DOCSLIB.ORG

Developement of Strategies for the Isotopic Labeling of Methyl Groups for the NMR Study of Large Protein Assemblies Rime Kerfah

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Developement of Strategies for the Isotopic Labeling of Methyl Groups for the NMR Study of Large Protein Assemblies Rime Kerfah Developement of strategies for the isotopic labeling of methyl groups for the NMR study of large protein assemblies Rime Kerfah To cite this version: Rime Kerfah. Developement of strategies for the isotopic labeling of methyl groups for the NMR study of large protein assemblies. Biomolecules [q-bio.BM]. Université de Grenoble, 2014. English. NNT : 2014GRENV043. tel-01343865 HAL Id: tel-01343865 https://tel.archives-ouvertes.fr/tel-01343865 Submitted on 10 Jul 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour obtenir le grade de DOCTEUR DE L’UNIVERSITÉ DE GRENOBLE Spécialité : Biologie structurale et nanobiologie Présentée par Rime Kerfah Thèse dirigée par Jérôme Boisbouvier Préparée au sein du Groupe de Spéctrosopie RMN Biomoléculaire École Doctorale Chimie et Sciences du Vivant Développement de stratégies de marquage isotopique des groupements méthyles pour l'étude d'assemblages protéiques de grande taille par RMN Date de soutenance le 26 Septembre 2014, devant le jury composé de : Bruno Kieffer Président Carine Tisné Rapporteur Ewen Lescop Rapporteur Olivier Hamelin Membre Michael Plevin Membre Jérôme Boisbouvier Directeur de thèse ACKNOWLEDGMENTS I wish to thank my supervisor, Dr. Boisbouvier, for the guidance and generosity that he has provided me. I consider it a privilege to have had the opportunity in working within his research group. I would like to acknowledge with sincere gratitude to Elodie and Pavel for their assistance in my early life in science and also Guillaume for his ingenious IT advises. I am also really grateful for the scientific support of Pierre and Dominique and for their cultural discussions. I would like to thank the whole NMR, group, especially Adrien, Karine, Catherine, Lionel, Isabel, Paul, Hugo and Jia-ying for the collaboration and the excellent work environment that have proportioned to me. My thesis would not be possible without the presence of my parents, brothers and my best friend, Amal. For all of them I would like to express my gratitude for being always by my side. To conclude, I would like to thank Victor, who has been my energy source to pursue this step of my life and who has always managed to put a smile on my face in difficult circumstances. Content 1. INTRODUCTION……………….. .......................................................................................... 1 1.1 Overview of isotope labeling in solution NMR spectroscopy: ....................................................... 2 1.2 Selective protonation and isotopic labeling in a perdeuterated biological system ........................ 5 1.2.1 Production of labeled proteins .................................................................................................. 5 1.2.1.1 In vivo protein production ................................................................................................ 5 1.2.1.2 In vitro protein production ............................................................................................... 8 1.2.2 Optimal sites for selective protonation and isotopic labeling ................................................. 13 1.2.2.1 Selective protonation and isotopic labeling on the backbone: ..................................... 13 1.2.2.1.1 Selective protonation and labeling of amide groups ................................................ 13 1.2.2.1.2 Selective protonation and isotopic labeling at the C position ................................. 19 1.2.2.2 Selective protonation and isotopic labeling on the side chain ...................................... 20 1.2.2.2.1 Stereo-array Isotope Labeling (SAIL) ......................................................................... 21 1.2.2.2.2 Specific protonation position in aromatic amino acids ............................................. 23 1.2.2.2.3 Methyl groups labeling ............................................................................................. 25 1.3 Selective protonation and isotopic labeling of methyl groups in perdeuterated biological systems ………………………………………………………………………………………………………………………………………………25 1.3.1 Why methyl groups? ............................................................................................................... 25 1.3.2 Labeling strategy for each methyl-containing amino acid ...................................................... 29 1.3.2.1 Amino acids involved in irreversible metabolic pathways ............................................. 29 1.3.2.1.1 Isoleucine residue methyl groups labeling ................................................................ 29 1.3.2.1.2 Leucine and valine residues methyl groups labeling................................................. 37 1.3.2.1.3 Methionine residue methyl group labeling ............................................................... 44 1.3.2.2 Amino acids involved in reversible metabolic pathways ............................................... 45 1.3.2.2.1 Alanine residue methyl group labeling ..................................................................... 45 1.3.2.2.2 Threonine residue methyl group labeling ................................................................. 49 1.3.2.3 Grafted Methyl group .................................................................................................... 56 1.3.2.3.1 Grafted methyl group on cysteine ............................................................................ 