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Gianazza E, Zoanni B, Mallia A, Brioschi M, Colombo GI, Banfi C. Proteomic studies on apoB-containing lipoprotein in cardiovascular research: A comprehensive review. MASS SPECTROMETRY REVIEWS 2023; 42:1397-1423. [PMID: 34747518 DOI: 10.1002/mas.21747] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/05/2021] [Accepted: 08/16/2021] [Indexed: 06/07/2023]
Abstract
The complexity of cardiovascular diseases (CVDs), which remains the leading cause of death worldwide, makes the current clinical pathway for cardiovascular risk assessment unsatisfactory, as there remains a substantial unexplained residual risk. Simultaneous assessment of a large number of plasma proteins may be a promising tool to further refine risk assessment, and lipoprotein-associated proteins have the potential to fill this gap. Technical advances now allow for high-throughput proteomic analysis in a reproducible and cost-effective manner. Proteomics has great potential to identify and quantify hundreds of candidate marker proteins in a sample and allows the translation from isolated lipoproteins to whole plasma, thus providing an individual multiplexed proteomic fingerprint. This narrative review describes the pathophysiological roles of atherogenic apoB-containing lipoproteins and the recent advances in their mass spectrometry-based proteomic characterization and quantitation for better refinement of CVD risk assessment.
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Affiliation(s)
| | | | - Alice Mallia
- Centro Cardiologico Monzino, IRCCS, Milano, Italy
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2
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Point AD, Crimmins BS, Holsen TM, Fernando S, Hopke PK, Darie CC. Can blood proteome diversity among fish species help explain perfluoroalkyl acid trophodynamics in aquatic food webs? THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162337. [PMID: 36848995 DOI: 10.1016/j.scitotenv.2023.162337] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/22/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are a diverse family of industrially significant synthetic chemicals infamous for extreme environmental persistence and global environmental distribution. Many PFAS are bioaccumulative and biologically active mainly due to their tendency to bind with various proteins. These protein interactions are important in determining the accumulation potential and tissue distribution of individual PFAS. Trophodynamics studies including aquatic food webs present inconsistent evidence for PFAS biomagnification. This study strives to identify whether the observed variability in PFAS bioaccumulation potential among species could correspond with interspecies protein composition differences. Specifically, this work compares the perfluorooctane sulfonate (PFOS) serum protein binding potential and the tissue distribution of ten perfluoroalkyl acids (PFAAs) detected in alewife (Alosa pseudoharengus), deepwater sculpin (Myoxocephalus thompsonii), and lake trout (Salvelinus namaycush) of the Lake Ontario aquatic piscivorous food web. These three fish sera and fetal bovine reference serum all had unique total serum protein concentrations. Serum protein-PFOS binding experiments showed divergent patterns between fetal bovine serum and fish sera, suggesting potentially two different PFOS binding mechanisms. To identify interspecies differences in PFAS-binding serum proteins, fish sera were pre-equilibrated with PFOS, fractionated by serial molecular weight cut-off filter fractionation, followed by liquid chromatography-tandem mass spectrometry analysis of the tryptic protein digests and the PFOS extracts of each fraction. This workflow identified similar serum proteins for all fish species. However, serum albumin was only identified in lake trout, suggesting apolipoproteins are likely the primary PFAA transporters in alewife and deepwater sculpin sera. PFAA tissue distribution analysis provided supporting evidence for interspecies variations in lipid transport and storage, which may also contribute to the varied PFAA accumulation in these species. Proteomics data are available via ProteomeXchange with identifier PXD039145.
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Affiliation(s)
- Adam D Point
- Institute for a Sustainable Environment, Clarkson University, Potsdam, NY, United States of America.
