Hydration of Cations: a Key to Understanding of Specific Cation Effects on Aggregation Behaviors of PEO-PPO-PEO Triblock Copolymers Jacob C
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Selective and Specific Ion Binding on Proteins at Physiologically-Relevant
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 585 (2011) 3126–3132 journal homepage: www.FEBSLetters.org Selective and specific ion binding on proteins at physiologically-relevant concentrations ⇑ Linlin Miao a, Haina Qin a, Patrice Koehl a,b, Jianxing Song a,c, a Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore b Department of Computer Science and Genome Center, University of California, Davis, CA 95616, USA c Department of Biochemistry, Yong Loo Lin School of Medicine and National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore article info abstract Article history: Insoluble proteins dissolved in unsalted water appear to have no well-folded tertiary structures. Received 30 July 2011 This raises a fundamental question as to whether being unstructured is due to the absence of salt Revised 25 August 2011 ions. To address this issue, we solubilized the insoluble ephrin-B2 cytoplasmic domain in unsalted Accepted 29 August 2011 water and first confirmed using NMR spectroscopy that it is only partially folded. Using NMR HSQC Available online 6 September 2011 titrations with 14 different salts, we further demonstrate that the addition of salt triggers no signif- Edited by Miguel De la Rosa icant folding of the protein within physiologically relevant ion concentrations. We reveal however that their 8 anions bind to the ephrin-B2 protein with high affinity and specificity at biologically-rel- evant concentrations. Interestingly, the binding is found to be both salt- and residue-specific. Keywords: Insoluble protein Ó 2011 Federation of European Biochemical Societies. -
Peptide Chemistry up to Its Present State
Appendix In this Appendix biographical sketches are compiled of many scientists who have made notable contributions to the development of peptide chemistry up to its present state. We have tried to consider names mainly connected with important events during the earlier periods of peptide history, but could not include all authors mentioned in the text of this book. This is particularly true for the more recent decades when the number of peptide chemists and biologists increased to such an extent that their enumeration would have gone beyond the scope of this Appendix. 250 Appendix Plate 8. Emil Abderhalden (1877-1950), Photo Plate 9. S. Akabori Leopoldina, Halle J Plate 10. Ernst Bayer Plate 11. Karel Blaha (1926-1988) Appendix 251 Plate 12. Max Brenner Plate 13. Hans Brockmann (1903-1988) Plate 14. Victor Bruckner (1900- 1980) Plate 15. Pehr V. Edman (1916- 1977) 252 Appendix Plate 16. Lyman C. Craig (1906-1974) Plate 17. Vittorio Erspamer Plate 18. Joseph S. Fruton, Biochemist and Historian Appendix 253 Plate 19. Rolf Geiger (1923-1988) Plate 20. Wolfgang Konig Plate 21. Dorothy Hodgkins Plate. 22. Franz Hofmeister (1850-1922), (Fischer, biograph. Lexikon) 254 Appendix Plate 23. The picture shows the late Professor 1.E. Jorpes (r.j and Professor V. Mutt during their favorite pastime in the archipelago on the Baltic near Stockholm Plate 24. Ephraim Katchalski (Katzir) Plate 25. Abraham Patchornik Appendix 255 Plate 26. P.G. Katsoyannis Plate 27. George W. Kenner (1922-1978) Plate 28. Edger Lederer (1908- 1988) Plate 29. Hennann Leuchs (1879-1945) 256 Appendix Plate 30. Choh Hao Li (1913-1987) Plate 31. -
A Global Review on Short Peptides: Frontiers and Perspectives †
molecules Review A Global Review on Short Peptides: Frontiers and Perspectives † Vasso Apostolopoulos 1 , Joanna Bojarska 2,* , Tsun-Thai Chai 3 , Sherif Elnagdy 4 , Krzysztof Kaczmarek 5 , John Matsoukas 1,6,7, Roger New 8,9, Keykavous Parang 10 , Octavio Paredes Lopez 11 , Hamideh Parhiz 12, Conrad O. Perera 13, Monica Pickholz 14,15, Milan Remko 16, Michele Saviano 17, Mariusz Skwarczynski 18, Yefeng Tang 19, Wojciech M. Wolf 2,*, Taku Yoshiya 20 , Janusz Zabrocki 5, Piotr Zielenkiewicz 21,22 , Maha AlKhazindar 4 , Vanessa Barriga 1, Konstantinos Kelaidonis 6, Elham Mousavinezhad Sarasia 9 and Istvan Toth 18,23,24 1 Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; [email