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Cisse A, Desfosses A, Stainer S, Kandiah E, Traore DAK, Bezault A, Schachner-Nedherer AL, Leitinger G, Hoerl G, Hinterdorfer P, Gutsche I, Prassl R, Peters J, Kornmueller K. Targeting structural flexibility in low density lipoprotein by integrating cryo-electron microscopy and high-speed atomic force microscopy. Int J Biol Macromol 2023; 252:126345. [PMID: 37619685 DOI: 10.1016/j.ijbiomac.2023.126345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/26/2023]
Abstract
Low-density lipoprotein (LDL) plays a crucial role in cholesterol metabolism. Responsible for cholesterol transport from the liver to the organs, LDL accumulation in the arteries is a primary cause of cardiovascular diseases, such as atherosclerosis. This work focuses on the fundamental question of the LDL molecular structure, as well as the topology and molecular motions of apolipoprotein B-100 (apo B-100), which is addressed by single-particle cryo-electron microscopy (cryo-EM) and high-speed atomic force microscopy (HS-AFM). Our results suggest a revised model of the LDL core organization with respect to the cholesterol ester (CE) arrangement. In addition, a high-density region close to the flattened poles could be identified, likely enriched in free cholesterol. The most remarkable new details are two protrusions on the LDL surface, attributed to the protein apo B-100. HS-AFM adds the dimension of time and reveals for the first time a highly dynamic direct description of LDL, where we could follow large domain fluctuations of the protrusions in real time. To tackle the inherent flexibility and heterogeneity of LDL, the cryo-EM maps are further assessed by 3D variability analysis. Our study gives a detailed explanation how to approach the intrinsic flexibility of a complex system comprising lipids and protein.
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Affiliation(s)
- Aline Cisse
- Université Grenoble Alpes, CNRS, LiPhy, Grenoble, France; Institut Laue-Langevin, Grenoble, France
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Sarah Stainer
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | | | - Daouda A K Traore
- Institut Laue-Langevin, Grenoble, France; Faculté de Pharmacie, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali; Faculty of Natural Sciences, School of Life Sciences, Keele University, Staffordshire, UK
| | - Armel Bezault
- Institut Européen de Chimie et Biologie, UAR3033/US001, Université de Bordeaux, CNRS, INSERM 2, Pessac, France; Structural Image Analysis Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3528, Paris, France
| | - Anna-Laurence Schachner-Nedherer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical Physics and Biophysics Division, Medical University of Graz, Graz, Austria
| | - Gerd Leitinger
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Gerd Hoerl
- Otto Loewi Research Center, Physiological Chemistry, Medical University of Graz, Graz, Austria
| | - Peter Hinterdorfer
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Ruth Prassl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical Physics and Biophysics Division, Medical University of Graz, Graz, Austria
| | - Judith Peters
- Université Grenoble Alpes, CNRS, LiPhy, Grenoble, France; Institut Laue-Langevin, Grenoble, France; Institut Universitaire de France, France.
| | - Karin Kornmueller
- Institut Laue-Langevin, Grenoble, France; Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical Physics and Biophysics Division, Medical University of Graz, Graz, Austria.
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2
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Almadhi S, Forth J, Rodriguez-Arco L, Duro-Castano A, Williams I, Ruiz-Pérez L, Battaglia G. Bottom-Up Preparation of Phase-Separated Polymersomes. Macromol Biosci 2023; 23:e2300068. [PMID: 37315231 DOI: 10.1002/mabi.202300068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/20/2023] [Indexed: 06/16/2023]
Abstract
A bottom-up approach to fabricating monodisperse, two-component polymersomes that possess phase-separated ("patchy") chemical topology is presented. This approach is compared with already-existing top-down preparation methods for patchy polymer vesicles, such as film rehydration. These findings demonstrate a bottom-up, solvent-switch self-assembly approach that produces a high yield of nanoparticles of the target size, morphology, and surface topology for drug delivery applications, in this case patchy polymersomes of a diameter of ≈50 nm. In addition, an image processing algorithm to automatically calculate polymersome size distributions from transmission electron microscope images based on a series of pre-processing steps, image segmentation, and round object identification is presented.
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Affiliation(s)
- Safa Almadhi
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
| | - Joe Forth
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
| | - Laura Rodriguez-Arco
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
- Department of Applied Physics, Faculty of Sciences, University of Granada, Granada, 18071, Spain
| | - Aroa Duro-Castano
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
- Curapath, Valencia, 46980, Spain
| | - Ian Williams
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
- Department of Physics, University of Surrey, Guildford, GU2 7XH, UK
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | - Lorena Ruiz-Pérez
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | - Giuseppe Battaglia
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
- Catalan Institution of Research and Advanced Studies, Barcelona, 08010, Spain
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3
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Xu Y, Li Y, Zhao W, Zhao C. Simple emulsion template method towards self-anticoagulant and high-efficiency carboxymethyl chitosan-based adsorbent for low-density lipoprotein from whole blood. J Colloid Interface Sci 2022; 631:231-244. [DOI: 10.1016/j.jcis.2022.10.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/02/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022]
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4
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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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Chemello K, García-Nafría J, Gallo A, Martín C, Lambert G, Blom D. Lipoprotein metabolism in familial hypercholesterolemia. J Lipid Res 2021; 62:100062. [PMID: 33675717 PMCID: PMC8050012 DOI: 10.1016/j.jlr.2021.100062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/20/2021] [Accepted: 02/21/2021] [Indexed: 02/06/2023] Open
Abstract
Familial hypercholesterolemia (FH) is one of the most common genetic disorders in humans. It is an extremely atherogenic metabolic disorder characterized by lifelong elevations of circulating LDL-C levels often leading to premature cardiovascular events. In this review, we discuss the clinical phenotypes of heterozygous and homozygous FH, the genetic variants in four genes (LDLR/APOB/PCSK9/LDLRAP1) underpinning the FH phenotype as well as the most recent in vitro experimental approaches used to investigate molecular defects affecting the LDL receptor pathway. In addition, we review perturbations in the metabolism of lipoproteins other than LDL in FH, with a major focus on lipoprotein (a). Finally, we discuss the mode of action and efficacy of many of the currently approved hypocholesterolemic agents used to treat patients with FH, with a special emphasis on the treatment of phenotypically more severe forms of FH.
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Affiliation(s)
- Kévin Chemello
- Inserm UMR 1188 DéTROI, Université de La Réunion, Saint- Denis de La Réunion, France
| | - Javier García-Nafría
- Institute for Biocomputation and Physics of complex systems (BIFI), University of Zaragoza, Zaragoza, Spain; Laboratorio de Microscopías Avanzadas, University of Zaragoza, Zaragoza, Spain
| | - Antonio Gallo
- Cardiovascular Prevention Unit, Department of Endocrinology and Metabolism, Pitié-Salpêtrière University Hospital, Paris, France; Laboratoire d'imagerie Biomédicale, INSERM 1146, CNRS 7371, Sorbonne University, Paris, France
| | - Cesar Martín
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco UPV/EHU, Bilbao, Spain
| | - Gilles Lambert
- Inserm UMR 1188 DéTROI, Université de La Réunion, Saint- Denis de La Réunion, France.
| | - Dirk Blom
- Hatter Institute for Cardiovascular Research in Africa and Division of Lipidology, Department of Medicine, University of Cape Town, Cape Town, South Africa
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6
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Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures. PHYSICAL REVIEW LETTERS 2020; 125:228101. [PMID: 33315453 DOI: 10.1103/physrevlett.125.228101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/06/2020] [Indexed: 06/12/2023]
Abstract
In this study, we investigate the role of the surface patterning of nanostructures for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations and explore the solution space of ligand patterns on a nanoparticle that promote efficient and reliable cell uptake. Surprisingly, we find that in the regime of low ligand number the best-performing structures are characterized by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. Our approach reveals a set of nonintuitive design rules that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry.