57 1.3.2.3.2 Grafted methyl group on lysine: ............................................................................... 57 2. COMBINATORIAL LABELING OF METHYL GROUPS............................................. 59 2.1 Context ....................................................................................................................................... 60 2.2 Article I: scrambling-free combinatorial labeling of alanine-, isoleucine-1, leucine-pro-S and valine-pro-S groups for the detection of long-range NOEs ................................................................... 64 3. ASSIGNMENT OF METHYL GROUPS ......................................................................... 83 3.1 Context ....................................................................................................................................... 84 3.2 Methyl groups assignment in large proteins ............................................................................... 84 3.2.1 Methyl groups assignment based on bond-transfer NMR experiments: ................................ 85 3.2.2 Methyl group assignment using structure-based methods .................................................... 85 3.2.3 Stereospecific assignment of methyl groups .......................................................................... 88 3.2.4 Article II: A single step regio- and stereo-specific NMR assignment of isoleucine, leucine and valine residues in large proteins ................................................................................................... 90 3.3 Methyl groups assignment in supramolecular assemblies ........................................................ 110 3.3.1 Historical overview ................................................................................................................ 110 3.3.2 Methyl groups assignment using the “divide and conquer” strategy ................................... 110 3.3.3 Methyl groups assignments using mutagenesis .................................................................... 111 13 3.3.4 Article III: A cost-effective protocol for the parallel production of libraries of CH3- specifically labeled mutants for NMR studies of high molecular weight proteins ........................... 113 4. APPLICATIONS OF METHYL GROUPS LABELING STRATEGY ......................... 134 4.1 Labeling of methyl groups for real-time NMR studies of protein oligomerization process ........ 135 4.1.1 Context .................................................................................................................................. 135 4.1.2 Article IV: Probing protein self-assembly by real-time NMR spectroscopy ........................ 136 4.2 Combinatorial methyl groups labeling for long-range nOes detection ..................................... 156 4.2.1 Context .................................................................................................................................. 156 4.2.2 Combinatorial labeling of methyl groups for the detection of long-range nOes in perdeuterated large systems ............................................................................................................... 158 4.2.3 Detection of long-range nOes in MSG labeled simultaneously at AI1(LV)proS ....................... 162 4.2.4 Generalization to a supramolecular protein (PhTET-2) ......................................................... 164 4.3 Combinatorial methyl groups labeling for the filetering of inter-monomeric nOes in homo- oligomeric proteins ...........................................................................................................................
Load more

Recommended publications
  • ISOTEC® Stable Isotopes Biomolecular NMR Isotope Labeling Methods for Protein Dynamics Studies
    ISOTEC® Stable Isotopes Biomolecular NMR Isotope Labeling Methods for Protein Dynamics Studies Eric D. Watt and J. Patrick Loria, Ph.D. Department of Chemistry, Yale University, Kline Chemistry Laboratory, 225 Prospect Street, New Haven, CT 06520 Protein structure determination by solution NMR spectroscopy use of 15N-enriched minimal or nutrient-rich growth media that are has long relied on the uniform stable isotopic enrichment with readily available, allowing for easy sample preparation. Uniform 15N 13C and 15N to alleviate resonance overlap and to allow multiple labeling results in an isolated spin system (1H-15N) that lends itself well distance and angular restraints, at as many atomic sites as possible, to relaxation experiments. Every 15N position whether in the protein to facilitate computing the optimal three-dimensional structural backbone or sidechain is separated from another 15N atom by at least (1) 1 model. Recently, the optimization of these labeling techniques has two bonds. Therefore there are no JNN couplings that could lead to increased the range of protein sizes amendable to study, enhanced complicated multiexponential relaxation behavior, which would be the quality of three-dimensional structures, and simplified the analysis difficult to accurately measure and would cloud the interpretation of of experimental data.(2) Similarly, the field of protein dynamics has the associated motions. benefited from advances in isotopic labeling techniques that have However, 15N enrichment by itself does not provide a complete picture allowed researchers to study the motional properties of ever larger of the motions a protein undergoes. Nitrogen makes up only 1/3 of proteins over a broad range of timescales while more accurately the protein backbone and is only sparsely populated in the sidechains describing the protein motions.
