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Wilkinson DJ, Crossland H, Atherton PJ. Metabolomic and proteomic applications to exercise biomedicine. TRANSLATIONAL EXERCISE BIOMEDICINE 2024; 1:9-22. [PMID: 38660119 PMCID: PMC11036890 DOI: 10.1515/teb-2024-2006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 04/26/2024]
Abstract
Objectives 'OMICs encapsulates study of scaled data acquisition, at the levels of DNA, RNA, protein, and metabolite species. The broad objectives of OMICs in biomedical exercise research are multifarious, but commonly relate to biomarker development and understanding features of exercise adaptation in health, ageing and metabolic diseases. Methods This field is one of exponential technical (i.e., depth of feature coverage) and scientific (i.e., in health, metabolic conditions and ageing, multi-OMICs) progress adopting targeted and untargeted approaches. Results Key findings in exercise biomedicine have led to the identification of OMIC features linking to heritability or adaptive responses to exercise e.g., the forging of GWAS/proteome/metabolome links to cardiovascular fitness and metabolic health adaptations. The recent addition of stable isotope tracing to proteomics ('dynamic proteomics') and metabolomics ('fluxomics') represents the next phase of state-of-the-art in 'OMICS. Conclusions These methods overcome limitations associated with point-in-time 'OMICs and can be achieved using substrate-specific tracers or deuterium oxide (D2O), depending on the question; these methods could help identify how individual protein turnover and metabolite flux may explain exercise responses. We contend application of these methods will shed new light in translational exercise biomedicine.
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Affiliation(s)
- Daniel J. Wilkinson
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
| | - Hannah Crossland
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
| | - Philip J. Atherton
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
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Personnaz J, Piccolo E, Dortignac A, Iacovoni JS, Mariette J, Rocher V, Polizzi A, Batut A, Deleruyelle S, Bourdens L, Delos O, Combes-Soia L, Paccoud R, Moreau E, Martins F, Clouaire T, Benhamed F, Montagner A, Wahli W, Schwabe RF, Yart A, Castan-Laurell I, Bertrand-Michel J, Burlet-Schiltz O, Postic C, Denechaud PD, Moro C, Legube G, Lee CH, Guillou H, Valet P, Dray C, Pradère JP. Nuclear HMGB1 protects from nonalcoholic fatty liver disease through negative regulation of liver X receptor. SCIENCE ADVANCES 2022; 8:eabg9055. [PMID: 35333579 PMCID: PMC8956270 DOI: 10.1126/sciadv.abg9055] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Dysregulations of lipid metabolism in the liver may trigger steatosis progression, leading to potentially severe clinical consequences such as nonalcoholic fatty liver diseases (NAFLDs). Molecular mechanisms underlying liver lipogenesis are very complex and fine-tuned by chromatin dynamics and multiple key transcription factors. Here, we demonstrate that the nuclear factor HMGB1 acts as a strong repressor of liver lipogenesis. Mice with liver-specific Hmgb1 deficiency display exacerbated liver steatosis, while Hmgb1-overexpressing mice exhibited a protection from fatty liver progression when subjected to nutritional stress. Global transcriptome and functional analysis revealed that the deletion of Hmgb1 gene enhances LXRα and PPARγ activity. HMGB1 repression is not mediated through nucleosome landscape reorganization but rather via a preferential DNA occupation in a region carrying genes regulated by LXRα and PPARγ. Together, these findings suggest that hepatocellular HMGB1 protects from liver steatosis development. HMGB1 may constitute a new attractive option to therapeutically target the LXRα-PPARγ axis during NAFLD.