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Affiliation(s)
- Joel C Forster
- Department of Physics and Astronomy, University College London, WC1E 6BS London, United Kingdom
- Institute for the Physics of Living Systems, University College London, WC1E 6BS London, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BS London, United Kingdom
| | - Johannes Krausser
- Department of Physics and Astronomy, University College London, WC1E 6BS London, United Kingdom
- Institute for the Physics of Living Systems, University College London, WC1E 6BS London, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BS London, United Kingdom
| | - Manish R Vuyyuru
- Department of Physics and Astronomy, University College London, WC1E 6BS London, United Kingdom
- Institute for the Physics of Living Systems, University College London, WC1E 6BS London, United Kingdom
| | - Buzz Baum
- Institute for the Physics of Living Systems, University College London, WC1E 6BS London, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BS London, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, WC1E 6BS London, United Kingdom
- Institute for the Physics of Living Systems, University College London, WC1E 6BS London, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BS London, United Kingdom
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7
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Klee EW, Zimmermann MT. Molecular modeling of LDLR aids interpretation of genomic variants. J Mol Med (Berl) 2019; 97:533-540. [PMID: 30778614 PMCID: PMC6440939 DOI: 10.1007/s00109-019-01755-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 01/14/2019] [Accepted: 02/05/2019] [Indexed: 11/24/2022]
Abstract
Abstract Genetic variants in low-density lipoprotein receptor (LDLR) are known to cause familial hypercholesterolemia (FH), occurring in up to 1 in 200 people (Youngblom E. et al. 1993 and Nordestgaard BG et al. 34:3478–3490a, 2013) and leading to significant risk for heart disease. Clinical genomics testing using high-throughput sequencing is identifying novel genomic variants of uncertain significance (VUS) in individuals suspected of having FH, but for whom the causal link to the disease remains to be established (Nordestgaard BG et al. 34:3478–3490a, 2013). Unfortunately, experimental data about the atomic structure of the LDL binding domains of LDLR at extracellular pH does not exist. This leads to an inability to apply protein structure-based methods for assessing novel variants identified through genetic testing. Thus, the ambiguities in interpretation of LDLR variants are a barrier to achieving the expected clinical value for personalized genomics assays for management of FH. In this study, we integrated data from the literature and related cellular receptors to develop high-resolution models of full-length LDLR at extracellular conditions and use them to predict which VUS alter LDL binding. We believe that the functional effects of LDLR variants can be resolved using a combination of structural bioinformatics and functional assays, leading to a better correlation with clinical presentation. We have completed modeling of LDLR in two major physiologic conditions, generating detailed hypotheses for how each of the 1007 reported protein variants may affect function. Key messages • Hundreds of variants are observed in the LDLR, but most lack interpretation. • Molecular modeling is aided by biochemical knowledge. • We generated context-specific 3D protein models of LDLR. • Our models allowed mechanistic interpretation of many variants. • We interpreted both rare and common genomic variants in their physiologic context. • Effects of genomic variants are often context-specific. Electronic supplementary material The online version of this article (10.1007/s00109-019-01755-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eric W Klee
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, 53226-0509, USA.
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8
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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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9
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Lei D, Yu Y, Kuang YL, Liu J, Krauss RM, Ren G. Single-molecule 3D imaging of human plasma intermediate-density lipoproteins reveals a polyhedral structure. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1864:260-270. [PMID: 30557627 PMCID: PMC6409128 DOI: 10.1016/j.bbalip.2018.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 11/25/2018] [Accepted: 12/09/2018] [Indexed: 11/25/2022]
Abstract
Intermediate-density lipoproteins (IDLs), the remnants of very-low-density lipoproteins via lipolysis, are rich in cholesteryl ester and are associated with cardiovascular disease. Despite pharmacological interest in IDLs, their three-dimensional (3D) structure is still undetermined due to their variation in size, composition, and dynamic structure. To explore the 3D structure of IDLs, we reconstructed 3D density maps from individual IDL particles using cryo-electron microscopy (cryo-EM) and individual-particle electron tomography (IPET, without averaging from different molecules). 3D reconstructions of IDLs revealed an unexpected polyhedral structure that deviates from the generally assumed spherical shape model (Frias et al., 2007; Olson, 1998; Shen et al., 1977). The polyhedral-shaped IDL contains a high-density shell formed by flat surfaces that are similar to those of very-low-density lipoproteins but have sharper dihedral angles between nearby surfaces. These flat surfaces would be less hydrophobic than the curved surface of mature spherical high-density lipoprotein (HDL), leading to a lower binding affinity of IDL to hydrophobic proteins (such as cholesteryl ester transfer protein) than HDL. This is the first visualization of the IDL 3D structure, which could provide fundamental clues for delineating the role of IDL in lipid metabolism and cardiovascular disease.
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Affiliation(s)
- Dongsheng Lei
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yadong Yu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yu-Lin Kuang
- Atherosclerosis Research, Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ronald M Krauss
- Atherosclerosis Research, Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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10
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Rodríguez-Arco L, Poma A, Ruiz-Pérez L, Scarpa E, Ngamkham K, Battaglia G. Molecular bionics - engineering biomaterials at the molecular level using biological principles. Biomaterials 2018; 192:26-50. [PMID: 30419394 DOI: 10.1016/j.biomaterials.2018.10.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/06/2018] [Accepted: 10/28/2018] [Indexed: 12/18/2022]
Abstract
Life and biological units are the result of the supramolecular arrangement of many different types of molecules, all of them combined with exquisite precision to achieve specific functions. Taking inspiration from the design principles of nature allows engineering more efficient and compatible biomaterials. Indeed, bionic (from bion-, unit of life and -ic, like) materials have gained increasing attention in the last decades due to their ability to mimic some of the characteristics of nature systems, such as dynamism, selectivity, or signalling. However, there are still many challenges when it comes to their interaction with the human body, which hinder their further clinical development. Here we review some of the recent progress in the field of molecular bionics with the final aim of providing with design rules to ensure their stability in biological media as well as to engineer novel functionalities which enable navigating the human body.
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Affiliation(s)
- Laura Rodríguez-Arco
- Department of Chemistry, University College London (UCL) 20 Gordon St, Kings Cross, London, WC1H 0AJ, UK; Institute for Physics of Living Systems, University College London, London, UK.
| | - Alessandro Poma
- Department of Chemistry, University College London (UCL) 20 Gordon St, Kings Cross, London, WC1H 0AJ, UK; Institute for Physics of Living Systems, University College London, London, UK
| | - Lorena Ruiz-Pérez
- Department of Chemistry, University College London (UCL) 20 Gordon St, Kings Cross, London, WC1H 0AJ, UK; Institute for Physics of Living Systems, University College London, London, UK; The EPRSC/Jeol Centre of Liquid Electron Microscopy, University College London, London, WC1H 0AJ, UK
| | - Edoardo Scarpa
- Department of Chemistry, University College London (UCL) 20 Gordon St, Kings Cross, London, WC1H 0AJ, UK; Institute for Physics of Living Systems, University College London, London, UK
| | - Kamolchanok Ngamkham
- Faculty of Engineering, King Mongkut's University of Technology Thonbury, 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok, 10140, Thailand
| | - Giuseppe Battaglia
- Department of Chemistry, University College London (UCL) 20 Gordon St, Kings Cross, London, WC1H 0AJ, UK; Institute for Physics of Living Systems, University College London, London, UK; The EPRSC/Jeol Centre of Liquid Electron Microscopy, University College London, London, WC1H 0AJ, UK.
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11
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Lehofer B, Golub M, Kornmueller K, Kriechbaum M, Martinez N, Nagy G, Kohlbrecher J, Amenitsch H, Peters J, Prassl R. High Hydrostatic Pressure Induces a Lipid Phase Transition and Molecular Rearrangements in Low-Density Lipoprotein Nanoparticles. PARTICLE & PARTICLE SYSTEMS CHARACTERIZATION : MEASUREMENT AND DESCRIPTION OF PARTICLE PROPERTIES AND BEHAVIOR IN POWDERS AND OTHER DISPERSE SYSTEMS 2018; 35:1800149. [PMID: 30283212 PMCID: PMC6166783 DOI: 10.1002/ppsc.201800149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Indexed: 06/08/2023]
Abstract
Low-density lipoproteins (LDL) are natural lipid transporter in human plasma whose chemically modified forms contribute to the progression of atherosclerosis and cardiovascular diseases accounting for a vast majority of deaths in westernized civilizations. For the development of new treatment strategies, it is important to have a detailed picture of LDL nanoparticles on a molecular basis. Through the combination of X-ray and neutron small-angle scattering (SAS) techniques with high hydrostatic pressure (HHP) this study describes structural features of normolipidemic, triglyceride-rich and oxidized forms of LDL. Due to the different scattering contrasts for X-rays and neutrons, information on the effects of HHP on the internal structure determined by lipid rearrangements and changes in particle shape becomes accessible. Independent pressure and temperature variations provoke a phase transition in the lipid core domain. With increasing pressure an inter-related anisotropic deformation and flattening of the particle are induced. All LDL nanoparticles maintain their structural integrity even at 3000 bar and show a reversible response toward pressure variations. The present work depicts the complementarity of pressure and temperature as independent thermodynamic parameters and introduces HHP as a tool to study molecular assembling and interaction processes in distinct lipoprotein particles in a nondestructive manner.