    [Show full text]
  • A Roadmap for Interpreting 13C Metabolite Labeling Patterns from Cells
    Available online at www.sciencedirect.com ScienceDirect 13 A roadmap for interpreting C metabolite labeling patterns from cells 1,2 3,* 4,* Joerg M Buescher , Maciek R Antoniewicz , Laszlo G Boros , 5,* 6,* 7,* Shawn C Burgess , Henri Brunengraber , Clary B Clish , 8,* 9,* 10,* Ralph J DeBerardinis , Olivier Feron , Christian Frezza , 1,2,* 11,* 12,* Bart Ghesquiere , Eyal Gottlieb , Karsten Hiller , 13,* 14,* 15,* Russell G Jones , Jurre J Kamphorst , Richard G Kibbey , 16,* 17,* 18,* Alec C Kimmelman , Jason W Locasale , Sophia Y Lunt , 11,* 19,* 20,* Oliver DK Maddocks , Craig Malloy , Christian M Metallo , 21,22,* 23,24,* Emmanuelle J Meuillet , Joshua Munger , 25,* 26,* 27,28,* Katharina No¨ h , Joshua D Rabinowitz , Markus Ralser , 29,* 30,* 31,* Uwe Sauer , Gregory Stephanopoulos , Julie St-Pierre , 32,* 33,* Daniel A Tennant , Christoph Wittmann , 34,35,* 11,* Matthew G Vander Heiden , Alexei Vazquez , 11,* 36,37,* 29,* Karen Vousden , Jamey D Young , Nicola Zamboni and 1,2 Sarah-Maria Fendt 13 Measuring intracellular metabolism has increasingly led to Goodman Cancer Research Centre, Department of Physiology, McGill 13 University, Montreal, QC, Canada important insights in biomedical research. C tracer analysis, 14 13 Institute of Cancer Sciences, University of Glasgow, Glasgow, UK although less information-rich than quantitative C flux 15 Internal Medicine, Cellular and Molecular Physiology, Yale University analysis that requires computational data integration, has been School of Medicine, New Haven, CT, USA 16 established as a time-efficient method to unravel relative Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA pathway activities, qualitative changes in pathway 17 Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA contributions, and nutrient contributions.
    [Show full text]
  • Isotope Distributions
    Isotope distributions This exposition is based on: • R. Martin Smith: Understanding Mass Spectra. A Basic Approach. Wiley, 2nd edition 2004. [S04] • Exact masses and isotopic abundances can be found for example at http: //www.sisweb.com/referenc/source/exactmaa.htm or http://education. expasy.org/student_projects/isotopident/htdocs/motza.html • IUPAC Compendium of Chemical Terminology - the Gold Book. http:// goldbook.iupac.org/ [GoldBook] • Sebastian Bocker,¨ Zzuzsanna Liptak:´ Efficient Mass Decomposition. ACM Symposium on Applied Computing, 2005. [BL05] • Christian Huber, lectures given at Saarland University, 2005. [H05] • Wikipedia: http://en.wikipedia.org/, http://de.wikipedia.org/ 10000 Isotopes This lecture addresses some more combinatorial aspect of mass spectrometry re- lated to isotope distributions and mass decomposition. Most elements occur in nature as a mixture of isotopes. Isotopes are atom species of the same chemical element that have different masses. They have the same number of protons and electrons, but a different number of neutrons. The main ele- ments occurring in proteins are CHNOPS. A list of their naturally occurring isotopes is given below. Isotope Mass [Da] % Abundance Isotope Mass [Da] % Abundance 1H 1.007825 99.985 16O 15.994915 99.76 2H 2.014102 0.015 17O 16.999131 0.038 18O 17.999159 0.20 12C 12. (exact) 98.90 13C 13.003355 1.10 31P 30.973763 100. 14N 14.003074 99.63 32S 31.972072 95.02 15N 15.000109 0.37 33S 32.971459 0.75 34S 33.967868 4.21 10001 Isotopes (2) Note that the lightest isotope is also the most abundant one for these elements.
