Acid-Base Equilibria of Amino Acids: Microscopic and Macroscopic Acidity Constants
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Direct Sensing and Discrimination Among Ubiquitin and Ubiquitin Chains Using Solid-State Nanopores
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector 2340 Biophysical Journal Volume 108 May 2015 2340–2349 Article Direct Sensing and Discrimination among Ubiquitin and Ubiquitin Chains Using Solid-State Nanopores Iftach Nir,1 Diana Huttner,1 and Amit Meller1,* 1Department of Biomedical Engineering, The Technion—Israel Institute of Technology, Haifa, Israel ABSTRACT Nanopore sensing involves an electrophoretic transport of analytes through a nanoscale pore, permitting label- free sensing at the single-molecule level. However, to date, the detection of individual small proteins has been challenging, primarily due to the poor signal/noise ratio that these molecules produce during passage through the pore. Here, we show that fine adjustment of the buffer pH, close to the isoelectric point, can be used to slow down the translocation speed of the analytes, hence permitting sensing and characterization of small globular proteins. Ubiquitin (Ub) is a small protein of 8.5 kDa, which is well conserved in all eukaryotes. Ub conjugates to proteins as a posttranslational modification called ubiquiti- nation. The immense diversity of Ub substrates, as well as the complexity of Ub modification types and the numerous physio- logical consequences of these modifications, make Ub and Ub chains an interesting and challenging subject of study. The ability to detect Ub and to identify Ub linkage type at the single-molecule level may provide a novel tool for investigation in the Ub field. This is especially adequate because, for most ubiquitinated substrates, Ub modifies only a few molecules in the cell at a given time. -
I. Gas Phase Proton Affinity of Zwitterionic Betaine N. High
I. Gas Phase Proton Affinity of Zwitterionic Betaine n. High Resolution Spectroscopy of Trapped Ions: Concept and Design Thesis by Hak-No Lee In Partial Fulfillment of the Requirements for the Degree o f Doctor of Philosophy California Institute of Technology Pasadena, California 1999 (Submitted September 30, 1998) Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Acknowledgements Much gratitude is owed to my thesis advisors, Professors Jack Beauchamp and Dan Weitekamp, for their guidance and support. I feel fortunate to have worked with advisors who value and emphasize the training of their students. I thank them for allowing me to pursue studies of my own interest, without the pressure to produce timely results. Such freedom has enabled me to obtain exposure to a wide variety of areas in physical chemistry and chemical physics: An invaluable training that would be difficult to attain after graduation. There are many people whose support and friendship enriched my years at Caltech, including fellow graduate students and the staff of the chemistry department. Special thanks go to the members of Beauchamp group, past and present: Sherrie Campbell, Elaine Marzluff, Kevin Crellin, Jim Smith, Sang Won Lee, Dmitri Kossakovski, Hyun Sik Kim, Thomas Schindler, Patrick Vogel, and Priscilla Boon. Always willing to help and answer questions, they contributed significantly to my learning and provided companionship for which I am grateful. Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Abstract In an ideal experiment, the system being investigated is isolated from the environment. The only external influences allowed on the system are the parameters that the experimenter chooses to vary, in effort to study their effects on the observables. -
Recent Advances in Chiral Analysis of Proteins and Peptides