protected] (V.A.); [email protected] (J.M.); [email protected] (V.B.) 2 Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego˙ 116, 90-924 Lodz, Poland 3 Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar 31900, Malaysia; [email protected] 4 Botany and Microbiology Department, Faculty of Science, Cairo University, Gamaa St., Giza 12613, Egypt; [email protected] (S.E.); [email protected] (M.A.) 5 Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego˙ 116, 90-924 Lodz, Poland; [email protected] (K.K.); [email protected] (J.Z.) 6 NewDrug, Patras Science Park, 26500 Patras, Greece; [email protected] 7 Department of Physiology and Pharmacology, -
Specific Salt Effects on the Formation and Thermal Transitions Among Β-Lactoglobulin and Pectin Electrostatic Complexes
Purdue University Purdue e-Pubs Open Access Theses Theses and Dissertations 2013 Specific altS Effects on the Formation and Thermal Transitions Among β-Lactoglobulin and Pectin Electrostatic Complexes Stacey Ann Hirt Purdue University, [email protected] Follow this and additional works at: https://docs.lib.purdue.edu/open_access_theses Part of the Agriculture Commons, Bioresource and Agricultural Engineering Commons, Food Science Commons, and the Physical Chemistry Commons Recommended Citation Hirt, Stacey Ann, "Specific altS Effects on the Formation and Thermal Transitions Among β-Lactoglobulin and Pectin Electrostatic Complexes" (2013). Open Access Theses. 34. https://docs.lib.purdue.edu/open_access_theses/34 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. Graduate School ETD Form 9 (Revised 12/07) PURDUE UNIVERSITY GRADUATE SCHOOL Thesis/Dissertation Acceptance This is to certify that the thesis/dissertation prepared Stacey A. Hirt By ! Entitled! Specific Salt Effects on the Formation and Thermal Transitions Among "-Lactoglobulin and Pectin Electrostatic Complexes! Master of Science For the degree of Is approved by the final examining committee: Owen Jones Chair Yuan Yao Ganesan Narsimhan To the best of my knowledge and as understood by the student in the Research Integrity and Copyright Disclaimer (Graduate School Form 20), this thesis/dissertation adheres to the provisions of Purdue University’s “Policy on Integrity -
Amino Acids-The Molecular Building Blocks of Life
Understanding the structure-property relationships of amino acids-the molecular building blocks of life Aravindhan Ganesan Dissertation submitted in fulfillment of requirements for the degree of Doctor of Philosophy Environmental and Biotechnology Centre Faculty of Life & Social Sciences Swinburne University of Technology Victoria, Australia 2013 ©2013 Aravindhan Ganesan Abstract Amino acids are significant molecular building blocks of proteins. Only 20 natural amino acids, whose structures differ in their side chain ‘R-’ groups, control the structures, functions and selectivity of almost all the proteins in biology. The structure-properties of the amino acids must be revealed, in order to understand the methodical behind the nature’s choices in using them as ‘building blocks’. There are several molecular level details of the amino acids, which are still unknown or limitedly known. In this project, the electronic structures, properties and dynamics of the aliphatic and the aromatic amino acids under isolated and defined environmental conditions are studied quantum mechanically. A rich tool chest of ab initio and density functional theory (DFT) methods has been employed. The impacts of alkyl side chain groups on the structure-properties of the aliphatic amino acids are revealed in the gas phase. A number of properties including geometries, molecular dipole moments, ionization energies and spectra, charge re-distributions, vibrational spectra (IR and Raman), vibrational optical activity spectra (VOA), molecular orbitals and momentum spectra are investigated. Dual space analyses (DSA) has been employed as an efficient analytical tool to understand the electronic structures of the amino acids in both the coordinate space and momentum space. Our quantum chemical calculations are validated against the synchrotron-sourced and other experiments, whenever possible. -
Plant Proteomics As a Tool for Elucidating the Molecular Mechanisms Underlying Signaling and Plant Interactions with the Environment
