity of other antigen systems at approximately 5 Å precision, as quantified by Root-Mean-Square Deviation (RMSD) among good-scoring models.
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13
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Kim HJ, Kim A, Miyata K, Kataoka K. Recent progress in development of siRNA delivery vehicles for cancer therapy. Adv Drug Deliv Rev 2016; 104:61-77. [PMID: 27352638 DOI: 10.1016/j.addr.2016.06.011] [Citation(s) in RCA: 311] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 05/21/2016] [Accepted: 06/16/2016] [Indexed: 12/13/2022]
Abstract
Recent progress in RNA biology has broadened the scope of therapeutic targets of RNA drugs for cancer therapy. However, RNA drugs, typically small interfering RNAs (siRNAs), are rapidly degraded by RNases and filtrated in the kidney, thereby requiring a delivery vehicle for efficient transport to the target cells. To date, various delivery formulations have been developed from cationic lipids, polymers, and/or inorganic nanoparticles for systemic delivery of siRNA to solid tumors. This review describes the current status of clinical trials related to siRNA-based cancer therapy, as well as the remaining issues that need to be overcome to establish a successful therapy. It, then introduces various promising design strategies of delivery vehicles for stable and targeted siRNA delivery, including the prospects for future design.
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14
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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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15
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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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16
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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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17
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Gutierrez R AV, Hedström M, Mattiasson B. Screening of self-assembled monolayer for aflatoxin B1 detection using immune-capacitive sensor. ACTA ACUST UNITED AC 2015; 8:144-151. [PMID: 28352584 PMCID: PMC4980746 DOI: 10.1016/j.btre.2015.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/23/2015] [Accepted: 10/04/2015] [Indexed: 02/07/2023]
Abstract
A capacitive biosensor was used for detection of aflatoxin B1. Two different methods for cleaning gold electrodes were evaluated using cyclic voltammetry in the presence of ferricyanide as redox couple. The methods involve use of a sequence of cleaning steps avoiding the use of Piranha solution and plasma cleaner. Anti-aflatoxin B1 was immobilized on self-assembled monolayers (SAM). The immune-capacitive biosensor is able to detect aflatoxin B1 concentrations in a linear range of 3.2 × 10−12 M to 3.2 × 10−9 M when thiourea was used to form the SAM; 3.2 × 10−9 M to 3.2 × 10−7 M when thioctic acid was used. When the gold surface was isolated with tyramine-electropolymerization linear ranges of 3.2 × 10−13 M to 3.2 × 10−7 M and 3.2 × 10−9 M to 3.2 × 10−7 M where obtained, respectively. The results obtained show the difference in linear range, limit of detection, and limit of quantification when different self-assembled monolayers are used for aflatoxin B1 detection.
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Affiliation(s)
- Alvaro V Gutierrez R
- Department of Biotechnology, Lund University, Lund, Sweden; IIFB, FCFB, Universidad Mayor de San Andres, La Paz, Bolivia
| | - Martin Hedström
- Department of Biotechnology, Lund University, Lund, Sweden; CapSenze HB, Medicon Village, Lund, Sweden
| | - Bo Mattiasson
- Department of Biotechnology, Lund University, Lund, Sweden; CapSenze HB, Medicon Village, Lund, Sweden
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18
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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: 95] [Impact Index Per Article: 10.6] [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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19
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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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20
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Neutron reflectometry from poly (ethylene-glycol) brushes binding anti-PEG antibodies: evidence of ternary adsorption. Biomaterials 2015; 46:95-104. [PMID: 25678119 DOI: 10.1016/j.biomaterials.2014.12.041] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/15/2014] [Accepted: 12/20/2014] [Indexed: 12/12/2022]
Abstract
Neutron reflectometry provides evidence of ternary protein adsorption within polyethylene glycol (PEG) brushes. Anti-PEG Immunoglobulin G antibodies (Abs) binding the methoxy terminated PEG chain segment specifically adsorb onto PEG brushes grafted to lipid monolayers on a solid support. The Abs adsorb at the outer edge of the brush. The thickness and density of the adsorbed Ab layer, as well as its distance from the grafting surface grow with increasing brush density. At high densities most of the protein is excluded from the brush. The results are consistent with an inverted "Y" configuration with the two FAB segments facing the brush. They suggest that increasing the grafting density favors narrowing of the angle between the FAB segments as well as overall orientation of the bound Abs perpendicular to the surface.