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Affiliation(s)
- Bernhard Lehofer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/IV, 8010 Graz, Austria
| | - Maksym Golub
- Institut Laue-Langevin, 71 avenue des Martyrs, 38044 Grenoble, France; Univ. Grenoble Alpes, CNRS + CEA, IBS, 38000 Grenoble, France
| | - Karin Kornmueller
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/IV, 8010 Graz, Austria
| | - Manfred Kriechbaum
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Nicolas Martinez
- Institut Laue-Langevin, 71 avenue des Martyrs, 38044 Grenoble, France; Univ. Grenoble Alpes, CNRS + CEA, IBS, 38000 Grenoble, France
| | - Gergely Nagy
- Paul Scherrer Institut, 5232 Villigen, Switzerland; Wigner Research Centre for Physics, 1121 Budapest, Hungary; European Spallation Source ERIC, 22363 Lund, Sweden
| | | | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Judith Peters
- Institut Laue-Langevin, 71 avenue des Martyrs, 38044 Grenoble, France; Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
| | - Ruth Prassl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/IV, 8010 Graz, Austria
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12
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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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13
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How multi-scale structural biology elucidated context-dependent variability in ectodomain conformation along with the ligand capture and release cycle for LDLR family members. Biophys Rev 2017; 10:481-492. [PMID: 29204877 DOI: 10.1007/s12551-017-0362-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/19/2017] [Indexed: 12/25/2022] Open
Abstract
The low-density lipoprotein receptor (LDLR) and its homologs capture and internalize lipoproteins into the cell. Due to the fact that LDLR family members possess a modular ectodomain that undergoes dynamic conformational changes, multi-scale structural analysis has been performed so as to understand the ligand capture and release mechanism. For example, crystallographic analyses have provided models for both the entire ectodomain and high-resolution structures of individual modules. In addition, nuclear magnetic resonance spectroscopic analyses have shown the rigidity and flexibility of inter-module linkers to restrict the mobility of ectodomain. Accumulated structural data suggest that the ectodomains of LDLR family members are flexible at the cell surface and switch between two metastable conformations, that is, the extended and contracted conformations. Recent structural analysis of ApoER2, a close homolog of LDLR, raised the possibility that the receptor binds with the ligand in the contracted conformation. After transport to an endosome by endocytosis, the receptor undergoes a conformational change to the closed conformation for completion of ligand release. In contrast, LDLR has been reported to adopt the extended conformation when it binds with a inhibitory regulator that recruits LDLR toward the degradation pathway. These findings support a mechanism of different ectodomain conformations for binding the ligand versus binding the regulatory protein. In this review, I provide an overview of studies that analyze the structural and biophysical properties of the ectodomains of LDLR family members and discuss a hypothetical model for ligand uptake and receptor recycling that integrates the known ectodomain conformational variability.
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14
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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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15
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Hirai H, Yasui N, Yamashita K, Tabata S, Yamamoto M, Takagi J, Nogi T. Structural basis for ligand capture and release by the endocytic receptor ApoER2. EMBO Rep 2017; 18:982-999. [PMID: 28446613 PMCID: PMC5452030 DOI: 10.15252/embr.201643521] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/09/2017] [Accepted: 03/15/2017] [Indexed: 11/09/2022] Open
Abstract
Apolipoprotein E receptor 2 (ApoER2) is a close homologue of low-density lipoprotein receptor (LDLR) that mediates the endocytosis of ligands, including LDL particles. LDLR family members have been presumed to explore a large conformational space to capture ligands in the extended conformation at the cell surface. Ligands are subsequently released through a pH-titrated structural transition to a self-docked, contracted-closed conformation. In addition to lipoprotein uptake, ApoER2 is implicated in signal transduction during brain development through capture of the extracellular protein reelin. From crystallographic analysis, we determine that the full-length ApoER2 ectodomain adopts an intermediate contracted-open conformation when complexed with the signaling-competent reelin fragment, and we identify a previously unappreciated auxiliary low-affinity binding interface. Based on mutational analyses, we propose that the pH shift during endocytosis weakens the affinity of the auxiliary interface and destabilizes the ligand-receptor complex. Furthermore, this study elucidates that the contracted-open conformation of ligand-bound ApoER2 at neutral pH resembles the contracted-closed conformation of ligand-unbound LDLR at acidic pH in a manner suggestive of being primed for ligand release even prior to internalization.
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Affiliation(s)
- Hidenori Hirai
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Norihisa Yasui
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | | | - Sanae Tabata
- Institute for Protein Research, Osaka University, Osaka, Japan
| | | | - Junichi Takagi
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Terukazu Nogi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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16
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Eid L, Parent M. Preparation of Non-human Primate Brain Tissue for Pre-embedding Immunohistochemistry and Electron Microscopy. J Vis Exp 2017. [PMID: 28448038 DOI: 10.3791/55397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Despite all the technological advances at the light microscopy level, electron microscopy remains the only tool in neuroscience to examine and characterize ultrastructural and morphological details of neurons, such as synaptic contacts. Good preservation of brain tissue for electron microscopy can be obtained by rigorous cryo-fixation methods, but these techniques are rather costly and limit the use of immunolabeling, which is crucial to understand the connectivity of identified neuronal systems. Freeze-substitution methods have been developed to allow the combination of cryo-fixation with immunolabeling. However, the reproducibility of these methodological approaches usually relies on costly freezing devices. Moreover, achieving reliable results with this technique is very time-consuming and skill-challenging. Hence, the traditional chemically fixed brain, particularly with acrolein fixative, remains a time-efficient and low-cost method to combine electron microscopy with immunohistochemistry. Here, we provide a reliable experimental protocol using chemical acrolein fixation that leads to the preservation of primate brain tissue and is compatible with pre-embedding immunohistochemistry and transmission electron microscopic examination.
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Affiliation(s)
- Lara Eid
- Centre de recherche de l'Institut universitaire en santé mentale de Québec, Department of Psychiatry and Neuroscience, Université Laval; Centre de recherche du CHU Sainte-Justine;
| | - Martin Parent
- Centre de recherche de l'Institut universitaire en santé mentale de Québec, Department of Psychiatry and Neuroscience, Université Laval
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17
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Maric S, Lind TK, Lyngsø J, Cárdenas M, Pedersen JS. Modeling Small-Angle X-ray Scattering Data for Low-Density Lipoproteins: Insights into the Fatty Core Packing and Phase Transition. ACS NANO 2017; 11:1080-1090. [PMID: 28048943 DOI: 10.1021/acsnano.6b08089] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Atherosclerosis and its clinical consequences are the leading cause of death in the western hemisphere. While many studies throughout the last decades have aimed at understanding the disease, the clinical markers in use today still fail to accurately predict the risks. The role of the current main clinical indicator, low density lipoprotein (LDL), in depositing fat to the vessel wall is believed to be the onset of the process. However, many subfractions of the LDL, which differ both in structure and composition, are present in the blood and among different individuals. Understanding the relationship between LDL structure and composition is key to unravel the specific role of various LDL components in the development and/or prevention of atherosclerosis. Here, we describe a model for analyzing small-angle X-ray scattering data for rapid and robust structure determination for the LDL. The model not only gives the overall structure but also the particular internal layering of the fats inside the LDL core. Thus, the melting of the LDL can be followed in situ as a function of temperature for samples extracted from healthy human patients and purified using a double protocol based on ultracentrifugation and size-exclusion chromatography. The model provides information on: (i) the particle-specific melting temperature of the core lipids, (ii) the structural organization of the core fats inside the LDL, (iii) the overall shape of the particle, and (iv) the flexibility and overall conformation of the outer protein/hydrophilic layer at a given temperature as governed by the organization of the core. The advantage of this method over other techniques such as cryo-TEM is the possibility of in situ experiments under near-physiological conditions which can be performed relatively fast (minutes at home source, seconds at synchrotron). This approach now allows the monitoring of structural changes in the LDL upon different stresses from the environment, such as changes in temperature, oxidation, or external agents used or currently in development against atherosclerotic plaque build-up and which are targeting the LDL.
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Affiliation(s)
- Selma Maric
- Biofilms- Research Center for Biointerfaces, Dept. of Biomedical Science, Faculty of Health and Society, Malmö University , Malmö 20506, Sweden
| | - Tania Kjellerup Lind
- Biofilms- Research Center for Biointerfaces, Dept. of Biomedical Science, Faculty of Health and Society, Malmö University , Malmö 20506, Sweden
| | - Jeppe Lyngsø
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University , 8000 Aarhus, Denmark
| | - Marité Cárdenas
- Biofilms- Research Center for Biointerfaces, Dept. of Biomedical Science, Faculty of Health and Society, Malmö University , Malmö 20506, Sweden
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University , 8000 Aarhus, Denmark
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18
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Fernández-Higuero JA, Benito-Vicente A, Etxebarria A, Milicua JCG, Ostolaza H, Arrondo JLR, Martín C. Structural changes induced by acidic pH in human apolipoprotein B-100. Sci Rep 2016; 6:36324. [PMID: 27824107 PMCID: PMC5099883 DOI: 10.1038/srep36324] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/14/2016] [Indexed: 11/16/2022] Open
Abstract
Acidification in the endosome causes lipoprotein release by promoting a conformational change in the LDLR allowing its recycling and degradation of LDL. Notwithstanding conformational changes occurring in the LDLR have expanded considerably, structural changes occurring in LDL particles have not been fully explored yet. The objectives of the present work were to study structural changes occurring in apoB100 by infrared spectroscopy (IR) and also LDL size and morphology by dynamic light scattering (DLS) and electron microscopy (EM) at both pH 7.4 and 5.0. We determined by IR that pH acidification from 7.4 to 5.0, resembling that occurring within endosomal environment, induces a huge reversible structural rearrangement of apoB100 that is characterized by a reduction of beta-sheet content in favor of alpha-helix structures. Data obtained from DLS and EM showed no appreciable differences in size and morphology of LDL. These structural changes observed in apoB100, which are likely implied in particle release from lipoprotein receptor, also compromise the apoprotein stability what would facilitate LDL degradation. In conclusion, the obtained results reveal a more dynamic picture of the LDL/LDLR dissociation process than previously perceived and provide new structural insights into LDL/LDLR interactions than can occur at endosomal low-pH milieu.