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Affiliation(s)
- Jean Personnaz
- Institut RESTORE, UMR 1301, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS-Université Paul Sabatier, Université de Toulouse, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Enzo Piccolo
- Institut RESTORE, UMR 1301, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS-Université Paul Sabatier, Université de Toulouse, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Alizée Dortignac
- Institut RESTORE, UMR 1301, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS-Université Paul Sabatier, Université de Toulouse, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Jason S. Iacovoni
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Jérôme Mariette
- MIAT, Université de Toulouse, INRAE, 31326 Castanet-Tolosan, France
| | - Vincent Rocher
- Molecular, Cellular, and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Arnaud Polizzi
- Toxalim, INRAE UMR 1331, ENVT, INP-Purpan, University of Toulouse, Paul Sabatier University, F-31027, Toulouse, France
| | - Aurélie Batut
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Simon Deleruyelle
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Lucas Bourdens
- Institut RESTORE, UMR 1301, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS-Université Paul Sabatier, Université de Toulouse, Toulouse, France
| | - Océane Delos
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
- MetaToul-MetaboHUB, Toulouse, France
| | - Lucie Combes-Soia
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Romain Paccoud
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Elsa Moreau
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Frédéric Martins
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
- Plateforme GeT, Genotoul, 31100 Toulouse, France
| | - Thomas Clouaire
- Molecular, Cellular, and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Fadila Benhamed
- Université de Paris, Institut Cochin, CNRS, INSERM, F- 75014 Paris, France
| | - Alexandra Montagner
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Walter Wahli
- Molecular, Cellular, and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
- Center for Integrative Genomics, University of Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, Singapore 308232, Singapore
| | | | - Armelle Yart
- Institut RESTORE, UMR 1301, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS-Université Paul Sabatier, Université de Toulouse, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Isabelle Castan-Laurell
- Institut RESTORE, UMR 1301, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS-Université Paul Sabatier, Université de Toulouse, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Justine Bertrand-Michel
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
- MetaToul-MetaboHUB, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Catherine Postic
- Université de Paris, Institut Cochin, CNRS, INSERM, F- 75014 Paris, France
| | - Pierre-Damien Denechaud
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Cédric Moro
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Gaelle Legube
- Molecular, Cellular, and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Chih-Hao Lee
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hervé Guillou
- Toxalim, INRAE UMR 1331, ENVT, INP-Purpan, University of Toulouse, Paul Sabatier University, F-31027, Toulouse, France
| | - Philippe Valet
- Institut RESTORE, UMR 1301, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS-Université Paul Sabatier, Université de Toulouse, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Cédric Dray
- Institut RESTORE, UMR 1301, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS-Université Paul Sabatier, Université de Toulouse, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Jean-Philippe Pradère
- Institut RESTORE, UMR 1301, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS-Université Paul Sabatier, Université de Toulouse, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1297/I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
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Cross KM, Granados JZ, Ten Have GAM, Thaden JJ, Engelen MPKJ, Lightfoot JT, Deutz NEP. Protein fractional synthesis rates within tissues of high- and low-active mice. PLoS One 2020; 15:e0242926. [PMID: 33253250 PMCID: PMC7703944 DOI: 10.1371/journal.pone.0242926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/11/2020] [Indexed: 11/19/2022] Open
Abstract
With the rise in physical inactivity and its related diseases, it is necessary to understand the mechanisms involved in physical activity regulation. Biological factors regulating physical activity are studied to establish a possible target for improving the physical activity level. However, little is known about the role metabolism plays in physical activity regulation. Therefore, we studied protein fractional synthesis rate (FSR) of multiple organ tissues of 12-week-old male mice that were previously established as inherently low-active (n = 15, C3H/HeJ strain) and high-active (n = 15, C57L/J strain). Total body water of each mouse was enriched to 5% deuterium oxide (D2O) via intraperitoneal injection and maintained with D2O enriched drinking water for about 24 h. Blood samples from the jugular vein and tissues (kidney, heart, lung, muscle, fat, jejunum, ileum, liver, brain, skin, and bone) were collected for enrichment analysis of alanine by LC-MS/MS. Protein FSR was calculated as -ln(1-enrichment). Data are mean±SE as fraction/day (unpaired t-test). Kidney protein FSR in the low-active mice was 7.82% higher than in high-active mice (low-active: 0.1863±0.0018, high-active: 0.1754±0.0028, p = 0.0030). No differences were found in any of the other measured organ tissues. However, all tissues resulted in a generally higher protein FSR in the low-activity mice compared to the high-activity mice (e.g. lung LA: 0.0711±0.0015, HA: 0.0643±0.0020, heart LA: 0.0649± 0.0013 HA: 0.0712±0.0073). Our observations suggest that high-active mice in most organ tissues are no more inherently equipped for metabolic adaptation than low-active mice, but there may be a connection between protein metabolism of kidney tissue and physical activity level. In addition, low-active mice have higher organ-specific baseline protein FSR possibly contributing to the inability to achieve higher physical activity levels.
