1
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Sacher S, Mukherjee A, Ray A. Deciphering structural aspects of reverse cholesterol transport: mapping the knowns and unknowns. Biol Rev Camb Philos Soc 2023; 98:1160-1183. [PMID: 36880422 DOI: 10.1111/brv.12948] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 02/03/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023]
Abstract
Atherosclerosis is a major contributor to the onset and progression of cardiovascular disease (CVD). Cholesterol-loaded foam cells play a pivotal role in forming atherosclerotic plaques. Induction of cholesterol efflux from these cells may be a promising approach in treating CVD. The reverse cholesterol transport (RCT) pathway delivers cholesteryl ester (CE) packaged in high-density lipoproteins (HDL) from non-hepatic cells to the liver, thereby minimising cholesterol load of peripheral cells. RCT takes place via a well-organised interplay amongst apolipoprotein A1 (ApoA1), lecithin cholesterol acyltransferase (LCAT), ATP binding cassette transporter A1 (ABCA1), scavenger receptor-B1 (SR-B1), and the amount of free cholesterol. Unfortunately, modulation of RCT for treating atherosclerosis has failed in clinical trials owing to our lack of understanding of the relationship between HDL function and RCT. The fate of non-hepatic CEs in HDL is dependent on their access to proteins involved in remodelling and can be regulated at the structural level. An inadequate understanding of this inhibits the design of rational strategies for therapeutic interventions. Herein we extensively review the structure-function relationships that are essential for RCT. We also focus on genetic mutations that disturb the structural stability of proteins involved in RCT, rendering them partially or completely non-functional. Further studies are necessary for understanding the structural aspects of RCT pathway completely, and this review highlights alternative theories and unanswered questions.
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Affiliation(s)
- Sukriti Sacher
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase III, New Delhi, 110019, India
| | - Abhishek Mukherjee
- Dhiti Life Sciences Pvt Ltd, B-107, Okhla Phase I, New Delhi, 110020, India
| | - Arjun Ray
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase III, New Delhi, 110019, India
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2
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Zhao Y, Hao D, Zhao Y, Zhang S, Zhang L, Yang Z. Dissecting the Structural Dynamics of Authentic Cholesteryl Ester Transfer Protein for the Discovery of Potential Lead Compounds: A Theoretical Study. Int J Mol Sci 2023; 24:12252. [PMID: 37569628 PMCID: PMC10418423 DOI: 10.3390/ijms241512252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Current structural and functional investigations of cholesteryl ester transfer protein (CETP) inhibitor design are nearly entirely based on a fully active mutation (CETPMutant) constructed for protein crystallization, limiting the study of the dynamic structural features of authentic CETP involved in lipid transport under physiological conditions. In this study, we conducted comprehensive molecular dynamics (MD) simulations of both authentic CETP (CETPAuthentic) and CETPMutant. Considering the structural differences between the N- and C-terminal domains of CETPAuthentic and CETPMutant, and their crucial roles in lipid transfer, we identified the two domains as binding pockets of the ligands for virtual screening to discover potential lead compounds targeting CETP. Our results revealed that CETPAuthentic displays greater flexibility and pronounced curvature compared to CETPMutant. Employing virtual screening and MD simulation strategies, we found that ZINC000006242926 has a higher binding affinity for the N- and C-termini, leading to reduced N- and C-opening sizes, disruption of the continuous tunnel, and increased curvature of CETP. In conclusion, CETPAuthentic facilitates the formation of a continuous tunnel in the "neck" region, while CETPMutant does not exhibit such characteristics. The ligand ZINC000006242926 screened for binding to the N- and C-termini induces structural changes in the CETP unfavorable to lipid transport. This study sheds new light on the relationship between the structural and functional mechanisms of CETP. Furthermore, it provides novel ideas for the precise regulation of CETP functions.