    [Show full text]
  • Large D/H Variations in Bacterial Lipids Reflect Central Metabolic Pathways
    Large D/H variations in bacterial lipids reflect central metabolic pathways Xinning Zhanga, Aimee L. Gillespieb, and Alex L. Sessionsa,b,1 aEnvironmental Science and Engineering Program and bDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 This Feature Article is part of a series identified by the Editorial Board as reporting findings of exceptional significance. Edited by John M. Hayes, Woods Hole Oceanographic Institution, Woods Hole, MA, and approved May 29, 2009 (received for review March 19, 2009) Large hydrogen-isotopic (D/H) fractionations between lipids and compositions. Jones et al. (17) measured fatty acids extracted growth water have been observed in most organisms studied to from coastal marine particulate organic matter (POM) and date. These fractionations are generally attributed to isotope found ␦D values ranging from Ϫ73 to Ϫ237‰. Measurements effects in the biosynthesis of lipids, and are frequently assumed to of lipids from marine sediments have extended this range from be approximately constant for the purpose of reconstructing cli- Ϫ32 to Ϫ348‰ for lipids with n-alkyl skeletons and Ϫ148 to matic variables. Here, we report D/H fractionations between lipids Ϫ469‰ for those with isoprenoid skeletons (18). Because the and water in 4 cultured members of the phylum Proteobacteria, lipids measured by both studies likely derive from marine and show that they can vary by up to 500‰ in a single organism. organisms inhabiting seawater of essentially constant ␦D value The variation cannot be attributed to lipid biosynthesis as there is (Ϸ0‰), such differences cannot be due to varying environmen- no significant change in these pathways between cultures, nor can tal water.
    [Show full text]
  • Selective Isotope Labeling Methods for Protein Structural Studies
    Cambridge Isotope Laboratories, Inc. www.isotope.com Biomolecular NMR Selective Isotope-Labeling Methods for Protein Structural Studies Hanudatta S. Atreya, PhD NMR Research Centre, Indian Institute of Science, Bangalore, India One of the major contributing factors to the rapid advance dynamic studies. Selective amino acid-type labeling also aids in of biomolecular NMR spectroscopy is the emergence of different sequence-specific resonance assignments by helping to identify isotope labeling methods. Recent developments in biotechnology resonances which are otherwise buried in the crowded regions have made it easier and economical to introduce 13C,15N and 2H of 2D and 3D NMR spectra. However, a disadvantage of this into proteins and nucleic acids. At the same time, there has been method is the possible mis-incorporation of 15N label in undesired an explosion in the number of NMR experiments that utilize such amino acids (also called as “isotope scrambling”).3 This happens isotope-labeled samples. Thus, a combination of isotopic labeling due to metabolic conversion of one amino acid to another in and multidimensional, multinuclear experiments has significantly the bio-synthetic pathway of the cell. The problem becomes expanded the range of problems in structural biology amenable more severe for amino acids higher up or intermediates in the to NMR. metabolic pathway such as Asp, Glu and Gln (See Figure 2 showing the biosynthetic pathway in E. coli ). For those which Isotope labeling in proteins can be broadly classified into four are end-products in the production pipeline (Ala, Arg, Asn, Cys, categories: Uniform, amino acid-type selective, site-specific His, Ile, Lys, Met, Pro and Trp) isotope scrambling is minimal and and random / fractional labeling.