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Affiliation(s)
- Kristina M. Cross
- Center for Translational Research in Aging & Longevity, Dept. Health and Kinesiology, Texas A&M University, College Station, TX, United States of America
- * E-mail:
| | - Jorge Z. Granados
- Biology of Physical Activity Laboratory, Dept. Health and Kinesiology, Texas A&M University, College Station, TX, United States of America
| | - Gabriella A. M. Ten Have
- Center for Translational Research in Aging & Longevity, Dept. Health and Kinesiology, Texas A&M University, College Station, TX, United States of America
| | - John J. Thaden
- Center for Translational Research in Aging & Longevity, Dept. Health and Kinesiology, Texas A&M University, College Station, TX, United States of America
| | - Marielle P. K. J. Engelen
- Center for Translational Research in Aging & Longevity, Dept. Health and Kinesiology, Texas A&M University, College Station, TX, United States of America
| | - J. Timothy Lightfoot
- Biology of Physical Activity Laboratory, Dept. Health and Kinesiology, Texas A&M University, College Station, TX, United States of America
| | - Nicolaas E. P. Deutz
- Center for Translational Research in Aging & Longevity, Dept. Health and Kinesiology, Texas A&M University, College Station, TX, United States of America
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Downes DP, Kasumov T, Daurio NA, Wood NB, Previs MJ, Sheth PR, McLaren DG, Previs SF. Isotope Fractionation during Gas Chromatography Can Enhance Mass Spectrometry-Based Measures of 2H-Labeling of Small Molecules. Metabolites 2020; 10:E474. [PMID: 33233825 PMCID: PMC7699861 DOI: 10.3390/metabo10110474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022] Open
Abstract
Stable isotope tracers can be used to quantify the activity of metabolic pathways. Specifically, 2H-water is quite versatile, and its incorporation into various products can enable measurements of carbohydrate, lipid, protein and nucleic acid kinetics. However, since there are limits on how much 2H-water can be administered and since some metabolic processes may be slow, it is possible that one may be challenged with measuring small changes in isotopic enrichment. We demonstrate an advantage of the isotope fractionation that occurs during gas chromatography, namely, setting tightly bounded integration regions yields a powerful approach for determining isotope ratios. We determined how the degree of isotope fractionation, chromatographic peak width and mass spectrometer dwell time can increase the apparent isotope labeling. Relatively simple changes in the logic surrounding data acquisition and processing can enhance gas chromatography-mass spectrometry measures of low levels of 2H-labeling, this is especially useful when asymmetrical peaks are recorded at low signal:background. Although we have largely focused attention on alanine (which is of interest in studies of protein synthesis), it should be possible to extend the concepts to other analytes and/or hardware configurations.
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Affiliation(s)
- Daniel P. Downes
- Department of Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA; (D.P.D.); (N.A.D.); (P.R.S.); (D.G.M.)
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA;
| | - Natalie A. Daurio
- Department of Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA; (D.P.D.); (N.A.D.); (P.R.S.); (D.G.M.)
| | - Neil B. Wood
- Department of Molecular Physiology & Biophysics, University of Vermont, Burlington, VT 05405, USA; (N.B.W.); (M.J.P.)
| | - Michael J. Previs
- Department of Molecular Physiology & Biophysics, University of Vermont, Burlington, VT 05405, USA; (N.B.W.); (M.J.P.)
| | - Payal R. Sheth
- Department of Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA; (D.P.D.); (N.A.D.); (P.R.S.); (D.G.M.)
| | - David G. McLaren
- Department of Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA; (D.P.D.); (N.A.D.); (P.R.S.); (D.G.M.)
| | - Stephen F. Previs
- Department of Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA; (D.P.D.); (N.A.D.); (P.R.S.); (D.G.M.)