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Affiliation(s)
- Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Dongxiao Hao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yifan Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
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3
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Moors J, Krishnan M, Sumpter N, Takei R, Bixley M, Cadzow M, Major TJ, Phipps-Green A, Topless R, Merriman M, Rutledge M, Morgan B, Carlson JC, Zhang JZ, Russell EM, Sun G, Cheng H, Weeks DE, Naseri T, Reupena MS, Viali S, Tuitele J, Hawley NL, Deka R, McGarvey ST, de Zoysa J, Murphy R, Dalbeth N, Stamp L, Taumoepeau M, King F, Wilcox P, Rapana N, McCormick S, Minster RL, Merriman TR, Leask M. A Polynesian -specific missense CETP variant alters the lipid profile. HGG ADVANCES 2023; 4:100204. [PMID: 37250494 PMCID: PMC10209881 DOI: 10.1016/j.xhgg.2023.100204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/31/2023] Open
Abstract
Identifying population-specific genetic variants associated with disease and disease-predisposing traits is important to provide insights into the genetic determinants of health and disease between populations, as well as furthering genomic justice. Various common pan-population polymorphisms at CETP associate with serum lipid profiles and cardiovascular disease. Here, sequencing of CETP identified a missense variant rs1597000001 (p.Pro177Leu) specific to Māori and Pacific people that associates with higher HDL-C and lower LDL-C levels. Each copy of the minor allele associated with higher HDL-C by 0.236 mmol/L and lower LDL-C by 0.133 mmol/L. The rs1597000001 effect on HDL-C is comparable with CETP Mendelian loss-of-function mutations that result in CETP deficiency, consistent with our data, which shows that rs1597000001 lowers CETP activity by 27.9%. This study highlights the potential of population-specific genetic analyses for improving equity in genomics and health outcomes for population groups underrepresented in genomic studies.
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Affiliation(s)
- Jaye Moors
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Mohanraj Krishnan
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nick Sumpter
- Division of Clinical Rheumatology and Immunology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Riku Takei
- Division of Clinical Rheumatology and Immunology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matt Bixley
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Murray Cadzow
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Tanya J. Major
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Ruth Topless
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Marilyn Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Malcolm Rutledge
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Ben Morgan
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Jenna C. Carlson
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jerry Z. Zhang
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emily M. Russell
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Guangyun Sun
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Hong Cheng
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Daniel E. Weeks
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Take Naseri
- Ministry of Health, Apia, Samoa
- International Health Institute, Department of Epidemiology, School of Public Health, Brown University, Providence, RI, USA
| | | | | | - John Tuitele
- Department of Public Health, Lyndon B. Johnson Tropical Medical Center, Faga’alu, American Samoa, USA
| | - Nicola L. Hawley
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Ranjan Deka
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Stephen T. McGarvey
- International Health Institute, Department of Epidemiology, School of Public Health, Brown University, Providence, RI, USA
| | - Janak de Zoysa
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Rinki Murphy
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Lisa Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Mele Taumoepeau
- Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Frances King
- Ngāti Porou Hauora, Te Puia Springs, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Nuku Rapana
- Pukapukan Community Centre, Māngere, Auckland, New Zealand
| | - Sally McCormick
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Ryan L. Minster
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tony R. Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Division of Clinical Rheumatology and Immunology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Megan Leask
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Division of Clinical Rheumatology and Immunology, University of Alabama at Birmingham, Birmingham, AL, USA
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4
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Xue H, Zhang M, Liu J, Wang J, Ren G. Structure-based mechanism and inhibition of cholesteryl ester transfer protein. Curr Atheroscler Rep 2023; 25:155-166. [PMID: 36881278 PMCID: PMC10027838 DOI: 10.1007/s11883-023-01087-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
PURPOSE OF REVIEW Cholesteryl ester transfer proteins (CETP) regulate plasma cholesterol levels by transferring cholesteryl esters (CEs) among lipoproteins. Lipoprotein cholesterol levels correlate with the risk factors for atherosclerotic cardiovascular disease (ASCVD). This article reviews recent research on CETP structure, lipid transfer mechanism, and its inhibition. RECENT FINDINGS Genetic deficiency in CETP is associated with a low plasma level of low-density lipoprotein cholesterol (LDL-C) and a profoundly elevated plasma level of high-density lipoprotein cholesterol (HDL-C), which correlates with a lower risk of atherosclerotic cardiovascular disease (ASCVD). However, a very high concentration of HDL-C also correlates with increased ASCVD mortality. Considering that the elevated CETP activity is a major determinant of the atherogenic dyslipidemia, i.e., pro-atherogenic reductions in HDL and LDL particle size, inhibition of CETP emerged as a promising pharmacological target during the past two decades. CETP inhibitors, including torcetrapib, dalcetrapib, evacetrapib, anacetrapib and obicetrapib, were designed and evaluated in phase III clinical trials for the treatment of ASCVD or dyslipidemia. Although these inhibitors increase in plasma HDL-C levels and/or reduce LDL-C levels, the poor efficacy against ASCVD ended interest in CETP as an anti-ASCVD target. Nevertheless, interest in CETP and the molecular mechanism by which it inhibits CE transfer among lipoproteins persisted. Insights into the structural-based CETP-lipoprotein interactions can unravel CETP inhibition machinery, which can hopefully guide the design of more effective CETP inhibitors that combat ASCVD. Individual-molecule 3D structures of CETP bound to lipoproteins provide a model for understanding the mechanism by which CETP mediates lipid transfer and which in turn, guide the rational design of new anti-ASCVD therapeutics.