    [Show full text]
  • Application of Isotope Labeling Experiments and 13C Flux Analysis
    Available online at www.sciencedirect.com ScienceDirect 13 Application of isotope labeling experiments and C flux analysis to enable rational pathway engineering 1 1 1,2 Allison G McAtee , Lara J Jazmin and Jamey D Young 13 Isotope labeling experiments (ILEs) and C flux analysis industries to date, despite the fact that these approaches provide actionable information for metabolic engineers to can provide direct readouts on in vivo metabolic pathway identify knockout, overexpression, and/or media optimization activities. This may be partly due to the fact that many targets. ILEs have been used in both academic and industrial companies lack the combined experimental and compu- labs to increase product formation, discover novel metabolic tational expertise needed to effectively analyze ILEs, but functions in previously uncharacterized organisms, and perhaps even more important is the perception that these enhance the metabolic efficiency of host cell factories. This studies are intrinsically difficult and there have not been review highlights specific examples of how ILEs have been enough success stories to justify the requisite effort. used in conjunction with enzyme or metabolic engineering to Therefore, the purpose of this review is to present some elucidate host cell metabolism and improve product titer, rate, recent examples where ILEs and MFA have been suc- or yield in a directed manner. We discuss recent progress and cessfully applied to close the ‘design-build-test-learn’ 13 future opportunities involving the use of ILEs and C flux metabolic engineering cycle. analysis to characterize non-model host organisms and to identify and subsequently eliminate wasteful byproduct Applications of isotope labeling experiments pathways or metabolic bottlenecks.
    [Show full text]
  • Short Stories in Pharmaceutical Discovery, Process and Isotopic
    Short Stories in Pharmaceutical Discovery, Q. Michaudel Process and Isotopic Labeling Baran Lab GM 2011-11-19 Some data about some common radiolabels: There are three different but complementary ways to explore medicinal chemistry, every having its own constraints: Isotope Type Decay Half-life Medical use Discovery, hit-to-lead, and lead optimization: * rapidity * development of a chemical library 3 natural 3He, – 12.32 years analytical Process chemistry and development: * scalable synthesis (yield optimization, ease of T (trace) β purification, cost, safety) for bulk industrial production 11C artificial 11B, β+ 20.38 min PET imaging Isotopic labeling: * availability and price of labeled reagents * reaction times for radiochemistry (tomography...) natural 14 14N, β– 5,730 ± 40 analytical C (trace) years Route Discovery Process Labeling 13N artificial 13C, β+ <10 min PET imaging 15 15 + Typical O artificial N, β 122 s PET imaging scale 1 mg < x < 1 kg > 100 kg ~100 mg synthesis 18F artificial 18O, β+ 109.77 min PET imaging Isotopic labeling synthesis, a few definitions: 99mTc artificial 99Tc, γ 6.01 h imaging This technique is used for metabolic and pharmacological studies. Radiolabeled compounds allow for measuring absorption, distribution, metabolism, and elimination of SPECT 123 123Te, EC compounds from the human body. Stable-labeled molecules often serve as internal I artificial 13.3 h imaging standards in mass spectrometry and NMR studies. Radioactive molecules are also used in imaging and radiation therapy. 131 – radiation 131I artificial Xe, β 8.02 h therapy Radioactive isotopes: 3T, 11C, 14C, 13N, 15O, 18F, 35S, 124I, 131I... Diagnostic medical imaging: 3 main techniques, all using gamma cameras Stable isotopes: 2D, 13C, 15N, 17O, 18O..
    [Show full text]
  • An Isotopic Technique to Marie:Mid-Sized Vertebrates Non-Lnvaslvelv
    Journal of Zoology. Print ISSN 0952-8369 An isotopic technique to marie:mid-sized vertebrates non-lnvaslvelv 1,2 ,2 1,2 3 J. N. Pauli , M. Ben-David1 , S. W. Buskirk , J. E. DePue2 & W. P. Smith 1 Prograrn in Ecology, University of Wyorning, Laramie, WY, USA 2 Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA 3 USDA Forest Service, Pacific Northwest Research Station, Forestry and Range Sciences Laboratory, La Grande, OR, USA Keywords Abstract carbon; deuterium; nitrogen; mesocarnivore; movement; ranging. Although dispersal is an important attribute of animal population ecology, knowledge of dispersal rates or distances for many wide-ranging species is lacking. Correspondence Current methods require capturing and restraining animals, which can be cost- Jonathan N. Pauli, Department of Zoology prohibitive, fail to collect sufficient samples or change animal ranging behaviors. and Physiology, University of Wyoming, Herein, we describe a novel, cost-effective and non-invasive method, using bait 1000 E. University Avenue, Laramie, enriched with stable isotopes to mark the hair of American martens Martes WY82071, USA. americana. Captive martens that consumed isotopically labeled glycine exhibited Email: [email protected] significant and progressive enrichment in the isotopic signature of 13C,lsN and 2H in both whole blood and hair. A distinct mark in hair, >2 standard deviations Editor: Nigel Bennett above natural abundance, occurred within 14 days of the second dose. The rate of isotopic labeling of hair was higher in spring, possibly because labeled amino acids Received 7 November 2008; revised 31 became diluted among the many hairs growing during the autumn.