PALACKÝ UNIVERESITY OLOMOUC Faculty of Science Plant proteomics as a tool for elucidating the molecular mechanisms underlying signaling and plant interactions with the environment Mgr. Martin Černý, Ph.D. MENDEL UNIVERSITY IN BRNO Faculty of AgriSciences Department of Molecular Biology and Radiobiology HABILITATION THESIS Study field: Biochemistry Brno 2021 Děkuji všem, kteří se přímo i nepřímo zasloužili o tuto práci. Mé rodině a přátelům za podporu a trpělivost. Těm, kteří se mnou spolupracovali a těm, co ve spolupráci pokračovali a pokračují i přes řadu experimentů, které nevedly k očekávaným cílům. V neposlední řadě patří poděkování prof. Břetislavu Brzobohatému, bez kterého by tato práce nevznikla. Contents 1. Introduction ....................................................................................................................... 1 2. Fractionation techniques to increase plant proteome coverage ......................................... 4 2.1. Tissue separation ........................................................................................................ 5 2.2. Subcellular plant proteome ......................................................................................... 7 2.3. Separations at the protein level ................................................................................... 9 2.4. Separation at the peptide level .................................................................................. 11 2.5. Comparison of fractionation techniques .................................................................. -
Methods in Biochemistry Metodologie Biochimiche Anno 2018-19 Stefania Brocca, Matilde Forcella, Paola Fusi
Methods in Biochemistry Metodologie Biochimiche Anno 2018-19 Stefania Brocca, Matilde Forcella, Paola Fusi [email protected] Tel. int.: 02 6448 3518 room: 5054, U3 - 5th floor https://elearning.unimib.it/ Metodologie Biochimiche 2018-19 01) Martedì 2/10 02) Venerdì 5/10 03) Martedì 9/10 Modulo frontale 04) Venerdì 12/10 Esercitazioni 4 crediti 05) Martedì 16/10 2 crediti (14 lezioni) 06) Venerdì 19/10 (20 h in 5 pomeriggi) 07) Martedì 23/10 Aule: U1-04; U1-10 08) Venerdì 26/10 3 turni da 1 settimana 09) Martedì 30/10 dicembre 2018, gennaio 2019, 10) Martedì 06/11 febbraio 2019 11) Venerdì 09/11 Lab 1026 12) Martedì 13/11 13) Venerdì 16/11 14) Martedì 20/11 Program (theoretical lessons) Protein «environments» Electrophoresis Hydrophobic effect Principles Solubility, salting in/salting out SDS-PAGE Hofmeister series (Blue)-native gel Denaturing agents Band-shift assay Dialysis Isoelectrophocusing Centrifugation techniques Bidimensional gel Principles Western blot Differential centrifugation Spectroscopies Density gradient centrifugation Principles Analytical ultracentrifugation Absorbance Chromatography Fluorescence Principles Circular dichroism Chromatographer set up Mass spectrometry Gel filtration Surface plasmon resonance Ion exchange Hydrophobic interactions Affinity tags Suggested references Wilson K. & Walker J. (2000) “Biochimica e Biologia Molecolare” Cortina, 2006 Numero di pagine: 777 Prezzo: ~ € 100 M. C. Bonaccorsi di Patti, R. Contestabile, M. L. Di Salvo Cited articles “Metodologie Biochimiche” Casa Editrice Ambrosiana, -
UNIVERSITY of CALIFORNIA, SAN DIEGO Biochemical Kinds And
UNIVERSITY OF CALIFORNIA, SAN DIEGO Biochemical Kinds and Selective Naturalism A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Philosophy (Science Studies) by Joyce Catherine Havstad Committee in charge: Professor William Bechtel, Chair Professor Craig Callender Professor Nancy Cartwright Professor Cathy Gere Professor James Griesemer 2014 © Joyce Catherine Havstad, 2014 All rights reserved. The Dissertation of Joyce Catherine Havstad is approved, and it is acceptable in quality and form for publication on microfilm and electronically: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Chair University of California, San Diego 2014 iii DEDICATION for my parents iv TABLE OF CONTENTS Signature Page…………………………………………………………………….. iii Dedication…………………………………………………………………………. iv Table of Contents………………………………………………………………….. v List of Figures……………………………………………………………………... viii Vita………………………………………………………………………………… x Abstract of the Dissertation………………………………………………………... xi Introduction………………………………………………………………………... 1 References……………………………………………………………………... 7 Chapter 1: Messy Chemical Kinds………………………………………………… 8 Section 1: Introduction………………………………………………………… 8 Section 2: Microstructuralism about Chemical Kinds…………………………. -