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21
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Rames M, Yu Y, Ren G. Optimized negative staining: a high-throughput protocol for examining small and asymmetric protein structure by electron microscopy. J Vis Exp 2014:e51087. [PMID: 25145703 PMCID: PMC4710468 DOI: 10.3791/51087] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Structural determination of proteins is rather challenging for proteins with molecular masses between 40 - 200 kDa. Considering that more than half of natural proteins have a molecular mass between 40 - 200 kDa1,2, a robust and high-throughput method with a nanometer resolution capability is needed. Negative staining (NS) electron microscopy (EM) is an easy, rapid, and qualitative approach which has frequently been used in research laboratories to examine protein structure and protein-protein interactions. Unfortunately, conventional NS protocols often generate structural artifacts on proteins, especially with lipoproteins that usually form presenting rouleaux artifacts. By using images of lipoproteins from cryo-electron microscopy (cryo-EM) as a standard, the key parameters in NS specimen preparation conditions were recently screened and reported as the optimized NS protocol (OpNS), a modified conventional NS protocol 3 . Artifacts like rouleaux can be greatly limited by OpNS, additionally providing high contrast along with reasonably high‐resolution (near 1 nm) images of small and asymmetric proteins. These high-resolution and high contrast images are even favorable for an individual protein (a single object, no average) 3D reconstruction, such as a 160 kDa antibody, through the method of electron tomography4,5. Moreover, OpNS can be a high‐throughput tool to examine hundreds of samples of small proteins. For example, the previously published mechanism of 53 kDa cholesteryl ester transfer protein (CETP) involved the screening and imaging of hundreds of samples 6. Considering cryo-EM rarely successfully images proteins less than 200 kDa has yet to publish any study involving screening over one hundred sample conditions, it is fair to call OpNS a high-throughput method for studying small proteins. Hopefully the OpNS protocol presented here can be a useful tool to push the boundaries of EM and accelerate EM studies into small protein structure, dynamics and mechanisms.
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Affiliation(s)
- Matthew Rames
- Lawrence Berkeley National Laboratory, The Molecular Foundry
| | - Yadong Yu
- Lawrence Berkeley National Laboratory, The Molecular Foundry
| | - Gang Ren
- Lawrence Berkeley National Laboratory, The Molecular Foundry;
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22
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Chaves RC, Teulon JM, Odorico M, Parot P, Chen SWW, Pellequer JL. Conformational dynamics of individual antibodies using computational docking and AFM. J Mol Recognit 2014; 26:596-604. [PMID: 24089367 DOI: 10.1002/jmr.2310] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/01/2013] [Accepted: 08/15/2013] [Indexed: 12/12/2022]
Abstract
Molecular recognition between a receptor and a ligand requires a certain level of flexibility in macromolecules. In this study, we aimed at analyzing the conformational variability of receptors portrayed by monoclonal antibodies that have been individually imaged using atomic force microscopy (AFM). Individual antibodies were chemically coupled to activated mica surface, and they have been imaged using AFM in ambient conditions. The resulting topographical surface of antibodies was used to assemble the three subunits constituting antibodies: two antigen-binding fragments and one crystallizable fragment using a surface-constrained computational docking approach. Reconstructed structures based on 10 individual topographical surfaces of antibodies are presented for which separation and relative orientation of the subunits were measured. When compared with three X-ray structures of antibodies present in the protein data bank database, results indicate that several arrangements of the reconstructed subunits are comparable with those of known structures. Nevertheless, no reconstructed structure superimposes adequately to any particular X-ray structure consequence of the antibody flexibility. We conclude that high-resolution AFM imaging with appropriate computational reconstruction tools is adapted to study the conformational dynamics of large individual macromolecules deposited on mica.
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Affiliation(s)
- Rui C Chaves
- CEA, iBEB, Service de Biochimie et Toxicologie Nucléaire, F-30207, Bagnols sur Cèze, France
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23
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DiLillo DJ, Tan GS, Palese P, Ravetch JV. Broadly neutralizing hemagglutinin stalk-specific antibodies require FcγR interactions for protection against influenza virus in vivo. Nat Med 2014; 20:143-51. [PMID: 24412922 PMCID: PMC3966466 DOI: 10.1038/nm.3443] [Citation(s) in RCA: 621] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 12/06/2013] [Indexed: 02/07/2023]
Abstract
Neutralizing antibodies against influenza viruses have traditionally been thought to provide protection exclusively through their variable region; the contributions of mechanisms conferred by the Fc domain remain controversial. We investigated the in vivo contributions of Fc interactions with their cognate receptors for a collection of neutralizing anti-influenza antibodies. Whereas five broadly neutralizing monoclonal antibodies (bNAbs) targeting the conserved stalk region of hemagglutinin (HA) required interactions between the antibody Fc and Fc receptors for IgG (FcγRs) to confer protection from lethal H1N1 challenge, three strain-specific monoclonal Abs (mAbs) against the variable head domain of HA were equally protective in the presence or absence of FcγR interactions. Although all antibodies blocked infection, only anti-stalk bNAbs were capable of mediating cytotoxicity of infected cells, which accounts for their FcγR dependence. Immune complexes generated with anti-HA stalk mAb efficiently interacted with FcγRs, but anti-HA head immune complexes did not. These results suggest that FcγR binding capacity by anti-HA antibodies was dependent on the interaction of the cognate Fab with antigen. We exploited these disparate mechanisms of mAb-mediated protection to reengineer an anti-stalk bNAb to selectively enhance FcγR engagement to augment its protective activity. These findings reveal a previously uncharacterized property of bNAbs and guide an approach toward enhancing mAb-mediated antiviral therapeutics.
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MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antigen-Antibody Complex/immunology
- Cell Line
- Chick Embryo
- Dogs
- Enzyme-Linked Immunosorbent Assay
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Influenza A Virus, H1N1 Subtype/immunology
- Kaplan-Meier Estimate
- Killer Cells, Natural/immunology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Neutralization Tests
- Receptors, IgG/immunology
- Receptors, IgG/metabolism
- Surface Plasmon Resonance
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Affiliation(s)
- David J DiLillo
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York, USA
| | - Gene S Tan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jeffrey V Ravetch
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York, USA
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