| | - Bernard S Crimmins
- Civil and Environmental Engineering, Clarkson University, Potsdam, NY, United States of America; AEACS, LLC, New Kensington, PA, United States of America
| | - Thomas M Holsen
- Civil and Environmental Engineering, Clarkson University, Potsdam, NY, United States of America; Center for Air and Aquatic Resources Engineering and Science, Clarkson University, Potsdam, NY, United States of America
| | - Sujan Fernando
- Center for Air and Aquatic Resources Engineering and Science, Clarkson University, Potsdam, NY, United States of America
| | - Philip K Hopke
- Institute for a Sustainable Environment, Clarkson University, Potsdam, NY, United States of America; Department of Public Health Sciences, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, United States of America
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3
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Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi. Curr Issues Mol Biol 2022; 44:2069-2088. [PMID: 35678669 PMCID: PMC9164042 DOI: 10.3390/cimb44050140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 11/17/2022] Open
Abstract
An important step in the proteomic analysis of missing proteins is the use of a wide range of tissues, optimal extraction, and the processing of protein material in order to ensure the highest sensitivity in downstream protein detection. This work describes a purification protocol for identifying low-abundance proteins in human chorionic villi using the proposed “1DE-gel concentration” method. This involves the removal of SDS in a short electrophoresis run in a stacking gel without protein separation. Following the in-gel digestion of the obtained holistic single protein band, we used the peptide mixture for further LC–MS/MS analysis. Statistically significant results were derived from six datasets, containing three treatments, each from two tissue sources (elective or missed abortions). The 1DE-gel concentration increased the coverage of the chorionic villus proteome. Our approach allowed the identification of 15 low-abundance proteins, of which some had not been previously detected via the mass spectrometry of trophoblasts. In the post hoc data analysis, we found a dubious or uncertain protein (PSG7) encoded on human chromosome 19 according to neXtProt. A proteomic sample preparation workflow with the 1DE-gel concentration can be used as a prospective tool for uncovering the low-abundance part of the human proteome.
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4
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Detection of simultaneous production of kurstakin, fengycin and surfactin lipopeptides in Bacillus mojavensis using a novel gel-based method and MALDI-TOF spectrometry. World J Microbiol Biotechnol 2021; 37:97. [PMID: 33969441 DOI: 10.1007/s11274-021-03064-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/23/2021] [Indexed: 10/21/2022]
Abstract
Bacterial lipopeptides have become a research focus of many studies owing to their industrial and pharmaceutical importance. Although such studies focused on researching purification procedures and qualitative analysis, much remains to be explored and developed to improve the current methods. To enable thorough studies of lipopeptides, this paper describes a new method for purification and characterization of in-gel anionic lipopeptides. Specifically, lipopeptides attributed to the anti-staphylococcal activity of Bacillus mojavensis HF were separated using SDS-PAGE (sodium dodecyl sulphate-polyacrylamide gel electrophoresis) and subsequently characterized using mass spectrometry. Lipopeptide band obtained by gel electrophoresis was first visualized using three different staining methods. Next, the lipopeptide isomers were efficiently recovered from the gel band and structural characterization of the extracted lipopeptides was carried out by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). MS analysis revealed that Bacillus mojavensis HF produced three types of lipopeptides including surfactin, fengycin, and kurstakin. 14 clusters of ion peaks were identified as fengycin A with fatty acid of C15-C17, fengycin B (C16, C17), surfactin (C13-C16), and kurstakin (C9-C12). Moreover, tandem mass spectrometric analysis (MS/MS) revealed the sequences of fengycin A and surfactin. In this study, we identified a high variety and number of surfactin and fengycin isomers, which previous reports lacked. To the best of our knowledge, we are the first to report the presence of kurstakin in Bacillus mojavensis species. Finally, we demonstrated that our gel-based study of lipopeptides allowed for a precise and reproducible investigation of these molecules.
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5
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Dolui AK, Vijayaraj P. A solvent-free delipidation method for functional validation of lipases. 3 Biotech 2020; 10:343. [PMID: 32714738 DOI: 10.1007/s13205-020-02338-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 07/12/2020] [Indexed: 10/23/2022] Open
Abstract
Extracting protein in its active form is critical for its functional characterization, and lipid removal is an essential step in the protein extraction process for further downstream applications. In the present study, we revisited the delipidation protocol and developed a rapid, solvent-free delipidation method using activated silica. The delipidated samples showed improved optical clarity and a significant reduction of endogenous lipids. The functional integrity of the lipases present in the delipidated sample was validated by in vitro enzyme assay using physiological substrate which includes neutral lipid as well as phospholipid. The accessibility of active site of the extracted enzymes was demonstrated by activity-based protein profiling (ABPP), a functional chemoproteomic approach. Detection of serine hydrolases using ABPP probe labeling was enhanced upon delipidation. Further, the total polyphenol content was significantly reduced, which helps to enhance the protein enrichment and small-molecule inhibitor screening by ABPP. Collectively, these results suggest that the present solvent-free delipidation approach is efficient and highly compatible with the functional characterization of the enzymes, particularly lipid hydrolases.