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6
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Daurio NA, Zhou H, Chen Y, Sheth PR, Imbriglio JE, McLaren DG, Tawa P, Rachdaoui N, Previs MJ, Kasumov T, O’Neil J, Previs SF. Examining Targeted Protein Degradation from Physiological and Analytical Perspectives: Enabling Translation between Cells and Subjects. ACS Chem Biol 2020; 15:2623-2635. [PMID: 32930572 DOI: 10.1021/acschembio.0c00380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ability to target specific proteins for degradation may open a new door toward developing therapeutics. Although effort in chemistry is essential for advancing this modality, i.e., one needs to generate proteolysis targeting chimeras (bifunctional molecules, also referred to as PROTACS) or "molecular glues" to accelerate protein degradation, we suspect that investigations could also benefit by directing attention toward physiological regulation surrounding protein homeostasis, including the methods that can be used to examine changes in protein kinetics. This perspective will first consider some metabolic scenarios that might be of importance when one aims to change protein abundance by increasing protein degradation. Specifically, could protein turnover impact the apparent outcome? We will then outline how to study protein dynamics by coupling stable isotope tracer methods with mass spectrometry-based detection; since the experimental conditions could have a dramatic effect on protein turnover, special attention is directed toward the application of methods for quantifying protein kinetics using in vitro and in vivo models. Our goal is to present key concepts that should enable mechanistically informed studies which test targeted protein degradation strategies.
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Affiliation(s)
- Natalie A. Daurio
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Haihong Zhou
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Ying Chen
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Payal R. Sheth
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Jason E. Imbriglio
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - David G. McLaren
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Paul Tawa
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Nadia Rachdaoui
- Department of Animal Sciences, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Michael J. Previs
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, Vermont 05454, United States
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272, United States
| | - Jennifer O’Neil
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Stephen F. Previs
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
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Ilchenko S, Haddad A, Sadana P, Recchia FA, Sadygov RG, Kasumov T. Calculation of the Protein Turnover Rate Using the Number of Incorporated 2H Atoms and Proteomics Analysis of a Single Labeled Sample. Anal Chem 2019; 91:14340-14351. [PMID: 31638786 DOI: 10.1021/acs.analchem.9b02757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Rate constant estimation with heavy water requires a long-term experiment with data collection at multiple time points (3-4 weeks for mitochondrial proteome dynamics in mice and much longer in other species). When tissue proteins are analyzed, this approach requires euthanizing animals at each time point or multiple tissue biopsies in humans. Although short-term protocols are available, they require knowledge of the maximum number of isotope labels (N) and accurate quantification of observed 2H-enrichment in the peptide. The high-resolution accurate mass spectrometers used for proteome dynamics studies are characterized by a systematic spectral error that compromises these measurements. To circumvent these issues, we developed a simple algorithm for the rate constant calculation based on a single labeled sample and comparable unlabeled (time 0) sample. The algorithm determines N for all proteogenic amino acids from a long-term experiment to calculate the predicted plateau 2H-labeling of peptides for a short-term protocol and estimates the rate constant based on the measured baseline and the predicted plateau 2H-labeling of peptides. The method was validated based on the rate constant estimation in a long-term experiment in mice and dogs. The improved 2 time-point method enables the rate constant calculation with less than 10% relative error compared to the bench-marked multi-point method in mice and dogs and allows us to detect diet-induced subtle changes in ApoAI turnover in mice. In conclusion, we have developed and validated a new algorithm for protein rate constant calculation based on 2-time point measurements that could also be applied to other biomolecules.
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Affiliation(s)
- Serguei Ilchenko
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Andrew Haddad
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Prabodh Sadana
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Fabio A Recchia
- Institute of Life Sciences , Scuola Superiore Sant'Anna, Pisa, Fondazione Gabriele Monasterio , 56100 Pisa , Italy.,Cardiovascular Research Center , Lewis Katz School of Medicine at Temple University , Philadelphia , Pennsylvania 19140 , United States
| | - Rovshan G Sadygov
- University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Takhar Kasumov
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
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