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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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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: 49] [Impact Index Per Article: 3.8] [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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Molecular structure of low density lipoprotein: current status and future challenges. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 38:145-58. [DOI: 10.1007/s00249-008-0368-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 08/28/2008] [Indexed: 01/01/2023]
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Johs A, Hammel M, Waldner I, May RP, Laggner P, Prassl R. Modular Structure of Solubilized Human Apolipoprotein B-100. J Biol Chem 2006; 281:19732-9. [PMID: 16704977 DOI: 10.1074/jbc.m601688200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Being intimately involved in cholesterol transport and lipid metabolism human low density lipoprotein (LDL) plays a prominent role in atherogenesis and cardiovascular diseases. The receptor-mediated cellular uptake of LDL is triggered by apolipoprotein B-100 (apoB-100), which represents the single protein moiety of LDL. Due to the size and hydrophobic nature of apoB-100, its structure is not well characterized. Here we present a low resolution structure of solubilized apoB-100. We have used small angle neutron scattering in combination with advanced shape reconstruction algorithms to generate a three-dimensional model of lipid-free apoB-100. Our model clearly reveals that apoB-100 is composed of distinct domains connected by flexible regions. The apoB-100 molecule adopts a curved shape with a central cavity. In comparison to LDL-associated apoB-100, the lipid-free protein is expanded, whereas according to spectroscopic data the secondary structure is widely preserved. Finally, the low resolution model was used as a template to reconstruct a hypothetical domain organization of apoB-100 on LDL, including information derived from a secondary structure prediction.
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Affiliation(s)
- Alexander Johs
- Institute of Biophysics and X-ray Structure Research, Austrian Academy of Sciences, Schmiedlstrasse 6, A-8042 Graz, Austria
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Bresson S, El Marssi M, Khelifa B. Raman spectroscopy investigation of various saturated monoacid triglycerides. Chem Phys Lipids 2005; 134:119-29. [PMID: 15784230 DOI: 10.1016/j.chemphyslip.2004.12.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Revised: 12/16/2004] [Accepted: 12/23/2004] [Indexed: 11/16/2022]
Abstract
A study of the vibrational behavior of five saturated monoacid triacylglycerides is performed by Raman spectroscopy at room temperature in the 3100-500 cm(-1) spectral range. The splitting of the CO stretching mode leads to conclude on the existence of two or three geometries of CO in the "knot" group OCO. The CO stretching mode seems to be a good tool for distinguishing the polymorphic forms of the studied triglycerides. The assignments of the different CH stretching modes are performed in the 1500-500 cm(-1) spectral range. The I(2845)/I(2880) (in the CH stretching spectral region) and I(1445)/I(1296) intensity ratios (between the maximal intensity I(1445) of the CH(2) scissoring mode and the maximal intensity I(1296) of the skeletal vibration of (CH(2))(n) in-phase twist) seem to depend on the type of polymorphic forms of these molecules.
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Affiliation(s)
- S Bresson
- Centre de Calcul et de Modélisation de Lens, Université d'Artois, Faculté Jean Perrin, SP 18, rue Jean Souvraz, 62307 LENS Cedex, France.
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Coronado-Gray A, van Antwerpen R. The physical state of the LDL core influences the conformation of apolipoprotein B-100 on the lipoprotein surface. FEBS Lett 2003; 533:21-4. [PMID: 12505152 DOI: 10.1016/s0014-5793(02)03731-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We assessed the influence of temperature on the secondary structure of apolipoprotein B-100 (apoB) in normal low-density lipoprotein (N-LDL) and triglyceride-rich LDL (T-LDL). Gradual heating from 7 degrees C to the phase-transition temperature of the lipoprotein core ( approximately 28 degrees C and approximately 15 degrees C for N-LDL and T-LDL, respectively) gradually altered the secondary structure of apoB, while further heating from the phase-transition temperature to 45 degrees C had no additional effect. Above the phase-transition temperature of the core, the apoBs of N-LDL and T-LDL had a similar secondary structure. These results indicate that the conformation of apoB on the LDL surface depends strongly on the physical state of the lipoprotein core, and less on the lipid composition of the core per se.