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6
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Awad D, Brueck T. Optimization of protein isolation by proteomic qualification from Cutaneotrichosporon oleaginosus. Anal Bioanal Chem 2020; 412:449-462. [PMID: 31797019 PMCID: PMC6992551 DOI: 10.1007/s00216-019-02254-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/23/2019] [Accepted: 10/30/2019] [Indexed: 11/03/2022]
Abstract
In the last decades, microbial oils have been extensively investigated as a renewable platform for biofuel and oleochemical production. Offering a potent alternative to plant-based oils, oleaginous microorganisms have been the target of ongoing metabolic engineering aimed at increasing growth and lipid yields, in addition to specialty fatty acids. Discovery proteomics is an attractive tool for elucidating lipogenesis and identifying metabolic bottlenecks, feedback regulation, and competing biosynthetic pathways. One prominent microbial oil producer is Cutaneotrichosporon oleaginosus, due to its broad feedstock catabolism and high lipid yield. However, this yeast has a recalcitrant cell wall and high cell lipid content, which complicates efficient and unbiased protein extraction for downstream proteomic analysis. Optimization efforts of protein sample preparation from C. oleaginosus in the present study encompasses the comparison of 8 lysis methods, 13 extraction buffers, and 17 purification methods with respect to protein abundance, proteome coverage, applicability, and physiochemical properties (pI, MW, hydrophobicity in addition to COG, and GO analysis). The optimized protocol presented in this work entails a one-step extraction method utilizing an optimal lysis method (liquid homogenization), which is augmented with a superior extraction buffer (50 mM Tris, 8/2 M Urea/Thiourea, and 1% C7BzO), followed by either of 2 advantageous purification methods (hexane/ethanol or TCA/acetone), depending on subsequent applications and target studies. This work presents a significant step forward towards implementation of efficient C. oleaginosus proteome mining for the identification of potential targets for genetic optimization of this yeast to improve lipogenesis and production of specialty lipids. Graphical abstract.
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Affiliation(s)
- Dania Awad
- Werner Siemens-Lehrstuhl für Synthetische Biotechnologie, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Thomas Brueck
- Werner Siemens-Lehrstuhl für Synthetische Biotechnologie, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany.
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7
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Bhattacharjee P, Öhrfelt A, Lashley T, Blennow K, Brinkmalm A, Zetterberg H. Mass Spectrometric Analysis of Lewy Body-Enriched α-Synuclein in Parkinson’s Disease. J Proteome Res 2019; 18:2109-2120. [DOI: 10.1021/acs.jproteome.8b00982] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Payel Bhattacharjee
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Annika Öhrfelt
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Tammaryn Lashley
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, U.K
- Queen Square Brain Bank for Neurological Diseases, UCL Institute of Neurology, London WC1N 3BG, U.K
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, S-431 80 Mölndal, Sweden
| | - Ann Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, S-431 80 Mölndal, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, U.K
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, S-431 80 Mölndal, Sweden
- UK Dementia Research Institute at UCL, London WC1N 3BG, U.K
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8
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Maternal consumption of fish oil programs reduced adiposity in broiler chicks. Sci Rep 2017; 7:13129. [PMID: 29030616 PMCID: PMC5640664 DOI: 10.1038/s41598-017-13519-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022] Open
Abstract
Maternal intake of eicosapentaenoic acid (EPA; 20:5 n-3) and docosahexaenoic acid (22:6 n-3) has been associated with reduced adiposity in children, suggesting the possibility to program adipose development through dietary fatty acids before birth. This study determined if enriching the maternal diet in fish oil, the primary source of EPA and DHA, affected adipose development in offspring. Broiler chickens were used because they are obesity-prone, and because fatty acids provided to the embryo can be manipulated through the hen diet. Hens were fed diets supplemented (2.8% wt:wt) with corn oil (CO; n-6) or fish oil (FO; n-3) for 28 d. Chicks from both maternal diet groups were fed the same diet after hatch. Maternal FO consumption enriched chick adipose tissue in EPA and DHA and reduced adiposity by promoting more, but smaller, adipocytes. This adipocyte profile was paralleled by lower expression of the adipogenic regulator PPARG and its co-activator PPARGC1B, and elevated expression of LPL. Proteomics identified 95 differentially abundant proteins between FO and CO adipose tissue, including components of glucose metabolism, lipid droplet trafficking, and cytoskeletal organization. These results demonstrate that the maternal dietary fatty acid profile programs offspring adipose development.