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Affiliation(s)
- José A. Fernández-Higuero
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
- Dpt. Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
| | - Asier Benito-Vicente
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
- Dpt. Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
| | - Aitor Etxebarria
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
- Dpt. Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
| | - José Carlos G. Milicua
- Dpt. Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
| | - Helena Ostolaza
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
- Dpt. Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
| | - José L. R. Arrondo
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
- Dpt. Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
| | - Cesar Martín
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
- Dpt. Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU, Spain, Apdo. 644, 48080 Bilbao, Spain
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19
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Gordon SM, Pourmousa M, Sampson M, Sviridov D, Islam R, Perrin BS, Kemeh G, Pastor RW, Remaley AT. Identification of a novel lipid binding motif in apolipoprotein B by the analysis of hydrophobic cluster domains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:135-145. [PMID: 27814978 DOI: 10.1016/j.bbamem.2016.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/11/2016] [Accepted: 10/27/2016] [Indexed: 02/05/2023]
Abstract
Apolipoprotein B (apoB) is a large amphipathic protein that is the structural scaffold for the formation of several classes of lipoproteins involved in lipid transport throughout the body. The goal of the present study was to identify specific domains in the apoB sequence that contribute to its lipid binding properties. A sequence analysis algorithm was developed to identify stretches of hydrophobic amino acids devoid of charged amino acids, which are referred to as hydrophobic cluster domains (HCDs). This analysis identified 78 HCDs in apoB with hydrophobic stretches ranging from 6 to 26 residues. Each HCD was analyzed in silico for secondary structure and lipid binding properties, and a subset was synthesized for experimental evaluation. One HCD peptide, B38, showed high affinity binding to both isolated HDL and LDL, and could exchange between lipoproteins. All-atom molecular dynamics simulations indicate that B38 inserts 3.7Å below the phosphate plane of the bilayer. B38 forms an unusual α-helix with a broad hydrophobic face and polar serine and threonine residues on the opposite face. Based on this structure, we hypothesized that B38 could efflux cholesterol from cells. B38 showed a 12-fold greater activity than the 5A peptide, a bihelical Class A amphipathic helix (EC50 of 0.2658 vs. 3.188μM; p<0.0001), in promoting cholesterol efflux from ABCA1 expressing BHK-1 cells. In conclusion, we have identified novel domains within apoB that contribute to its lipid biding properties. Additionally, we have discovered a unique amphipathic helix design for efficient ABCA1-specific cholesterol efflux.
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Affiliation(s)
- Scott M Gordon
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Mohsen Pourmousa
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Maureen Sampson
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Denis Sviridov
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rafique Islam
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - B Scott Perrin
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Georgina Kemeh
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Alan T Remaley
- Lipoprotein Metabolism Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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20
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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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21
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Lei D, Rames M, Zhang X, Zhang L, Zhang S, Ren G. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations. J Biol Chem 2016; 291:14034-14044. [PMID: 27143480 PMCID: PMC4933163 DOI: 10.1074/jbc.m116.715565] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Indexed: 12/31/2022] Open
Abstract
Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases.
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Affiliation(s)
- Dongsheng Lei
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Department of Applied Physics, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Matthew Rames
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Xing Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Department of Applied Physics, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Lei Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - 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, California 94720.
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22
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Ruiz-Pérez L, Messager L, Gaitzsch J, Joseph A, Sutto L, Gervasio FL, Battaglia G. Molecular engineering of polymersome surface topology. SCIENCE ADVANCES 2016; 2:e1500948. [PMID: 27152331 PMCID: PMC4846435 DOI: 10.1126/sciadv.1500948] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 03/21/2016] [Indexed: 05/03/2023]
Abstract
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from the molecular to mesoscopic level. We report an example of using fully synthetic systems that mimic two levels of self-assembly. We show the formation of vesicles using amphiphilic copolymers whose chemical nature is chosen to control both membrane formation and membrane-confined interactions. We report polymersomes with patterns that emerge by engineering interfacial tension within the polymersome surface. This allows the formation of domains whose topology is tailored by chemical synthesis, paving the avenue to complex supramolecular designs functionally similar to those found in viruses and trafficking vesicles.
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23
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Pan L, Segrest JP. Computational studies of plasma lipoprotein lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2401-2420. [PMID: 26969087 DOI: 10.1016/j.bbamem.2016.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 12/27/2022]
Abstract
Plasma lipoproteins are macromolecular assemblies of proteins and lipids found in the blood. The lipid components of lipoproteins are amphipathic lipids such as phospholipids (PLs), and unesterified cholesterols (UCs) and hydrophobic lipids such as cholesteryl esters (CEs) and triglycerides (TGs). Since lipoproteins are soft matter supramolecular assemblies easily deformable by thermal fluctuations and they also exist in varying densities and protein/lipid components, a detailed understanding of their structure/function is experimentally difficult. Molecular dynamics (MD) simulation has emerged as a particularly promising way to explore the structure and dynamics of lipoproteins. The purpose of this review is to survey the current status of computational studies of the lipid components of the lipoproteins. Computational studies aim to explore three levels of complexity for the 3-dimensional structural dynamics of lipoproteins at various metabolic stages: (i) lipoprotein particles consist of protein with minimal lipid; (ii) lipoprotein particles consist of PL-rich discoidal bilayer-like lipid particles; (iii) mature circulating lipoprotein particles consist of CE-rich or TG-rich spheroidal lipid-droplet-like particles. Due to energy barriers involved in conversion between these species, other biomolecules also participate in lipoprotein biological assembly. For example: (i) lipid-poor apolipoprotein A-I (apoA-I) interacts with ATP-binding cassette transporter A1 (ABCA1) to produce nascent discoidal high density lipoprotein (dHDL) particles; (ii) lecithin-cholesterol acyltransferase (LCAT) mediates the conversion of UC to CE in dHDL, driving spheroidal HDL (sHDL) formation; (iii) transfer proteins, cholesterol ester transfer protein (CETP) and phospholipid transfer protein (PLTP), transfer both CE and TG and PL, respectively, between lipoprotein particles. Computational studies have the potential to explore different lipoprotein particles at each metabolic stage in atomistic detail. This review discusses the current status of computational methods including all-atom MD (AAMD), coarse-grain MD (CGMD), and MD-simulated annealing (MDSA) and their applications in lipoprotein structural dynamics and biological assemblies. Results from MD simulations are discussed and compared across studies in order to identify key findings, controversies, issues and future directions. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Lurong Pan
- Division of Gerontology, Geriatrics, & Palliative Care, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Jere P Segrest
- Division of Gerontology, Geriatrics, & Palliative Care, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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Angarica VE, Orozco M, Sancho J. Exploring the complete mutational space of the LDL receptor LA5 domain using molecular dynamics: linking SNPs with disease phenotypes in familial hypercholesterolemia. Hum Mol Genet 2016; 25:1233-46. [PMID: 26755827 PMCID: PMC4764198 DOI: 10.1093/hmg/ddw004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/05/2016] [Indexed: 11/18/2022] Open
Abstract
Familial hypercholesterolemia (FH), a genetic disorder with a prevalence of 0.2%, represents a high-risk factor to develop cardiovascular and cerebrovascular diseases. The majority and most severe FH cases are associated to mutations in the receptor for low-density lipoproteins receptor (LDL-r), but the molecular basis explaining the connection between mutation and phenotype is often unknown, which hinders early diagnosis and treatment of the disease. We have used atomistic simulations to explore the complete SNP mutational space (227 mutants) of the LA5 repeat, the key domain for interacting with LDL that is coded in the exon concentrating the highest number of mutations. Four clusters of mutants of different stability have been identified. The majority of the 50 FH known mutations (33) appear distributed in the unstable clusters, i.e. loss of conformational stability explains two-third of FH phenotypes. However, one-third of FH phenotypes (17 mutations) do not destabilize the LR5 repeat. Combining our simulations with available structural data from different laboratories, we have defined a consensus-binding site for the interaction of the LA5 repeat with LDL-r partner proteins and have found that most (16) of the 17 stable FH mutations occur at binding site residues. Thus, LA5-associated FH arises from mutations that cause either the loss of stability or a decrease in domain's-binding affinity. Based on this finding, we propose the likely phenotype of each possible SNP in the LA5 repeat and outline a procedure to make a full computational diagnosis for FH.