separations Review Recent Advances in Chiral Analysis of Proteins and Peptides Marine Morvan 1,2,* and Ivan Mikšík 1,2,* 1 Institute of Physiology of the Czech Academy of Sciences, Vídeˇnská 1083, 142 20 Prague, Czech Republic 2 Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic * Correspondence: [email protected] (M.M.); [email protected] (I.M.) Abstract: Like many biological compounds, proteins are found primarily in their homochiral form. However, homochirality is not guaranteed throughout life. Determining their chiral proteinogenic sequence is a complex analytical challenge. This is because certain D-amino acids contained in proteins play a role in human health and disease. This is the case, for example, with D-Asp in elastin, b-amyloid and a-crystallin which, respectively, have an action on arteriosclerosis, Alzheimer’s disease and cataracts. Sequence-dependent and sequence-independent are the two strategies for detecting the presence and position of D-amino acids in proteins. These methods rely on enzymatic digestion by a site-specific enzyme and acid hydrolysis in a deuterium or tritium environment to limit the natural racemization of amino acids. In this review, chromatographic and electrophoretic techniques, such as LC, SFC, GC and CE, will be recently developed (2018–2020) for the enantioseparation of amino acids and peptides. For future work, the discovery and development of new chiral stationary phases and derivatization reagents could increase the resolution of chiral separations. Keywords: chiral separation; proteins; peptides; D-amino acids Citation: Morvan, M.; Mikšík, I. Recent Advances in Chiral Analysis of Proteins and Peptides. -
Marginal Protein Stability Drives Subcellular Proteome Isoelectric Point
Marginal protein stability drives subcellular proteome isoelectric point Kaiser Loella,b and Vikas Nandaa,b,1 aCenter for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854; and bDepartment of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854 Edited by David Baker, University of Washington, Seattle, WA, and approved October 3, 2018 (received for review May 26, 2018) There exists a positive correlation between the pH of subcellular matching subcellular pH. Such selection could apply broadly compartments and the median isoelectric point (pI) for the across many proteins, resulting in proteome-wide effects (12). associated proteomes. Proteins in the human lysosome—a highly However, rather than exhibiting high stability under physiolog- acidic compartment in the cell—have a median pI of ∼6.5, whereas ical conditions, the majority of proteins are marginally stable, with proteins in the more basic mitochondria have a median pI of ∼8.0. free energy differences of only 5 kcal/mol to 15 kcal/mol between Proposed mechanisms reflect potential adaptations to pH. For ex- the folded and unfolded states (16). Neutral evolution theory ample, enzyme active site general acid/base residue pKs are likely posits most diversity can be explained by the accumulation of evolved to match environmental pH. However, such effects would random mutations that have minimal impact on fitness (17). be limited to a few residues on specific proteins, and might not Models of protein evolution demonstrate that proteome-wide affect the proteome at large. A protein model that considers res- marginal stability can be understood as neutral, rather than pos- idue burial upon folding recapitulates the correlation between itive selection for instability (18, 19). -
PC22 Doc. 22.1 Annex (In English Only / Únicamente En Inglés / Seulement En Anglais)
Original language: English PC22 Doc. 22.1 Annex (in English only / únicamente en inglés / seulement en anglais) Quick scan of Orchidaceae species in European commerce as components of cosmetic, food and medicinal products Prepared by Josef A. Brinckmann Sebastopol, California, 95472 USA Commissioned by Federal Food Safety and Veterinary Office FSVO CITES Management Authorithy of Switzerland and Lichtenstein 2014 PC22 Doc 22.1 – p. 1 Contents Abbreviations and Acronyms ........................................................................................................................ 7 Executive Summary ...................................................................................................................................... 