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Affiliation(s)
- Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jianjun Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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5
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Deng S, Liu J, Niu C. HDL and Cholesterol Ester Transfer Protein (CETP). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1377:13-26. [PMID: 35575918 DOI: 10.1007/978-981-19-1592-5_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cholesterol ester transfer protein (CETP) is important clinically and is one of the major targets in cardiovascular disease studies. With high conformational flexibility, its tunnel structure allows unforced movement of high-density lipoproteins (HDLs), VLDLs, and LDLs. Research in reverse cholesterol transports (RCT) reveals that the regulation of CETP activity can change the concentration of cholesteryl esters (CE) in HDLs, VLDLs, and LDLs. These molecular insights demonstrate the mechanisms of CETP activities and manifest the correlation between CETP and HDL. However, animal and cell experiments focused on CETP give controversial results. Inhibiting CETP is found to be beneficial to anti-atherosclerosis in terms of increasing plasma HDL-C, while it is also claimed that CETP weakens atherosclerosis formation by promoting RCT. Currently, the CETP-related drugs are still immature. Research on CETP inhibitors is targeted at improving efficacy and minimizing adverse reactions. As for CETP agonists, research has proved that they also can be used to resist atherosclerosis.
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Affiliation(s)
- Siying Deng
- Beijing Tiantan Hospital, China National Clinical Research Center for Neurological Diseases, Advanced Innovation Center for Human Brain Protection, The Capital Medical University, Beijing, China
| | | | - Chenguang Niu
- Key Laboratory of Clinical Resources Translation, First Affiliated Hospital, Henan University, Kaifeng, Henan, China.
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6
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Hao D, Wang H, Zang Y, Zhang L, Yang Z, Zhang S. Mechanism of Glycans Modulating Cholesteryl Ester Transfer Protein: Unveiled by Molecular Dynamics Simulation. J Chem Inf Model 2021; 62:5246-5257. [PMID: 33858135 DOI: 10.1021/acs.jcim.1c00233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Inhibition of the cholesteryl ester transfer protein (CETP) has been considered as a promising way for the treatment of cardiovascular disease (CVD) for three decades. However, clinical trials of several CETP inhibitors with various potencies have been marginally successful at best, raising doubts on the target drugability of CETP. The in-depth understanding of the glycosylated CETP structure could be beneficial to more definitive descriptions of the CETP function and the underlying mechanism. In this work, large-scale molecular dynamics simulations were performed to thoroughly explore the mechanism of glycans modulating CETP. Here, the extensive simulation results intensely suggest that glycan88 tends to assist CETP in forming a continuous tunnel throughout interacting with the upper-right region of the N-barrel, while it also could prevent the formation of a continuous tunnel by swinging toward the right-rear of the N-barrel. Furthermore, glycan240 formed stable H-bonds with Helix-B and might further stabilize the central cavity of CETP. Furthermore, the nonspecific involvement of the hydroxyl groups from the various glycans with protein core interactions and the similar influence of different glycans trapped at similar regions on the protein structure suggest that physiological glycan may lead to a similar effect. This study would provide valuable insights into devising novel methods for CVD treatment targeting CETP and functional studies about glycosylation for other systems.