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Affiliation(s)
- Vladimir Espinosa Angarica
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain, Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Mariano Esquillor, Edificio I + D, 50018 Zaragoza, Spain
| | - Modesto Orozco
- Institut de Recerca Biomèdica (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain, and
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain, Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Mariano Esquillor, Edificio I + D, 50018 Zaragoza, Spain, Aragon Institute for Health Research (IIS Aragón), Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
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25
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Van der Horst DJ, Rodenburg KW. Lipoprotein assembly and function in an evolutionary perspective. Biomol Concepts 2015; 1:165-83. [PMID: 25961995 DOI: 10.1515/bmc.2010.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Circulatory fat transport in animals relies on members of the large lipid transfer protein (LLTP) superfamily, including mammalian apolipoprotein B (apoB) and insect apolipophorin II/I (apoLp-II/I). ApoB and apoLp-II/I, constituting the structural (non-exchangeable) basis for the assembly of various lipoproteins, acquire lipids through microsomal triglyceride-transfer protein, another LLTP family member, and bind them by means of amphipathic α-helical and β-sheet structural motifs. Comparative research reveals that LLTPs evolved from the earliest animals and highlights the structural adaptations in these lipid-binding proteins. Thus, in contrast to apoB, apoLp-II/I is cleaved post-translationally by a furin, resulting in the appearance of two non-exchangeable apolipoproteins in the single circulatory lipoprotein in insects, high-density lipophorin (HDLp). The remarkable structural similarities between mammalian and insect lipoproteins notwithstanding important functional differences relate to the mechanism of lipid delivery. Whereas in mammals, partial delipidation of apoB-containing lipoproteins eventually results in endocytic uptake of their remnants, mediated by members of the low-density lipoprotein receptor (LDLR) family, and degradation in lysosomes, insect HDLp functions as a reusable lipid shuttle capable of alternate unloading and reloading of lipid. Also, during muscular efforts (flight activity), an HDLp-based lipoprotein shuttle provides for the transport of lipid for energy generation. Although a lipophorin receptor - a homolog of LDLR - was identified that mediates endocytic uptake of HDLp during specific developmental periods, the endocytosed lipoprotein appears to be recycled in a transferrin-like manner. These data highlight that the functional adaptations in the lipoprotein lipid carriers in mammals and insects also emerge with regard to the functioning of their cognate receptors.
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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: 41] [Impact Index Per Article: 4.6] [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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Oliveira CLP, Santos PR, Monteiro AM, Figueiredo Neto AM. Effect of oxidation on the structure of human low- and high-density lipoproteins. Biophys J 2015; 106:2595-605. [PMID: 24940777 DOI: 10.1016/j.bpj.2014.04.049] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/20/2014] [Accepted: 04/30/2014] [Indexed: 10/25/2022] Open
Abstract
This work presents a controlled study of low-density lipoprotein (LDL) and high-density lipoprotein (HDL) structural changes due to in vitro oxidation with copper ions. The changes were studied by small-angle x-ray scattering (SAXS) and dynamic light scattering (DLS) techniques in the case of LDL and by SAXS, DLS, and Z-scan (ZS) techniques in the case of HDL. SAXS data were analyzed with a to our knowledge new deconvolution method. This method provides the electron density profile of the samples directly from the intensity scattering of the monomers. Results show that LDL particles oxidized for 18 h show significant structural changes when compared to nonoxidized particles. Changes were observed in the electrical density profile, in size polydispersity, and in the degree of flexibility of the APO-B protein on the particle. HDL optical results obtained with the ZS technique showed a decrease of the amplitude of the nonlinear optical signal as a function of oxidation time. In contrast to LDL results reported in the literature, the HDL ZS signal does not lead to a complete loss of nonlinear optical signal after 18 h of copper oxidation. Also, the SAXS results did not indicate significant structural changes due to oxidation of HDL particles, and DLS results showed that a small number of oligomers formed in the sample oxidized for 18 h. All experimental results for the HDL samples indicate that this lipoprotein is more resistant to the oxidation process than are LDL particles.
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28
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Khoshi A, Mortazavi Y, Sokhanvar S, Tanzifi A, Akbari A, Kalantari S, Mazloomzadeh S. Determination of PON1 Gene Polymorphisms in Iranian Individuals with High LDL/HDL Ratios. Indian J Clin Biochem 2015. [DOI: 10.1007/s12291-015-0479-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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29
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Analysis of human T-cell leukemia virus type 1 particles by using cryo-electron tomography. J Virol 2014; 89:2430-5. [PMID: 25473052 DOI: 10.1128/jvi.02358-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The particle structure of human T-cell leukemia virus type 1 (HTLV-1) is poorly characterized. Here, we have used cryo-electron tomography to analyze HTLV-1 particle morphology. Particles produced from MT-2 cells were polymorphic, roughly spherical, and varied in size. Capsid cores, when present, were typically poorly defined polyhedral structures with at least one curved region contacting the inner face of the viral membrane. Most of the particles observed lacked a defined capsid core, which likely impacts HTLV-1 particle infectivity.
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30
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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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31
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Lancaster JL, Antonijevic T, Starobin JM. Ordering and stability in lipid droplets with applications to low-density lipoproteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:062708. [PMID: 25019815 DOI: 10.1103/physreve.89.062708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Indexed: 06/03/2023]
Abstract
In this article, we present a framework for investigating the order-disorder transition in lipid droplets using the standard Ising model. While a single lipid droplet is itself a complex system whose constituent cholesteryl esters each possesses many degrees of freedom, we present justification for using this effective approach to isolate the underlying physics. It is argued that the behavior of the esters confined within lipid droplets is significantly different from that of a bulk system of similar esters, which is adequately described by continuum mean-field theory in the thermodynamic limit. When the droplet's shell is modeled as an elastic membrane, a simple picture emerges for a transition between two ordered phases within the core which is tuned by the strength of interactions between the esters. Triglyceride concentration is proposed as a variable which strongly influences the strength of interactions between cholesteryl esters within droplets. The possible relevance of this mechanism to the well known atherogenic nature of small low-density lipoprotein particles is discussed in detail.
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Affiliation(s)
- Jarrett L Lancaster
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, 2907 E. Lee Street, Greensboro, North Carolina 27401, USA
| | - Todor Antonijevic
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, 2907 E. Lee Street, Greensboro, North Carolina 27401, USA
| | - Joseph M Starobin
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, 2907 E. Lee Street, Greensboro, North Carolina 27401, USA
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32
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Martínez-Oliván J, Arias-Moreno X, Velazquez-Campoy A, Millet O, Sancho J. LDL receptor/lipoprotein recognition: endosomal weakening of ApoB and ApoE binding to the convex face of the LR5 repeat. FEBS J 2014; 281:1534-46. [DOI: 10.1111/febs.12721] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 01/02/2014] [Accepted: 01/13/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Juan Martínez-Oliván
- Biocomputation and Complex Systems Physics Institute (BIFI). BIFI-Instituto de Química Física Rocasolano (Consejo Superior de Investigaciones Científicas) Joint Unit; Universidad de Zaragoza; Spain
- Departamento de Bioquímica y Biología Molecular y Celular; Universidad de Zaragoza; Spain
| | - Xabier Arias-Moreno
- Biocomputation and Complex Systems Physics Institute (BIFI). BIFI-Instituto de Química Física Rocasolano (Consejo Superior de Investigaciones Científicas) Joint Unit; Universidad de Zaragoza; Spain
- Departamento de Bioquímica y Biología Molecular y Celular; Universidad de Zaragoza; Spain
| | - Adrián Velazquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI). BIFI-Instituto de Química Física Rocasolano (Consejo Superior de Investigaciones Científicas) Joint Unit; Universidad de Zaragoza; Spain
- Departamento de Bioquímica y Biología Molecular y Celular; Universidad de Zaragoza; Spain
- Fundación Agencia Aragonesa para la Investigación y Desarrollo; Diputación General de Aragón; Spain
| | - Oscar Millet
- Structural Biology Unit; CIC bioGUNE; Derio Spain
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI). BIFI-Instituto de Química Física Rocasolano (Consejo Superior de Investigaciones Científicas) Joint Unit; Universidad de Zaragoza; Spain
- Departamento de Bioquímica y Biología Molecular y Celular; Universidad de Zaragoza; Spain
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33
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Akinc A, Battaglia G. Exploiting endocytosis for nanomedicines. Cold Spring Harb Perspect Biol 2013; 5:a016980. [PMID: 24186069 DOI: 10.1101/cshperspect.a016980] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this article, we briefly review the endocytic pathways used by cells, pointing out their defining characteristics and highlighting physical limitations that may direct the internalization of nanoparticles to a subset of these pathways. A more detailed description of these pathways is presented in the literature. We then focus on the endocytosis of nanomedicines and present how various nanomaterial parameters impact these endocytic processes. This topic is an area of active research, motivated by the recognition that an improved understanding of how nanomaterials interact at the molecular, cellular, and whole-organism level will lead to the design of better nanomedicines in the future. Next, we briefly review some of the important nanomedicines already on the market or in clinical development that serve to exemplify how endocytosis can be exploited for medical benefit. Finally, we present some key unanswered questions and remaining challenges to be addressed by the field.