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9
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Moore S, Hess S, Jorgenson J. Characterization of an immobilized enzyme reactor for on-line protein digestion. J Chromatogr A 2016; 1476:1-8. [PMID: 27876348 PMCID: PMC5136339 DOI: 10.1016/j.chroma.2016.11.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/29/2016] [Accepted: 11/13/2016] [Indexed: 01/05/2023]
Abstract
Despite the developments for faster liquid chromatographic and mass spectral detection techniques, the standard in-solution protein digestion for proteomic analyses has remained relatively unchanged. The typical in-solution trypsin protein digestion is usually the slowest part of the workflow, albeit one of the most important. The development of a highly efficient immobilized enzyme reactor (IMER) with rapid performance for on-line protein digestion would greatly decrease the analysis time involved in a proteomic workflow. Presented here is the development of a silica based IMER for on-line protein digestion, which produced rapid digestions in the presence of organic mobile phase for both model proteins and a complex sample consisting of the insoluble portion of a yeast cell lysate. Protein sequence coverage and identifications evaluated between the IMER and in-solution digestions were comparable. Overall, for a yeast cell lysate with only a 10s volumetric residence time on-column, the IMER identified 507 proteins while the in-solution digestion identified 490. There were no significant differences observed based on identified protein's molecular weight or isoelectric point between the two digestion methods. Implementation of the IMER into the proteomic workflow provided similar protein identification results, automation for sample analysis, and reduced the analysis time by 15h.
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Affiliation(s)
- Stephanie Moore
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States
| | - Stephanie Hess
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States
| | - James Jorgenson
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States.
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10
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Moore SM, Hess SM, Jorgenson JW. Extraction, Enrichment, Solubilization, and Digestion Techniques for Membrane Proteomics. J Proteome Res 2016; 15:1243-52. [PMID: 26979493 PMCID: PMC5488330 DOI: 10.1021/acs.jproteome.5b01122] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The importance of membrane proteins in biological systems is indisputable; however, their amphipathic nature makes them difficult to analyze. In this study, the most popular techniques for extraction, enrichment, solubilization, and digestion are compared, resulting in an overall improved workflow for the insoluble portion of Saccharomyces cerevisiae cell lysate. Yeast cells were successfully lysed using a French press pressure cell at 20 000 psi, and resulting proteins were fractionated prior to digestion to reduce sample complexity. The proteins were best solubilized with the addition of ionic detergent sodium deoxycholate (1%) and through the application of high-frequency sonication prior to a tryptic digestion at 37 °C. Overall, the improved membrane proteomic workflow resulted in a 26% increase in membrane protein identifications for baker's yeast. In addition, more membrane protein identifications were unique to the improved protocol. When comparing membrane proteins that were identified in the improved protocol and the standard operating procedure (176 proteins), 93% of these proteins were present in greater abundance (higher intensity) when using the improved method.
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Affiliation(s)
- Stephanie M. Moore
- Chemistry Department University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephanie M. Hess
- Chemistry Department University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - James W. Jorgenson
- Chemistry Department University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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11
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Mangrum JB, Martin EJ, Brophy DF, Hawkridge AM. Intact stable isotope labeled plasma proteins from the SILAC-labeled HepG2 secretome. Proteomics 2015; 15:3104-15. [DOI: 10.1002/pmic.201400369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/05/2014] [Accepted: 12/05/2014] [Indexed: 01/26/2023]
Affiliation(s)
- John B. Mangrum
- Department of Pharmaceutics; Virginia Commonwealth University; Richmond VA USA
| | - Erika J. Martin
- Department of Pharmacotherapy & Outcomes Science; Virginia Commonwealth University; Richmond VA USA
| | - Donald F. Brophy
- Department of Pharmacotherapy & Outcomes Science; Virginia Commonwealth University; Richmond VA USA
| | - Adam M. Hawkridge
- Department of Pharmaceutics; Virginia Commonwealth University; Richmond VA USA
- Department of Pharmacotherapy & Outcomes Science; Virginia Commonwealth University; Richmond VA USA
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12
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Kontush A, Lindahl M, Lhomme M, Calabresi L, Chapman MJ, Davidson WS. Structure of HDL: particle subclasses and molecular components. Handb Exp Pharmacol 2015; 224:3-51. [PMID: 25522985 DOI: 10.1007/978-3-319-09665-0_1] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
A molecular understanding of high-density lipoprotein (HDL) will allow a more complete grasp of its interactions with key plasma remodelling factors and with cell-surface proteins that mediate HDL assembly and clearance. However, these particles are notoriously heterogeneous in terms of almost every physical, chemical and biological property. Furthermore, HDL particles have not lent themselves to high-resolution structural study through mainstream techniques like nuclear magnetic resonance and X-ray crystallography; investigators have therefore had to use a series of lower resolution methods to derive a general structural understanding of these enigmatic particles. This chapter reviews current knowledge of the composition, structure and heterogeneity of human plasma HDL. The multifaceted composition of the HDL proteome, the multiple major protein isoforms involving translational and posttranslational modifications, the rapidly expanding knowledge of the HDL lipidome, the highly complex world of HDL subclasses and putative models of HDL particle structure are extensively discussed. A brief history of structural studies of both plasma-derived and recombinant forms of HDL is presented with a focus on detailed structural models that have been derived from a range of techniques spanning mass spectrometry to molecular dynamics.