8 Information about the Databases Used ...................................................................................................... 11 1. Anoectochilus formosanus .................................................................................................................. 13 1.1. Countries of origin ................................................................................................................. 13 1.2. Commercially traded forms ................................................................................................... 13 1.2.1. Anoectochilus Formosanus Cell Culture Extract (CosIng) ............................................ 13 1.2.2. Anoectochilus Formosanus Extract (CosIng) ................................................................ 13 1.3. Selected finished -
Chronological List of Correspondence, 1895–1920
CHRONOLOGICAL LIST OF CORRESPONDENCE, 1895–1920 In this chronological list of correspondence, the volume and document numbers follow each name. Documents abstracted in the calendars are listed in the Alphabetical List of Texts in this volume. 1895 13 or 20 Mar To Mileva Maric;;, 1, 45 29 Apr To Rosa Winteler, 1, 46 Summer To Caesar Koch, 1, 6 18 May To Rosa Winteler, 1, 47 28 Jul To Julia Niggli, 1, 48 Aug To Rosa Winteler, 5: Vol. 1, 48a 1896 early Aug To Mileva Maric;;, 1, 50 6? Aug To Julia Niggli, 1, 51 21 Apr To Marie Winteler, with a 10? Aug To Mileva Maric;;, 1, 52 postscript by Pauline Einstein, after 10 Aug–before 10 Sep 1,18 From Mileva Maric;;, 1, 53 7 Sep To the Department of Education, 10 Sep To Mileva Maric;;, 1, 54 Canton of Aargau, 1, 20 11 Sep To Julia Niggli, 1, 55 4–25 Nov From Marie Winteler, 1, 29 11 Sep To Pauline Winteler, 1, 56 30 Nov From Marie Winteler, 1, 30 28? Sep To Mileva Maric;;, 1, 57 10 Oct To Mileva Maric;;, 1, 58 1897 19 Oct To the Swiss Federal Council, 1, 60 May? To Pauline Winteler, 1, 34 1900 21 May To Pauline Winteler, 5: Vol. 1, 34a 7 Jun To Pauline Winteler, 1, 35 ? From Mileva Maric;;, 1, 61 after 20 Oct From Mileva Maric;;, 1, 36 28 Feb To the Swiss Department of Foreign Affairs, 1, 62 1898 26 Jun To the Zurich City Council, 1, 65 29? Jul To Mileva Maric;;, 1, 68 ? To Maja Einstein, 1, 38 1 Aug To Mileva Maric;;, 1, 69 2 Jan To Mileva Maric;; [envelope only], 1 6 Aug To Mileva Maric;;, 1, 70 13 Jan To Maja Einstein, 8: Vol. -
Anxiety & Depression.Pptx
Doc Talks: Natural Approaches to Anxiety & Depression Prosper Natural Health Dr. Molly Force & Dr. Alicia McCubbins www.ProsperNaturalHealth.com This presentation is meant for educational use only, not as a form of diagnosis, management or treatment of any medical concerns. Anxiety l What is it? l Physical symptoms l Mental symptoms l Common causes Depression l What is it? l Physical symptoms l Mental symptoms l Common causes Plasticity- ability to change l Adaptive plasticity - improves function l Ex. Stroke rehabilitiation l Maladaptive plasticity- dysfunction l Ex. PTSD (post traumatic stress disorder) l Long term potentiation l Enhanced communication (post synaptic neuron receptor more efficient) The Brain & Neurons l Neurons l Cells of the nervous system l Become electrically charged to transmit information (Sodium-potassium pumps) l Neurons need: l Energy- ATP for sodium potassium pumps 1. Oxygen 2. Glucose 3. Mitochondria- Methyl donor (folic acid / 5MTHF, B12) l Neurotransmitters l Stimulation The Synapse Neurotransmitters l Chemical signals Excitatory Inhibitory Epinephrine GABA Norepinephrine Dopamine Acetylcholine Serotonin Neurotransmitter testing l Urinary l Problems: l Blood brain barrier l Peripheral marker only Natural Approach: Balance & Support Function l Stress levels l Oxygen l Blood sugar l Energy production (methyl donors) l Neurotransmitters Overall Brain Health l Sleep l Safe environmental input l Oxygen l Blood circulation (hypertension/ hypotension) l Iron (anemia) l Glucose (hypoglycemia/ hyperglycemia/ diabetes) -
The Interaction Between Selected Antidepressants and Zinc Oxide Nanoparticles