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Affiliation(s)
- Akin Akinc
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142
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34
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Chu HL, Cheng TM, Chen HW, Chou FH, Chang YC, Lin HY, Liu SY, Liang YC, Hsu MH, Wu DS, Li HY, Ho LP, Wu PC, Chen FR, Chen GS, Shieh DB, Chang CS, Su CH, Yao Z, Chang CC. Synthesis of apolipoprotein B lipoparticles to deliver hydrophobic/amphiphilic materials. ACS APPLIED MATERIALS & INTERFACES 2013; 5:7509-16. [PMID: 23834261 PMCID: PMC3744920 DOI: 10.1021/am401808e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/08/2013] [Indexed: 05/23/2023]
Abstract
To develop a drug delivery system (DDS), it is critical to address challenging tasks such as the delivery of hydrophobic and amphiphilic compounds, cell uptake, and the metabolic fate of the drug delivery carrier. Low-density lipoprotein (LDL) has been acknowledged as the human serum transporter of natively abundant lipoparticles such as cholesterol, triacylglycerides, and lipids. Apolipoprotein B (apo B) is the only protein contained in LDL, and possesses a binding moiety for the LDL receptor that can be internalized and degraded naturally by the cell. Therefore, synthetic/reconstituting apoB lipoparticle (rABL) could be an excellent delivery carrier for hydrophobic or amphiphilic materials. Here, we synthesized rABL in vitro, using full-length apoB through a five-step solvent exchange method, and addressed its potential as a DDS. Our rABL exhibited good biocompatibility when evaluated with cytotoxicity and cell metabolic response assays, and was stable during storage in phosphate-buffered saline at 4 °C for several months. Furthermore, hydrophobic superparamagnetic iron oxide nanoparticles (SPIONPs) and the anticancer drug M4N (tetra-O-methyl nordihydroguaiaretic acid), used as an imaging enhancer and lipophilic drug model, respectively, were incorporated into the rABL, leading to the formation of SPIONPs- and M4N- containing rABL (SPIO@rABL and M4N@rABL, respectively). Fourier transform infrared spectroscopy suggested that rABL has a similar composition to that of LDL, and successfully incorporated SPIONPs or M4N. SPIO@rABL presented significant hepatic contrast enhancement in T2-weighted magnetic resonance imaging in BALB/c mice, suggesting its potential application as a medical imaging contrast agent. M4N@rABL could reduce the viability of the cancer cell line A549. Interestingly, we developed solution-phase high-resolution transmission electron microscopy to observe both LDL and SPIO@rABL in the liquid state. In summary, our LDL-based DDS, rABL, has significant potential as a novel DDS for hydrophobic and amphiphilic materials, with good cell internalization properties and metabolicity.
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Affiliation(s)
- Hsueh-Liang Chu
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Tsai-Mu Cheng
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
- Graduate Institute of Translational
Medicine, College of Medicine and Technology, Taipei
Medical University, Taipei 11031, Taiwan
| | - Hung-Wei Chen
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Fu-Hsuan Chou
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
- Department of Materials Science
and Engineering, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Yu-Chuan Chang
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Hsin-Yu Lin
- Department
of Engineering and System Science and Nuclear Science and Technology Development
Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Shih-Yi Liu
- Department
of Engineering and System Science and Nuclear Science and Technology Development
Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yu-Chuan Liang
- Agricultural
Biotechnology Research Center and Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Ming-Hua Hsu
- Department
of Engineering and System Science and Nuclear Science and Technology Development
Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Dian-Shyeu Wu
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Hsing-Yuan Li
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Li-Ping Ho
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Ping-Ching Wu
- Institute of Oral Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Fu-Rong Chen
- Department
of Engineering and System Science and Nuclear Science and Technology Development
Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Gong-Shen Chen
- Department of Hematology, Mackay Memorial Hospital, Taipei 10449, Taiwan
| | - Dar-Bin Shieh
- Institute of Oral Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chia-Seng Chang
- Agricultural
Biotechnology Research Center and Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Chia-Hao Su
- Center for Translational Research
in Biomedical Sciences, Kaohsiung Chang Gung Memorial
Hospital, Kaohsiung 83342, Taiwan
| | - Zemin Yao
- Department of Biochemistry,
Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Chia-Ching Chang
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
- Agricultural
Biotechnology Research Center and Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
- E-mail: . Tel: 886-3-5731633. Fax: 886-3-5733259
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35
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Tong H, Zhang L, Kaspar A, Rames MJ, Huang L, Woodnutt G, Ren G. Peptide-conjugation induced conformational changes in human IgG1 observed by optimized negative-staining and individual-particle electron tomography. Sci Rep 2013; 3:1089. [PMID: 23346347 PMCID: PMC3549606 DOI: 10.1038/srep01089] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 12/11/2012] [Indexed: 12/20/2022] Open
Abstract
Peptides show much promise as potent and selective drug candidates. Fusing peptides to a scaffold monoclonal antibody produces a conjugated antibody which has the advantages of peptide activity yet also has the pharmacokinetics determined by the scaffold antibody. However, the conjugated antibody often has poor binding affinity to antigens that may be related to unknown structural changes. The study of the conformational change is difficult by conventional techniques because structural fluctuation under equilibrium results in multiple structures co-existing. Here, we employed our two recently developed electron microscopy (EM) techniques: optimized negative-staining (OpNS) EM and individual-particle electron tomography (IPET). Two-dimensional (2D) image analyses and three-dimensional (3D) maps have shown that the domains of antibodies present an elongated peptide-conjugated conformational change, suggesting that our EM techniques may be novel tools to monitor the structural conformation changes in heterogeneous and dynamic macromolecules, such as drug delivery vehicles after pharmacological synthesis and development.
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Affiliation(s)
- Huimin Tong
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049, China
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Garewal M, Zhang L, Ren G. Optimized negative-staining protocol for examining lipid-protein interactions by electron microscopy. Methods Mol Biol 2013; 974:111-8. [PMID: 23404274 PMCID: PMC10546916 DOI: 10.1007/978-1-62703-275-9_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A large number of proteins are capable of inserting themselves into lipids, and interacting with membranes, such as transmembrane proteins and apolipoproteins. Protein-lipid interactions have been identified as one of the keys in understanding biological processes, while the structure of proteins at the lipid-binding stage can provide evidence to help identify their roles and critical functions. However, structure determination of proteins at the lipid-binding stage is rather difficult, because conformational and compositional heterogeneities of the protein-lipid complexes are major barriers to unravel their structures using traditional methods, such as X-ray crystallography. Electron microscopy (EM) is an alternative approach to determine protein structure and has demonstrated a capability in visualizing lipid-protein interactions directly. Among various EM techniques, negative-staining (NS) is an easy, rapid, qualitative approach that is a well-established technique, frequently used in research laboratories. Conventional NS protocols, unfortunately, often generate artifacts with lipid-related proteins, such as the rouleau formation of lipoproteins. To overcome this artifact formation, Ren and his colleagues recently developed an optimized NS protocol that was validated by comparing images of lipoproteins from cryo-electron microscopy (cryo-EM). The optimized NS protocol could produce "near native-state" particle images and high contrast images of the protein in its lipid-binding state that is favorable for three-dimensional (3D) reconstruction by single-particle analysis and individual-particle electron tomography (IPET), suggesting this optimized protocol can be used widely to examine the structure of proteins at lipid-binding stage.
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Affiliation(s)
- Mark Garewal
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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37
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Tong H, Zhang L, Huang L, Ren G. PROG BIOCHEM BIOPHYS 2012; 39:972-978. [DOI: 10.3724/sp.j.1206.2012.00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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38
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Zhang L, Tong H, Garewal M, Ren G. Optimized negative-staining electron microscopy for lipoprotein studies. Biochim Biophys Acta Gen Subj 2012; 1830:2150-9. [PMID: 23032862 DOI: 10.1016/j.bbagen.2012.09.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 09/20/2012] [Accepted: 09/23/2012] [Indexed: 12/16/2022]
Abstract
BACKGROUND Negative-staining (NS), a rapid, simple and conventional technique of electron microscopy (EM), has been commonly used to initially study the morphology and structure of proteins for half a century. Certain NS protocols however can cause artifacts, especially for structurally flexible or lipid-related proteins, such as lipoproteins. Lipoproteins were often observed in the form of rouleau as lipoprotein particles appeared to be stacked together by conventional NS protocols. The flexible components of lipoproteins, i.e. lipids and amphipathic apolipoproteins, resulted in the lipoprotein structure being sensitive to the NS sample preparation parameters, such as operational procedures, salt concentrations, and the staining reagents. SCOPE OF REVIEW The most popular NS protocols that have been used to examine lipoprotein morphology and structure were reviewed. MAJOR CONCLUSIONS The comparisons show that an optimized NS (OpNS) protocol can eliminate the rouleau artifacts of lipoproteins, and that the lipoproteins are similar in size and shape as statistically measured from two EM methods, OpNS and cryo-electron microscopy (cryo-EM). OpNS is a high-throughput, high-contrast and high-resolution (near 1nm, but rarely better than 1nm) method which has been used to discover the mechanics of a small protein, 53kDa cholesterol ester transfer protein (CETP), and the structure of an individual particle of a single protein by individual-particle electron tomography (IPET), i.e. a 14Å-resolution IgG antibody three-dimensional map. GENERAL SIGNIFICANCE It is suggested that OpNS can be used as a general protocol to study the structure of proteins, especially highly dynamic proteins with equilibrium-fluctuating structures.