    [Show full text]
  • Polymer Dynamics in Hydrogenous Systems by Neutron Reflectivity
    Polymer Dynamics in Hydrogenous Systems by Neutron Reflectivity A. R. ESKER,1 H. GRU¨ LL,2 S. K. SATIJA,3 C. C. HAN4 1Department of Chemistry (0212), Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 2Philips Research Laboratories, 5656 AA Eindhoven, The Netherlands 3Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899 4State Key Laboratory of Polymer Physics and Chemistry, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China, 100080 Received 2 September 2003; revised 6 February 2004; accepted 18 February 2004 DOI: 10.1002/polb.20176 Published online in Wiley InterScience (www.interscience.wiley.com). ABSTRACT: Neutron reflectivity is a powerful tool for exploring polymer dynamics above the glass-transition temperature at short diffusion times in layered thin-film systems. Recent studies of membrane-mediated interdiffusion in deuterium-labeled systems have shown that ultrathin membranes can track the position of the interface in binary polymeric diffusion couples and also can discriminate between perdeuterated and hydrogenous polymers of the same molecular weight. This report shows that similar dynamic information can be obtained for binary hydrogenous polystyrene (hPS) diffusion couples separated by an ultrathin (6-nm) isopentylcellulose cinnamate (IPCC) membrane on Si wafers (air//hPS/IPCC/hPS//Si, where “//” represents an interface between obviously different phases and “/” represents a dynamic interface between polymeric species). In particular, the air//hPS/IPCC/hPS//Si system provides the same information as perdeuterium-labeled polystyrene (dPS) diffusion couples separated by the same IPCC membrane (air//dPS/IPCC/dPS//Si). This technique has potential appli- cations for the study of confinement effects on thin-film dynamics and macromolecular transport across membranes.
    [Show full text]
  • Interplay of Temperature, Productivity, and Community Assemblage on Hydrogen Isotope Signatures of Algal Lipid Biomarkers S
    Biogeosciences Discuss., doi:10.5194/bg-2017-60, 2017 Manuscript under review for journal Biogeosciences Discussion started: 27 February 2017 c Author(s) 2017. CC-BY 3.0 License. Interplay of temperature, productivity, and community assemblage on hydrogen isotope signatures of algal lipid biomarkers S. Nemiah Ladd1, Nathalie Dubois1, 2, Carsten J. Schubert1, 3 1Department of Surface Waters – Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and 5 Technology, Kastanienbaum, 6047, Switzerland 2Department of Earth Sciences, ETH Zürich, Zürich, 8092, Switzerland 3Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, 8092, Switzerland Correspondence to: S. Nemiah Ladd ([email protected]) Abstract. The hydrogen isotope composition (δ2H) of biomarkers produced by algae is strongly influenced by the 10 δ2H values of the water in which they grew. δ2H values of algal biomarkers preserved in lake sediments are thus a useful tool for reconstructing past changes in lake water δ2H values, which can be used to infer hydroclimate variability. However, studies from laboratory cultures of marine algae have shown that a number of factors can influence the magnitude of hydrogen isotope fractionation between algal lipids and their source water, including temperature and growth rates. Quantifying the natural extent of these changes in freshwater lacustrine settings and identifying their causes is essential for 15 robust application of δ2H values of algal lipids as paleohydroclimate proxies, yet the influence of these factors remains poorly constrained. This work targets the effect of temperature and productivity on 2H/1H fractionation in algal biomarkers through a comparative time series in two central Swiss lakes: eutrophic Lake Greifen and oligotrophic Lake Lucerne.