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Affiliation(s)
- Anatol Kontush
- National Institute for Health and Medical Research (INSERM), UMR-ICAN 1166, Paris, France,
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13
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Zheleznova NN, Yang C, Ryan RP, Halligan BD, Liang M, Greene AS, Cowley AW. Mitochondrial proteomic analysis reveals deficiencies in oxygen utilization in medullary thick ascending limb of Henle in the Dahl salt-sensitive rat. Physiol Genomics 2012; 44:829-42. [PMID: 22805345 DOI: 10.1152/physiolgenomics.00060.2012] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The renal medullary thick ascending limb (mTAL) of the Dahl salt-sensitive (SS) rat is the site of enhanced NaCl reabsorption and excess superoxide production. In the present studies we isolated mitochondria from mTAL of SS and salt-resistant control strain SS.13(BN) rats on 0.4 and 8% salt diet for 7 days and performed a proteomic analysis. Purity of mTAL and mitochondria isolations exceeded 93.6 and 55%, respectively. Using LC/MS spectral analysis techniques we identified 96 mitochondrial proteins in four biological mTAL mitochondria samples, run in duplicate, as defined by proteins with a false discovery rate <5% and scan count ≥2. Seven of these 96 proteins, including IDH2, ACADM, SCOT, Hsp60, ATPA, EFTu, and VDAC2 were differentially expressed between the two rat strains. Oxygen consumption and high-resolution respirometry analyses showed that mTAL cells and the mitochondria in the outer medulla of SS rats fed high-salt diet exhibited lower rates of oxygen utilization compared with those from SS.13(BN) rats. These studies advance the conventional proteomic paradigm of focusing exclusively upon whole tissue homogenates to a focus upon a single cell type and specific subcellular organelle. The results reveal the importance of a largely unexplored role for deficiencies of mTAL mitochondrial metabolism and oxygen utilization in salt-induced hypertension and renal medullary oxidative stress.
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Affiliation(s)
- Nadezhda N Zheleznova
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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14
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Zhang S, Chang Z, Li Z, DuanMu H, Li Z, Li K, Liu Y, Qiu F, Xu Y. Calculating phenotypic similarity between genes using hierarchical structure data based on semantic similarity. Gene 2012; 497:58-65. [PMID: 22305981 DOI: 10.1016/j.gene.2012.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 01/16/2012] [Accepted: 01/18/2012] [Indexed: 01/25/2023]
Abstract
Phenotypic similarity is correlated with a number of measures of gene function, such as relatedness at the level of direct protein-protein interaction. The phenotypic effect of a deleted or mutated gene, which is one part of gene annotation, has caught broad attention. However, there have been few measures to study phenotypic similarity with the data from Human Phenotype Ontology (HPO) database, therefore more analogous measures should be developed and investigated. We used five semantic similarity-based measures (Jiang and Conrath, Lin, Schlicker, Yu and Wu) to calculate the human phenotypic similarity between genes (PSG) with data from HPO database, and evaluated their accuracy with information of protein-protein interaction, protein complex, protein family, gene function or DNA sequence. Compared with the gene pairs that were random selected, the results of these methods were statistically significant (all P<0.001). Furthermore, we assessed the performance of these five measures by receiver operating characteristic (ROC) curve analysis, and found that most of them performed better than the previous methods. This work had proved that these measures based on semantic similarity for calculation of PSG were effective for hierarchical structure data. Our study contributes to the development and optimization of novel algorithms of PSG calculation and provides more alternative methods to researchers as well as tools and directions for PSG study.