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Affiliation(s)
- Lei Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Charles MA, Kane JP. New molecular insights into CETP structure and function: a review. J Lipid Res 2012; 53:1451-8. [PMID: 22679067 DOI: 10.1194/jlr.r027011] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cholesteryl ester transfer protein (CETP) is important clinically and is the current target for new drug development. Its structure and mechanism of action has not been well understood. We have combined current new structural and functional methods to compare with relevant prior data. These analyses have led us to propose several steps in CETP's function at the molecular level, in the context of its interactions with lipoproteins, e.g., sensing, penetration, docking, selectivity, ternary complex formation, lipid transfer, and HDL dissociation. These new molecular insights improve our understanding of CETP's mechanisms of action.
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Affiliation(s)
- M Arthur Charles
- Department of Medicine University of California, San Francisco, CA 94158, USA.
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40
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Zhang L, Yan F, Zhang S, Lei D, Charles MA, Cavigiolio G, Oda M, Krauss RM, Weisgraber KH, Rye KA, Pownall HJ, Qiu X, Ren G. Structural basis of transfer between lipoproteins by cholesteryl ester transfer protein. Nat Chem Biol 2012; 8:342-9. [PMID: 22344176 DOI: 10.1038/nchembio.796] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 12/02/2011] [Indexed: 01/17/2023]
Abstract
Human cholesteryl ester transfer protein (CETP) mediates the net transfer of cholesteryl ester mass from atheroprotective high-density lipoproteins to atherogenic low-density lipoproteins by an unknown mechanism. Delineating this mechanism would be an important step toward the rational design of new CETP inhibitors for treating cardiovascular diseases. Using EM, single-particle image processing and molecular dynamics simulation, we discovered that CETP bridges a ternary complex with its N-terminal β-barrel domain penetrating into high-density lipoproteins and its C-terminal domain interacting with low-density lipoprotein or very-low-density lipoprotein. In our mechanistic model, the CETP lipoprotein-interacting regions, which are highly mobile, form pores that connect to a hydrophobic central cavity, thereby forming a tunnel for transfer of neutral lipids from donor to acceptor lipoproteins. These new insights into CETP transfer provide a molecular basis for analyzing mechanisms for CETP inhibition.
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Affiliation(s)
- Lei Zhang
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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41
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Zhang L, Ren G. IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure. PLoS One 2012; 7:e30249. [PMID: 22291925 PMCID: PMC3265479 DOI: 10.1371/journal.pone.0030249] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 12/14/2011] [Indexed: 02/06/2023] Open
Abstract
The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a “focused electron tomography reconstruction” (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single “snapshot” molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules.
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Affiliation(s)
- Lei Zhang
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Gang Ren
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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42
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Lo Surdo P, Bottomley MJ, Calzetta A, Settembre EC, Cirillo A, Pandit S, Ni YG, Hubbard B, Sitlani A, Carfí A. Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH. EMBO Rep 2011; 12:1300-5. [PMID: 22081141 DOI: 10.1038/embor.2011.205] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 08/26/2011] [Accepted: 09/12/2011] [Indexed: 12/19/2022] Open
Abstract
The protein PCSK9 (proprotein convertase subtilisin/kexin type 9) is a key regulator of low-density lipoprotein receptor (LDLR) levels and cardiovascular health. We have determined the crystal structure of LDLR bound to PCSK9 at neutral pH. The structure shows LDLR in a new extended conformation. The PCSK9 C-terminal domain is solvent exposed, enabling cofactor binding, whereas the catalytic domain and prodomain interact with LDLR epidermal growth factor(A) and β-propeller domains, respectively. Thus, PCSK9 seems to hold LDLR in an extended conformation and to interfere with conformational rearrangements required for LDLR recycling.
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Affiliation(s)
- Paola Lo Surdo
- Department of Biochemistry and Molecular Biology, IRBM P. Angeletti, Via Pontina Km 30.600, Pomezia, Rome I-00040, Italy
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43
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Guttman M, Komives EA. The structure, dynamics, and binding of the LA45 module pair of the low-density lipoprotein receptor suggest an important role for LA4 in ligand release. Biochemistry 2011; 50:11001-8. [PMID: 22091758 DOI: 10.1021/bi2014486] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The low-density lipoprotein receptor (LDLR), the primary receptor for cholesterol uptake, binds ligands through its seven LDL-A modules (LAs). We present nuclear magnetic resonance (NMR) and ligand binding measurements on the fourth and fifth modules of the LDLR (LA45), the modules critical for ApoE binding, at physiological pH. Unlike LA5 and all other modules in LDLR, LA4 has a very weak calcium affinity, which probably plays a critical role in endosomal ligand release. The NMR solution structure of each module in the LA45 pair only showed minor differences compared to the analogous domains in previously determined crystal structures. The 12-residue linker connecting the modules, though slightly structured through an interaction with LA4, is highly flexible. Although no intermodule nuclear Overhauser effects were detected, chemical shift perturbations and backbone dynamics suggest cross talk between the two modules. The ligand affinity of both modules is enhanced when the two are linked. LA4 is more flexible than LA5 and remains so even in the module pair, which likely is related to its weaker calcium binding affinity.
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Affiliation(s)
- Miklos Guttman
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0378, United States
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44
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Calandra S, Tarugi P, Speedy HE, Dean AF, Bertolini S, Shoulders CC. Mechanisms and genetic determinants regulating sterol absorption, circulating LDL levels, and sterol elimination: implications for classification and disease risk. J Lipid Res 2011; 52:1885-926. [PMID: 21862702 DOI: 10.1194/jlr.r017855] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This review integrates historical biochemical and modern genetic findings that underpin our understanding of the low-density lipoprotein (LDL) dyslipidemias that bear on human disease. These range from life-threatening conditions of infancy through severe coronary heart disease of young adulthood, to indolent disorders of middle- and old-age. We particularly focus on the biological aspects of those gene mutations and variants that impact on sterol absorption and hepatobiliary excretion via specific membrane transporter systems (NPC1L1, ABCG5/8); the incorporation of dietary sterols (MTP) and of de novo synthesized lipids (HMGCR, TRIB1) into apoB-containing lipoproteins (APOB) and their release into the circulation (ANGPTL3, SARA2, SORT1); and receptor-mediated uptake of LDL and of intestinal and hepatic-derived lipoprotein remnants (LDLR, APOB, APOE, LDLRAP1, PCSK9, IDOL). The insights gained from integrating the wealth of genetic data with biological processes have important implications for the classification of clinical and presymptomatic diagnoses of traditional LDL dyslipidemias, sitosterolemia, and newly emerging phenotypes, as well as their management through both nutritional and pharmaceutical means.
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Affiliation(s)
- Sebastiano Calandra
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena, Italy.
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45
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Kumar V, Butcher SJ, Öörni K, Engelhardt P, Heikkonen J, Kaski K, Ala-Korpela M, Kovanen PT. Three-dimensional cryoEM reconstruction of native LDL particles to 16Å resolution at physiological body temperature. PLoS One 2011; 6:e18841. [PMID: 21573056 PMCID: PMC3090388 DOI: 10.1371/journal.pone.0018841] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 03/21/2011] [Indexed: 11/20/2022] Open
Abstract
Background Low-density lipoprotein (LDL) particles, the major carriers of cholesterol in the human circulation, have a key role in cholesterol physiology and in the development of atherosclerosis. The most prominent structural components in LDL are the core-forming cholesteryl esters (CE) and the particle-encircling single copy of a huge, non-exchangeable protein, the apolipoprotein B-100 (apoB-100). The shape of native LDL particles and the conformation of native apoB-100 on the particles remain incompletely characterized at the physiological human body temperature (37°C). Methodology/Principal Findings To study native LDL particles, we applied cryo-electron microscopy to calculate 3D reconstructions of LDL particles in their hydrated state. Images of the particles vitrified at 6°C and 37°C resulted in reconstructions at ∼16 Å resolution at both temperatures. 3D variance map analysis revealed rigid and flexible domains of lipids and apoB-100 at both temperatures. The reconstructions showed less variability at 6°C than at 37°C, which reflected increased order of the core CE molecules, rather than decreased mobility of the apoB-100. Compact molecular packing of the core and order in a lipid-binding domain of apoB-100 were observed at 6°C, but not at 37°C. At 37°C we were able to highlight features in the LDL particles that are not clearly separable in 3D maps at 6°C. Segmentation of apoB-100 density, fitting of lipovitellin X-ray structure, and antibody mapping, jointly revealed the approximate locations of the individual domains of apoB-100 on the surface of native LDL particles. Conclusions/Significance Our study provides molecular background for further understanding of the link between structure and function of native LDL particles at physiological body temperature.