    [Show full text]
  • Mass Spectrometry and Proteomics - Lecture 5
    Mass Spectrometry and Proteomics - Lecture 5 - Matthias Trost Newcastle University [email protected] Previously • Proteomics • Sample prep 144 Lecture 5 • Quantitation techniques • Search Algorithms • Proteomics software 145 Current limitations of MS-based Proteomics • Cellular proteins span a wide range of expression and current mass spectrometric technologies typically sample only a fraction of all the proteins present in a sample. • Due to limited data quality, only a fraction of all identified proteins can also be reliably quantified. Bantscheff et al, Anal Bioanal Chem, 2007 146 Limitations of Proteomics – concentration of proteins in plasma Anderson & Anderson, MCP, 2002 147 Quantitation techniques Label-free • Ion intensity • Spectral counting Chemical isotopic labeling • ICAT • iTRAQ/TMT • mTRAQ • Formaldehyde label • Enzymatic label Metabolic isotopic labeling • SILAC • 15N 148 The three different spectral sources of quantitative information Wilm, Proteomics, 2010 149 Quantitation methods Isotope label Fragmentation-based label Label-free (SILAC, ICAT, demethyl label etc) (iTRAQ) X Da MS MS/MS 150 Quantitation strategies Bantscheff et al, Anal Bioanal Chem, 2007 151 Characteristics of quantitative MS methods Bantscheff et al, Anal Bioanal Chem, 2007 152 Label-free quantitation Condition A Condition B MS/MS • MASCOT • identification driven peptide assignment Peak detection (in triplicate) Peak detection (in triplicate) Hierarchical clustering 153 Label-free proteomics RLEIpSPDpSpSPER Cond. A Advantages and Disadvantages + Lower complexity + Lower cost + Primary tissue possible (+) Repetitions increase Cond. B identification rates - High LC-reproducibility necessary - Good clustering dependent on high mass accuracy Stdev Cond. A 0.089 - Several peptides for reliable Stdev Cond. B 0.067 quantitation required Ratio Cond. A/Cond. B 0.49 154 Another label-free quantitation: Spectral counting • The number of spectra matched to peptides from a protein is used as a surrogate measure of protein abundance.
    [Show full text]
  • Deficiencies of Deuterium As an Internal Standard in MS Deficiencies of Deuterium As an Internal Standard in MS Presentation
    Deficiencies of Deuterium as an Internal Standard in MS Deficiencies of Deuterium as an Internal Standard in MS Presentation Scott Landvatter, Ph.D. (President) Rich Tyburski (Vice President) About IsoSciences • Formed in 2002 by Scott Landvatter and David Saunders • Both were isotope chemists at SmithKline Beecham and have >35 years labeling experience • Custom Synthesis of Labeled Standards • Catalog of Labeled Internal Standards • Work with NIST on Vitamin Internal Standards • Supplier of high purity unlabeled vitamin standards to NIST • Worked with International Vitamin D Harmonization group • Collaborator with Diagnostic Labs to develop the next generation of internal standards (e.g. steroids) Which 25-OH D3 Internal Standard Do I Choose? 13 D3 or D6 or C3 or 13 13 C5 or C3 (Not Yet Available) Which Testosterone Internal Standard Do I Choose? OH OH OH D D D D D 13C 13C O O O 13C D D D 13 D5 or D3 or C3 Selecting a Labeled Internal Standard: What is Typical Now • ‘Old’ Internal Standards Continued to be Used • ‘SOP’s Complete • Validation Complete • Why Change? Selecting a Labeled Internal Standard: What is Typical Now • ‘Old’ Standards Continue to be Used • ‘SOP’s complete • Validation Complete • Why Change? • What Do ‘Old’ Internal Standards Look Like? • Usually Deuterated • Usually the Least Expensive Selecting a Labeled Internal Standard: What about New Internal Standards? • ‘New’ Standards Rapidly Being Developed • ‘New’ Standards Represent a Shift in Approach • Minimizing the use of Deuterium • 13C • 15N • D in more stable Positions • Combination of Labels • Minimize chance of unlabeled material Selecting a Labeled Internal Standard: What about New Internal Standards? • ‘New’ Standards Rapidly Being Developed • ‘New’ Standards Represent a Shift in Approach • Minimizing the use of Deuterium • 13C • 15N • D in more stable Positions • Combination of Labels • Minimize chance of unlabeled material Question: Are There Reasons to Switch Standards? Answer: In Many Cases the Answer is Yes.
    [Show full text]