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Affiliation(s)
- Dongxiao Hao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - He Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yongjian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.,School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
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7
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Moqadam M, Tubiana T, Moutoussamy EE, Reuter N. Membrane models for molecular simulations of peripheral membrane proteins. ADVANCES IN PHYSICS: X 2021. [DOI: 10.1080/23746149.2021.1932589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Mahmoud Moqadam
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Thibault Tubiana
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Emmanuel E. Moutoussamy
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
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8
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Izem L, Liu Y, Morton RE. Exon 9-deleted CETP inhibits full length-CETP synthesis and promotes cellular triglyceride storage. J Lipid Res 2020; 61:422-431. [PMID: 31988147 DOI: 10.1194/jlr.ra120000583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/27/2020] [Indexed: 11/20/2022] Open
Abstract
Cholesteryl ester transfer protein (CETP) exists as full-length (FL) and exon 9 (E9)-deleted isoforms. The function of E9-deleted CETP is poorly understood. Here, we investigated the role of E9-deleted CETP in regulating the secretion of FL-CETP by cells and explored its possible role in intracellular lipid metabolism. CETP overexpression in cells that naturally express CETP confirmed that E9-deleted CETP is not secreted, and showed that cellular FL- and E9-deleted CETP form an isolatable complex. Coexpression of CETP isoforms lowered cellular levels of both proteins and impaired FL-CETP secretion. These effects were due to reduced synthesis of both isoforms; however, the predominate consequence of FL- and E9-deleted CETP coexpression is impaired FL-CETP synthesis. We reported previously that reducing both CETP isoforms or overexpressing FL-CETP impairs cellular triglyceride (TG) storage. To investigate this further, E9-deleted CETP was expressed in SW872 cells that naturally synthesize CETP and in mouse 3T3-L1 cells that do not. E9-deleted CETP overexpression stimulated SW872 triglyceride synthesis and increased stored TG 2-fold. Expression of E9-deleted CETP in mouse 3T3-L1 cells produced a similar lipid phenotype. In vitro, FL-CETP promotes the transfer of TG from ER-enriched membranes to lipid droplets. E9-deleted CETP also promoted this transfer, although less effectively, and it inhibited the transfer driven by FL-CETP. We conclude that FL- and E9-deleted CETP isoforms interact to mutually decrease their intracellular levels and impair FL-CETP secretion by reducing CETP biosynthesis. E9-deleted CETP, like FL-CETP, alters cellular TG metabolism and storage but in a contrary manner.
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Affiliation(s)
- Lahoucine Izem
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Yan Liu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Richard E Morton
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
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9
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Cuban Sugar Cane Wax Acid and Policosanol Showed Similar Atheroprotective Effects with Inhibition of LDL Oxidation and Cholesteryl Ester Transfer via Enhancement of High-Density Lipoproteins Functionality. Cardiovasc Ther 2019; 2019:8496409. [PMID: 31772618 PMCID: PMC6739770 DOI: 10.1155/2019/8496409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/23/2019] [Accepted: 02/11/2019] [Indexed: 11/17/2022] Open
Abstract
Background Cuban sugarcane wax acids (SCWA) and policosanol (PCO) are mixtures of higher aliphatic acids and alcohols, respectively, purified from sugarcane wax with different chief components. Although it has been known that they have antioxidant and anti-inflammatory activities, physiological properties on molecular mechanism of SCWA have been less studied than PCO. Methods In this study, we compared antiatherogenic activities of SCWA and PCO via encapsulation with reconstituted high-density lipoproteins (rHDL). Results After reconstitution, SCWA-rHDL showed smaller particle size than PCO-rHDL with increase of content. PCO-rHDL or SCWA-rHDL showed distinct inhibition of glycation with similar extent in the presence of fructose. PCO-rHDL or SCWA-rHDL showed strong antioxidant activity against cupric ion-mediated oxidation of low-density lipoproteins (LDL), and inhibition of oxLDL uptake into macrophages. Although PCO-rHDL showed 1.2-fold stronger inhibition against cholesteryl ester transfer protein (CETP) activity than SCWA-rHDL, SCWA-rHDL enhanced 15% more brain cell (BV-2) growth and 23% more regeneration of tail fin in zebrafish. Conclusion PCO and SCWA both enhance the beneficial functions of HDL to maximize its antioxidant, antiglycation, and antiatherosclerotic activities and the inhibition of CETP. These enhancements of HDL functionality by PCO and SCWA could exert antiaging and rejuvenation activity.