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Affiliation(s)
- Shanzhen Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
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15
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Barrera NP, Robinson CV. Advances in the mass spectrometry of membrane proteins: from individual proteins to intact complexes. Annu Rev Biochem 2011; 80:247-71. [PMID: 21548785 DOI: 10.1146/annurev-biochem-062309-093307] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rapid advances in structural genomics and in large-scale proteomic projects have yielded vast amounts of data on soluble proteins and their complexes. Despite these advances, progress in studying membrane proteins using mass spectrometry (MS) has been slow. This is due in part to the inherent solubility and dynamic properties of these proteins, but also to their low abundance and the absence of polar side chains in amino acid residues. Considerable progress in overcoming these challenges is, however, now being made for all levels of structural characterization. This progress includes MS studies of the primary structure of membrane proteins, wherein sophisticated enrichment and trapping procedures are allowing multiple posttranslational modifications to be defined through to the secondary structure level in which proteins and peptides have been probed using hydrogen exchange, covalent, or radiolytic labeling methods. Exciting possibilities now exist to go beyond primary and secondary structure to reveal the tertiary and quaternary interactions of soluble and membrane subunits within intact assemblies of more than 700 kDa.
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Affiliation(s)
- Nelson P Barrera
- Department of Physiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile.
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16
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Sajic T, Hopfgartner G, Szanto I, Varesio E. Comparison of three detergent-free protein extraction protocols for white adipose tissue. Anal Biochem 2011; 415:215-7. [PMID: 21565151 DOI: 10.1016/j.ab.2011.04.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/04/2011] [Accepted: 04/08/2011] [Indexed: 12/13/2022]
Abstract
A comparative study of three detergent-free protein extraction protocols--a differential centrifugal fractionation, a delipidation protocol based on the Bligh and Dyer method, and the trifluoroethanol addition as cosolvent to an aqueous buffer--was performed on white adipose tissue. The performance of the protocols directly compatible with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) was evaluated based on the total protein extraction yield and the protein recovery from different functional and cellular compartments. The most suitable method for the extraction of white adipose tissue proteins from a wide range of cellular and structural compartments was the delipidation protocol based on the Bligh and Dyer method.
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Affiliation(s)
- Tatjana Sajic
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
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Hoofnagle AN, Heinecke JW. Lipoproteomics: using mass spectrometry-based proteomics to explore the assembly, structure, and function of lipoproteins. J Lipid Res 2010; 50:1967-75. [PMID: 19738003 DOI: 10.1194/jlr.r900015-jlr200] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Lipoproteins are centrally important in lipid transport, fuel metabolism, and cardiovascular disease. The prototypic lipoprotein has an outer shell of amphipathic lipids and proteins that solubilizes a hydrophobic lipid core. Lipoprotein-associated proteins have classically been viewed as structural elements and factors important in lipid metabolism. Recent mass spectrometric analyses reveal that the protein cargo of lipoproteins is much more diverse than previously appreciated, raising the possibility that lipoproteins play previously unsuspected roles in host defense mechanisms and inflammation. They further suggest that lipoprotein-associated proteins can identify humans at increased risk of cardiovascular disease. Here, we summarize recent developments in lipoproteomics, the proteomic analysis of lipoproteins. We also discuss the promises and challenges this powerful analytical strategy offers for expanding our understanding of the biology and structures of lipoproteins.
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Affiliation(s)
- Andrew N Hoofnagle
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
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Kontush A, Chapman MJ. Lipidomics as a tool for the study of lipoprotein metabolism. Curr Atheroscler Rep 2010; 12:194-201. [PMID: 20425259 DOI: 10.1007/s11883-010-0100-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Although technologies for lipidomic and proteomic investigations have developed very recently, lipidomic and proteomic studies of plasma lipoproteins have already provided several impressive examples of detailed characterization of distinct metabolic pathways potentially involved in lipoprotein metabolism in both health and disease states (obesity, insulin resistance, fatty liver disease) as well as under lifestyle and dietary modification (fish consumption, carbohydrates, probiotics) and lipid-modifying treatments (statins, low-density lipoprotein apheresis). Available lipidomic methodologies have facilitated detailed characterization of lipid classes and molecular species present in plasma as well as in lipoprotein fractions. Together with emerging proteomic techniques, lipidomics of plasma lipoproteins will soon provide molecular details of lipoprotein composition, which will ultimately be translated into integrated knowledge of the structure, metabolism, and function of lipoproteins in health and disease.
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Affiliation(s)
- Anatol Kontush
- Université Pierre et Marie Curie-Paris 6, Paris, 75013, France.
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