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Affiliation(s)
- Vibhor Kumar
- Department of Biomedical Engineering and Computational Science, School of Science and Technology, Centre of Excellence in Computational Complex Systems Research, Aalto University Aalto, Finland
- Computational and Mathematical Biology, Genome Institute of Singapore, A*STAR, Singapore
| | - Sarah J. Butcher
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Katariina Öörni
- Wihuri Research Institute, Kalliolinnantie 4, Helsinki, Finland
| | - Peter Engelhardt
- Department of Biomedical Engineering and Computational Science, School of Science and Technology, Centre of Excellence in Computational Complex Systems Research, Aalto University Aalto, Finland
- Department of Pathology, Haartman Institute, Haartmaninkatu 3, University of Helsinki, Helsinki, Finland
- Department of Applied Physics, Nanomicroscopy Center, School of Science and Technology, Puumiehenkuja 2, Aalto University, Espoo, Finland
| | - Jukka Heikkonen
- Department of Biomedical Engineering and Computational Science, School of Science and Technology, Centre of Excellence in Computational Complex Systems Research, Aalto University Aalto, Finland
- Department of Information Technology, University of Turku, Turku, Finland
| | - Kimmo Kaski
- Department of Biomedical Engineering and Computational Science, School of Science and Technology, Centre of Excellence in Computational Complex Systems Research, Aalto University Aalto, Finland
| | - Mika Ala-Korpela
- Computational Medicine Research Group, Institute of Clinical Medicine, Faculty of Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Internal Medicine and Biocenter Oulu, Clinical Research Center, University of Oulu, Oulu, Finland
| | - Petri T. Kovanen
- Wihuri Research Institute, Kalliolinnantie 4, Helsinki, Finland
- * E-mail:
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46
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Liu Y, Atkinson D. Immuno-electron cryo-microscopy imaging reveals a looped topology of apoB at the surface of human LDL. J Lipid Res 2011; 52:1111-1116. [PMID: 21460103 DOI: 10.1194/jlr.m013946] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A single copy of apoB is the sole protein component of human LDL. ApoB is crucial for LDL particle stabilization and is the ligand for LDL receptor, through which cholesterol is delivered to cells. Dysregulation of the pathways of LDL metabolism is well documented in the pathophysiology of atherosclerosis. However, an understanding of the structure of LDL and apoB underlying these biological processes remains limited. In this study, we derived a 22 Å-resolution three-dimensional (3D) density map of LDL using cryo-electron microscopy and image reconstruction, which showed a backbone of high-density regions that encircle the LDL particle. Additional high-density belts complemented this backbone high density to enclose the edge of the LDL particle. Image reconstructions of monoclonal antibody-labeled LDL located six epitopes in five putative domains of apoB in 3D. Epitopes in the LDL receptor binding domain were located on one side of the LDL particle, and epitopes in the N-terminal and C-terminal domains of apoB were in close proximity at the front side of the particle. Such image information revealed a looped topology of apoB on the LDL surface and demonstrated the active role of apoB in maintaining the shape of the LDL particle.
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Affiliation(s)
- Yuhang Liu
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118
| | - David Atkinson
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118.
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47
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Nieland TJ, Xu S, Penman M, Krieger M. Negatively cooperative binding of high-density lipoprotein to the HDL receptor SR-BI. Biochemistry 2011; 50:1818-30. [PMID: 21254782 PMCID: PMC3065119 DOI: 10.1021/bi101657j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Scavenger receptor class B, type I (SR-BI), is a high-density lipoprotein (HDL) receptor, which also binds low-density lipoprotein (LDL), and mediates the cellular selective uptake of cholesteryl esters from lipoproteins. SR-BI also is a coreceptor for hepatitis C virus and a signaling receptor that regulates cell metabolism. Many investigators have reported that lipoproteins bind to SR-BI via a single class of independent (not interacting), high-affinity binding sites (one site model). We have reinvestigated the ligand concentration dependence of (125)I-HDL binding to SR-BI and SR-BI-mediated specific uptake of [(3)H]CE from [(3)H]CE-HDL using an expanded range of ligand concentrations (<1 μg of protein/mL, lower than previously reported). Scatchard and nonlinear least-squares model fitting analyses of the binding and uptake data were both inconsistent with a single class of independent binding sites binding univalent lipoprotein ligands. The data are best fit by models in which SR-BI has either two independent classes of binding sites or one class of sites exhibiting negative cooperativity due to either classic allostery or ensemble effects ("lattice model"). Similar results were observed for LDL. Application of the "infinite dilution" dissociation rate method established that the binding of (125)I-HDL to SR-BI at 4 °C exhibits negative cooperativity. The unexpected complexity of the interactions of lipoproteins with SR-BI should be taken into account when interpreting the results of experiments that explore the mechanism(s) by which SR-BI mediates ligand binding, lipid transport, and cell signaling.
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Affiliation(s)
- Thomas J.F. Nieland
- Department of Biology, Massachusetts Institute of Technology, Room 68-483, 77 Massachusetts Avenue, Cambridge, MA 02139
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142
| | - Shangzhe Xu
- Department of Biology, Massachusetts Institute of Technology, Room 68-483, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Marsha Penman
- Department of Biology, Massachusetts Institute of Technology, Room 68-483, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Monty Krieger
- Department of Biology, Massachusetts Institute of Technology, Room 68-483, 77 Massachusetts Avenue, Cambridge, MA 02139
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48
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Nieland TJF, Xu S, Penman M, Krieger M. Negatively cooperative binding of high-density lipoprotein to the HDL receptor SR-BI. Biochemistry 2011. [PMID: 21254782 DOI: 10.1021/bi1011657j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Scavenger receptor class B, type I (SR-BI), is a high-density lipoprotein (HDL) receptor, which also binds low-density lipoprotein (LDL), and mediates the cellular selective uptake of cholesteryl esters from lipoproteins. SR-BI also is a coreceptor for hepatitis C virus and a signaling receptor that regulates cell metabolism. Many investigators have reported that lipoproteins bind to SR-BI via a single class of independent (not interacting), high-affinity binding sites (one site model). We have reinvestigated the ligand concentration dependence of (125)I-HDL binding to SR-BI and SR-BI-mediated specific uptake of [(3)H]CE from [(3)H]CE-HDL using an expanded range of ligand concentrations (<1 μg of protein/mL, lower than previously reported). Scatchard and nonlinear least-squares model fitting analyses of the binding and uptake data were both inconsistent with a single class of independent binding sites binding univalent lipoprotein ligands. The data are best fit by models in which SR-BI has either two independent classes of binding sites or one class of sites exhibiting negative cooperativity due to either classic allostery or ensemble effects ("lattice model"). Similar results were observed for LDL. Application of the "infinite dilution" dissociation rate method established that the binding of (125)I-HDL to SR-BI at 4 °C exhibits negative cooperativity. The unexpected complexity of the interactions of lipoproteins with SR-BI should be taken into account when interpreting the results of experiments that explore the mechanism(s) by which SR-BI mediates ligand binding, lipid transport, and cell signaling.
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Affiliation(s)
- Thomas J F Nieland
- Department of Biology, Massachusetts Institute of Technology, Room 68-483, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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49
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Liu Y, Atkinson D. Enhancing the contrast of ApoB to locate the surface components in the 3D density map of human LDL. J Mol Biol 2011; 405:274-83. [PMID: 21029740 PMCID: PMC3006490 DOI: 10.1016/j.jmb.2010.10.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 10/14/2010] [Accepted: 10/19/2010] [Indexed: 11/25/2022]
Abstract
A 26 Å resolution map of the structure of human low-density lipoprotein (LDL) was obtained from electron cryomicroscopy and single-particle image reconstruction. The structure showed a discoidal-shaped LDL particle with high-density regions mainly distributed at the edge of the particle and low-density regions at the flat surface that covers the core region. To determine the chemical components that correspond to these density regions and to delineate the distribution of protein and phospholipid located at the particle surface at the resolution of the map, we used Mono-Sulfo-NHS-Undecagold labeling to increase preferentially the contrast of the apolipoprotein B component on the LDL particle. In the three-dimensional map from the image reconstruction of the undecagold-labeled LDL particles, the high-density region from the undecagold label was distributed mainly at the edge of the particle, and lower density regions were found at the flat surfaces that cover the neutral lipid core. This suggests that apolipoprotein B mainly encircles LDL at the edge of the particle and the phospholipid monolayers are located at the flat surfaces, which are parallel to the cholesterol ester layers in the core and may interact with the core lipid layers through the acyl chains.
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Affiliation(s)
- Yuhang Liu
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts, 02118 USA
| | - David Atkinson
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts, 02118 USA
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50
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Prassl R. Human low density lipoprotein: the mystery of core lipid packing. J Lipid Res 2010; 52:187-8. [PMID: 21131533 DOI: 10.1194/jlr.e013417] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Ruth Prassl
- Institute of Biophysics and Nanosystems Research, Austrian Academy of Sciences, Graz, Austria.
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