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10
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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11
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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12
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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: 1.4] [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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13
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Revanasiddappa PD, Sankar R, Senapati S. Role of the Bound Phospholipids in the Structural Stability of Cholesteryl Ester Transfer Protein. J Phys Chem B 2018; 122:4239-4248. [DOI: 10.1021/acs.jpcb.7b12095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Prasanna D. Revanasiddappa
- BJM School of Biosciences and Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
| | - Revathi Sankar
- BJM School of Biosciences and Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sanjib Senapati
- BJM School of Biosciences and Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
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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: 1.9] [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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Yang Z, Cao Y, Hao D, Yuan X, Zhang L, Zhang S. Binding profiles of cholesterol ester transfer protein with current inhibitors: a look at mechanism and drawback. J Biomol Struct Dyn 2017; 36:2567-2580. [PMID: 28777919 DOI: 10.1080/07391102.2017.1363661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Zhiwei Yang
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
- Department of Applied Chemistry, School of Science, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yang Cao
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
| | - Dongxiao Hao
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Lei Zhang
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
| | - Shengli Zhang
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
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16
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Wong LH, Levine TP. Tubular lipid binding proteins (TULIPs) growing everywhere. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1439-1449. [PMID: 28554774 PMCID: PMC5507252 DOI: 10.1016/j.bbamcr.2017.05.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/11/2017] [Accepted: 05/17/2017] [Indexed: 12/27/2022]
Abstract
Tubular lipid binding proteins (TULIPs) have become a focus of interest in the cell biology of lipid signalling, lipid traffic and membrane contact sites. Each tubular domain has an internal pocket with a hydrophobic lining that can bind a hydrophobic molecule such as a lipid. This allows TULIP proteins to carry lipids through the aqueous phase. TULIP domains were first found in a large family of extracellular proteins related to the bacterial permeability-inducing protein (BPI) and cholesterol ester transfer protein (CETP). Since then, the same fold and lipid transfer capacity have been found in SMP domains (so-called for their occurrence in synaptotagmin, mitochondrial and lipid binding proteins), which localise to intracellular membrane contact sites. Here the methods for identifying known TULIPs are described, and used to find previously unreported TULIPs, one in the silk polymer and another in prokaryotes illustrated by the E. coli protein YceB. The bacterial TULIP alters views on the likely evolution of the domain, suggesting its presence in the last universal common ancestor. The major function of TULIPs is to handle lipids, but we still do not know how they work in detail, or how many more remain to be discovered. This article is part of a Special Issue entitled: Membrane Contact Sites edited by Christian Ungermann and Benoit Kornmann. Proteins with the tubular lipid binding fold exist in a wider variety than is usually appreciated. TULIPs are found in prokaryotes, altering views on their evolution. It is not yet known whether TULIPs transfer lipids as tunnels or as shuttles. Tests have not yet been done to say if TULIPs with SMP domains (for example E-syts and ERMES components) tether contact sites. It is likely that more TULIPs remain to be discovered.
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Affiliation(s)
- Louise H Wong
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Tim P Levine
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK.