Oct 21st – 23rd 2020, Brno, Czech Republic, EU THE INTERACTION BETWEEN SELECTED ANTIDEPRESSANTS AND ZINC OXIDE NANOPARTICLES 1Roman MARŠÁLEK, 1Martin ŠVIDRNOCH 1University of Ostrava, Ostrava, Czech Republic, EU, [email protected] https://doi.org/10.37904/nanocon.2020.3737 Abstract Interactions between tricyclic antidepressants and zinc oxide nanoparticles have been studied. Amitriptyline and nortriptyline, which were immobilized from buffer medium at 37 °C, were selected as models. The key factor influencing the adsorption of these substances on zinc oxide is pH. During the adsorption, an acid-base equilibrium was established between the buffer, zinc oxide and the antidepressant. These pH changes were also reflected in the surface charge of the adsorbent and the values of the zeta potential, which was also monitored. Both substances have a similar structure, yet they differ in their acid-base properties and also in their ability to form micelles. These different properties caused different values of the amount adsorbed on the surface of the zinc oxide. Adsorption isotherms show a sigmoidal course. The highest adsorbed amount of amitriptyline on ZnO is 6.38 mmol g-1, in the case of nortriptyline it is 3.68 mmol g-1. The adsorption is directed in accordance with the pseudo-second-order kinetic equation. The values from the kinetic equations, as well as the changes in the zeta potential, indicate different mechanisms of immobilization of amitriptyline and nortriptyline on the surface of zinc oxide nanoparticles. In the case of both substances, due to the interaction with zinc oxide, they were significantly removed from the liquid medium; in the case of amitriptyline, the residual concentration was less than 10% at an initial concentration of 5 mmol L-1. -
Virtual 2-D Map of the Fungal Proteome
www.nature.com/scientificreports OPEN Virtual 2‑D map of the fungal proteome Tapan Kumar Mohanta1,6*, Awdhesh Kumar Mishra2,6, Adil Khan1, Abeer Hashem3,4, Elsayed Fathi Abd‑Allah5 & Ahmed Al‑Harrasi1* The molecular weight and isoelectric point (pI) of the proteins plays important role in the cell. Depending upon the shape, size, and charge, protein provides its functional role in diferent parts of the cell. Therefore, understanding to the knowledge of their molecular weight and charges is (pI) is very important. Therefore, we conducted a proteome‑wide analysis of protein sequences of 689 fungal species (7.15 million protein sequences) and construct a virtual 2‑D map of the fungal proteome. The analysis of the constructed map revealed the presence of a bimodal distribution of fungal proteomes. The molecular mass of individual fungal proteins ranged from 0.202 to 2546.166 kDa and the predicted isoelectric point (pI) ranged from 1.85 to 13.759 while average molecular weight of fungal proteome was 50.98 kDa. A non‑ribosomal peptide synthase (RFU80400.1) found in Trichoderma arundinaceum was identifed as the largest protein in the fungal kingdom. The collective fungal proteome is dominated by the presence of acidic rather than basic pI proteins and Leu is the most abundant amino acid while Cys is the least abundant amino acid. Aspergillus ustus encodes the highest percentage (76.62%) of acidic pI proteins while Nosema ceranae was found to encode the highest percentage (66.15%) of basic pI proteins. Selenocysteine and pyrrolysine amino acids were not found in any of the analysed fungal proteomes. -
Power and Limitations of Electrophoretic Separations in Proteomics Strategies