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Affiliation(s)
- Andrea Coronado-Gray
- Department of Biochemistry and Molecular Biophysics, Medical College of Virginia Campus, Virginia Commonwealth University, P.O. Box 980614, Richmond, VA 23298, USA
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Segrest JP, Jones MK, De Loof H, Dashti N. Structure of apolipoprotein B-100 in low density lipoproteins. J Lipid Res 2001. [DOI: 10.1016/s0022-2275(20)30267-4] [Citation(s) in RCA: 359] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Orlova EV, Sherman MB, Chiu W, Mowri H, Smith LC, Gotto AM. Three-dimensional structure of low density lipoproteins by electron cryomicroscopy. Proc Natl Acad Sci U S A 1999; 96:8420-5. [PMID: 10411890 PMCID: PMC17531 DOI: 10.1073/pnas.96.15.8420] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human low density lipoproteins (LDL) are the major cholesterol carriers in the blood. Elevated concentration of LDL is a major risk factor for atherosclerotic disease. Purified LDL particles appear heterogeneous in images obtained with a 400-kV electron cryomicroscope. Using multivariate statistical and cluster analyses, an ensemble of randomly oriented particle images has been subdivided into homogeneous subpopulations, and the largest subset was used for three-dimensional reconstruction. In contrast to the general belief that below the lipid phase-transition temperature (30 degrees C) LDL are quasi-spherical microemulsion particles with a radially layered core-shell organization, our three-dimensional map shows that LDL have a well-defined and stable organization. Particles consist of a higher-density outer shell and lower-density inner lamellae-like layers that divide the core into compartments. The outer shell consists of apolipoprotein B-100, phospholipids, and some free cholesterol.
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Affiliation(s)
- E V Orlova
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
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Halle M, Berg A, Garwers U, Baumstark MW, Knisel W, Grathwohl D, König D, Keul J. Influence of 4 weeks' intervention by exercise and diet on low-density lipoprotein subfractions in obese men with type 2 diabetes. Metabolism 1999; 48:641-4. [PMID: 10337867 DOI: 10.1016/s0026-0495(99)90064-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Insulin resistance is associated with dyslipoproteinemia characterized by increased serum triglycerides, reduced high-density lipoprotein 2 (HDL2) cholesterol, and increased small, dense low-density lipoprotein (LDL) subfraction particles. Physical activity and weight reduction are known to improve insulin resistance and dyslipoproteinemia, but their influence on LDL subfractions in diabetic patients is unknown. Therefore, we investigated the effect of a 4-week intervention program of exercise (2,200 kcal/wk) and diet (1,000 kcal/d: 50% carbohydrate, 25% protein, and 25% fat; polyunsaturated/saturated fat ratio, 1.0) on glycemic control and HDL and LDL subfractions in 34 obese patients with non-insulin-dependent diabetes (age, 49 +/- 9 years; body mass index [BMI], 33.1 +/- 5.1 kg/m2). Reductions in body weight (P < .001) and improvements in fasting blood glucose, insulin, fructosamine (P < .001), and free fatty acids (P < .01) by intervention were associated with reductions in serum cholesterol and apolipoprotein B (apo B) concentrations in very-low-density lipoprotein (VLDL) (P < .01), intermediate-density lipoprotein (IDL), and small, dense (>1.040 g/mL) LDL particles (P < .001). These data underlie the positive influence of weight reduction induced by exercise and diet on insulin resistance and lipoprotein metabolism in obese diabetic patients, particularly showing improvements of the LDL subfraction profile with a decrease of small, dense LDL particles. This is of particular importance, as these particles have been shown to be associated with coronary artery disease.
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Affiliation(s)
- M Halle
- Center for Internal Medicine, Department of Rehabilitation, Prevention and Sports Medicine, Freiburg University Hospital, Germany
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