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17
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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: 2.4] [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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18
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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: 2.1] [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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19
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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: 22] [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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20
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Lee EY, Yoo JA, Lim SM, Cho KH. Anti-Aging and Tissue Regeneration Ability of Policosanol Along with Lipid-Lowering Effect in Hyperlipidemic Zebrafish via Enhancement of High-Density Lipoprotein Functionality. Rejuvenation Res 2016; 19:149-58. [PMID: 26413884 PMCID: PMC4841090 DOI: 10.1089/rej.2015.1745] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We investigated the tissue regeneration and lipid-lowering effects of policosanol (PCO) by employing a hyperlipidemic zebrafish model. A reconstituted high-density lipoprotein containing policosanol (PCO-rHDL) facilitated greater cell growth and replication with less apoptosis and reactive oxygen species (ROS) production in BV-2 microglial cell lines. From in vivo study, injection of rHDL containing apolipoprotein A-I (ApoA-I) caused 76 ± 4% (p = 0.01) greater tissue regeneration activity than the phosphate-buffered saline (PBS) control, whereas PCO-rHDL caused 94 ± 7% (p = 0.002) increased regeneration. PCO in ethanol (EtOH) showed lower cholesteryl ester transfer protein (CETP) inhibitory ability than did anacetrapib, whereas PCO-rHDL showed higher inhibitory ability than anacetrapib, suggesting a synergistic effect between PCO and rHDL. Following 9 weeks of PCO consumption, the PCO group (0.003% PCO in Tetrabit) showed the highest survivability (80%), whereas normal diet (ND) and high-cholesterol diet (HCD) control groups showed 67% and 70% survival rates, respectively. Supplementation with a HCD resulted in two-fold elevation of CETP activity along with 3- and 2.5-fold increases in serum total cholesterol (TC) and triglycerides (TGs) levels, respectively. Consumption of PCO for 9 weeks resulted in 40 ± 5% (p = 0.01 vs. HCD) and 33 ± 4% (p = 0.02 vs. HCD) reduction of TC and TGs levels, respectively. Serum high-density lipoprotein cholesterol (HDL-C) level increased up to 37 ± 2 mg/dL (p = 0.004), whereas the percentage of HDL-C/TC increased up to 20 ± 2% from 5 ± 1% compared to the HCD control. The serum glucose level was reduced to 47 ± 2% (p = 0.002) compared to the HCD control. Fatty liver change and hepatic inflammation levels were remarkably increased upon HCD consumption and were two-fold higher than that under ND. However, the PCO group showed 58 ± 5% (p = 0.001) and 50 ± 3% (p = 0.006) reduction of inflammation enzyme levels and lipid content in hepatic tissue under HCD. In conclusion, PCO supplementation showed lipid-lowering and HDL-C-elevating effects with ameliorating fatty liver change. These in vivo anti-atherosclerotic and anti-diabetic effects of PCO are well associated with in vitro anti-apoptotic activities.
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Affiliation(s)
- Eun-Young Lee
- 1 School of Biotechnology, Yeungnam University , Gyeongsan, Republic of Korea.,2 Research Institute of Protein Sensor, Yeungnam University , Gyeongsan, Republic of Korea.,3 BK21plus Program Serum Biomedical Research and Education Team, Yeungnam University , Gyeongsan, Republic of Korea
| | - Jeong-Ah Yoo
- 1 School of Biotechnology, Yeungnam University , Gyeongsan, Republic of Korea.,2 Research Institute of Protein Sensor, Yeungnam University , Gyeongsan, Republic of Korea.,3 BK21plus Program Serum Biomedical Research and Education Team, Yeungnam University , Gyeongsan, Republic of Korea
| | - So-Mang Lim
- 1 School of Biotechnology, Yeungnam University , Gyeongsan, Republic of Korea.,2 Research Institute of Protein Sensor, Yeungnam University , Gyeongsan, Republic of Korea.,3 BK21plus Program Serum Biomedical Research and Education Team, Yeungnam University , Gyeongsan, Republic of Korea
| | - Kyung-Hyun Cho
- 1 School of Biotechnology, Yeungnam University , Gyeongsan, Republic of Korea.,2 Research Institute of Protein Sensor, Yeungnam University , Gyeongsan, Republic of Korea.,3 BK21plus Program Serum Biomedical Research and Education Team, Yeungnam University , Gyeongsan, Republic of Korea
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21
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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: 44] [Impact Index Per Article: 4.4] [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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