Power and limitations of electrophoretic separations in proteomics strategies Thierry. Rabilloud 1,2, Ali R.Vaezzadeh 3 , Noelle Potier 4, Cécile Lelong1,5, Emmanuelle Leize-Wagner 4, Mireille Chevallet 1,2 1: CEA, IRTSV, LBBSI, 38054 GRENOBLE, France. 2: CNRS, UMR 5092, Biochimie et Biophysique des Systèmes Intégrés, Grenoble France 3: Biomedical Proteomics Research Group, Central Clinical Chemistry Laboratory, Geneva University Hospitals, Geneva, Switzerland 4: CNRS, UMR 7177. Institut de Chime de Strasbourg, Strasbourg, France 5: Université Joseph Fourier, Grenoble France Correspondence : Thierry Rabilloud, iRTSV/LBBSI, UMR CNRS 5092, CEA-Grenoble, 17 rue des martyrs, F-38054 GRENOBLE CEDEX 9 Tel (33)-4-38-78-32-12 Fax (33)-4-38-78-44-99 e-mail: Thierry.Rabilloud@ cea.fr Abstract: Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry( i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed. Keywords: electrophoresis, two-dimensional electrophoresis, isoelectric focusing, immobilized pH gradients, peptides, proteins, proteomics. Table of contents I. Introduction II. The principles at play III. How to use electrophoresis in a proteomics strategy III.A. -
Betaine, CNS, Amix-C
GHS SAFETY DATA SHEET AMERICAN CRYSTAL SUGAR COMPANY Prepared to U.S. OSHA Standards in compliance with the GHS system (29 CFR 1910.1200(g), rev. 2012 Section Identification CONCENTRATED BETAINE 1 SOLUTION, Used for supplemental BETAINE LIQUID SOLUTION, dietary nitrogen in livestock AMIX –C, (not for human CNS (CROSS-OVER NON- consumption) SUGARS) Manufacturer's Name No restrictions on use American Crystal Sugar Co. rd 101 North 3 Street Preparation Date: Moorhead, MN 56560 14 Jan 2015 Emergency Telephone Number: Revised: 20 June 2018 (218) 236-4400 Telephone Number for Information (218) 236-4324 Section Hazard(s) Identification No Hazardous Components 2 CNS is non-hazardous under normal conditions of use, storage, and handling. CNS is not considered combustible though in a dried state the organic components may provide secondary fuel for an existing fire. Section Composition / No Hazardous Components; it is a concentrated mixture of aqueous 3 Information on soluble material (composition may vary: betaine and other amino Ingredients acids) from the processing of the sugar beet root (Beta vulgaris) from which virtually all the sucrose and salts have been removed. Betaine (glycine betaine; Oxyneurine; N,N,N-trimethylglycine; Carboxymethyl)trimethylammonium inner salt): 30 – 40% anhydrous monohydrate C5H11NO2 C5H11NO2 · H2O Molecular Weight : 117.15 g/mol Molecular Weight : 135.16 g/mol CAS-No. : 107-43-7 CAS-No. : 590-47-6 EC-No. : 203-490-6 EC-No. : 203-490-6 Water, 30 – 45% CAS: 7732-18-5 Miscellaneous Organics, including other Amino Acids ~25% Cross-over Non-sugars (CNS)—American Crystal Sugar Company— 21 Jan 2015 Page 1 of 4 pages Section First Aid Measures SKIN: Redness and/or blistering of skin. -
Genes for Direct Methylation of Glycine Provide High Levels of Glycinebetaine and Abiotic-Stress Tolerance in Synechococcus and Arabidopsis
Genes for direct methylation of glycine provide high levels of glycinebetaine and abiotic-stress tolerance in Synechococcus and Arabidopsis Rungaroon Waditee*†, Md. Nazmul H. Bhuiyan*†, Vandna Rai*, Kenji Aoki‡, Yoshito Tanaka‡, Takashi Hibino‡, Shigetoshi Suzuki§, Jun Takano¶, Andre´ T. Jagendorfʈ, Tetsuko Takabe**, and Teruhiro Takabe*†† *Research Institute, ‡Graduate School of Environmental and Human Sciences, and §School of Agriculture, Meijo University, Nagoya 468-8502, Japan; ¶Shimadzu Company, Nakagyou-ku, Kyoto 604-8511, Japan; ʈDepartment of Plant Biology, Cornell University, Ithaca, NY 14853; and **Graduate School of Agricultural Science, Nagoya University, Nagoya 464-8601, Japan Contributed by Andre´T. Jagendorf, December 8, 2004 Betaine is an important osmoprotectant, synthesized by many methylation (20). Two N-methyltransferase enzymes were involved plants in response to abiotic stresses. Almost all known biosyn- in betaine synthesis. One enzyme [A. halophytica glycine sarcosine thetic pathways of betaine are two-step oxidations of choline. methyltransferase (ApGSMT)] catalyzed the methylation reactions Recently, a biosynthetic pathway of betaine from glycine, cata- of glycine to sarcosine and sarcosine to dimethylglycine, respec- lyzed by two N-methyltransferase enzymes, was found. Here, the tively, and the other enzyme [A. halophytica dimethylglycine meth- potential role of N-methyltransferase genes for betaine synthesis yltransferase (ApDMT)] catalyzed the specific methylation of dim- was examined in a freshwater cyanobacterium,