Protein Precipitation Using Ammonium Sulfate
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Curr Protoc Manuscript Author Protein Sci. Manuscript Author Author manuscript; available in PMC 2016 April 01. Published in final edited form as: Curr Protoc Protein Sci. 2001 May ; APPENDIX 3: Appendix–3F. doi:10.1002/0471140864.psa03fs13. Protein Precipitation Using Ammonium Sulfate Paul T. Wingfield Protein Expression Laboratory (HNB-27), National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) - NIH, Bldg 6B, Room 1B130, 6 Center Drive, Bethesda MD 20814, Tel: 301-594-1313 Paul T. Wingfield: [email protected] Abstract The basic theory of protein precipitation by addition of ammonium sulfate is presented and the most common applications are listed, Tables are provided for calculating the appropriate amount of ammonium sulfate to add to a particular protein solution. Key terms for indexing Ammonium sulfate; ammonium sulfate tables; protein concentration; protein purification BASIC THEORY The solubility of globular proteins increases upon the addition of salt (<0.15 M), an effect termed salting-in. At higher salt concentrations, protein solubility usually decreases, leading to precipitation; this effect is termed salting-out ((Green and Hughes, 1955). Salts that reduce the solubility of proteins also tend to enhance the stability of the native conformation. In contrast, salting-in ions are usually denaturants. The mechanism of salting-out is based on preferential solvation due to exclusion of the cosolvent (salt) from the layer of water closely associated with the surface of the protein (hydration layer). The hydration layer, typically 0.3 to 0.4 g water per gram protein (Rupley et al., 1983), plays a critical role in maintaining solubility and the correctly folded native conformation. -
Models and Mechanisms of Hofmeister Effects in Electrolyte
Chem Soc Rev View Article Online REVIEW ARTICLE View Journal | View Issue Models and mechanisms of Hofmeister effects in electrolyte solutions, and colloid and protein Cite this: Chem. Soc. Rev., 2014, 43,7358 systems revisited Andrea Salis*ab and Barry W. Ninhamb Specific effects of electrolytes have posed a challenge since the 1880’s. The pioneering work was that of Franz Hofmeister who studied specific salt induced protein precipitation. These effects are the rule rather the exception and are ubiquitous in chemistry and biology. Conventional electrostatic theories (Debye– Hu¨ckel, DLVO, etc.) cannot explain such effects. Over the past decades it has been recognised that addi- tional quantum mechanical dispersion forces with associated hydration effects acting on ions are missing from theory. In parallel Collins has proposed a phenomenological set of rules (the law of matching water affinities, LMWA) which explain and bring to order the order of ion–ion and ion–surface site interactions at a qualitative level. The two approaches appear to conflict. Although the need for inclusion of quantum Creative Commons Attribution 3.0 Unported Licence. dispersion forces in one form or another is not questioned, the modelling has often been misleading and inappropriate. It does not properly describe the chemical nature (kosmotropic/chaotropic or hard/soft) of the interacting species. The success of the LMWA rules lies in the fact that they do. Here we point to the Received 30th April 2014 way that the two apparently opposing approaches might be reconciled. Notwithstanding, there are more DOI: 10.1039/c4cs00144c challenges, which deal with the effect of dissolved gas and its connection to ‘hydrophobic’ interactions, the problem of water at different temperatures and ‘water structure’ in the presence of solutes. -
Are Hofmeister Series Relevant to Modern Ion-Specific Effects Research?
Scholarly Research Exchange Volume 2008 • Article ID 818461 • doi:10.3814/2008/818461 Research Article Are Hofmeister Series Relevant to Modern Ion-Specific Effects Research? Terence J. Evens and Randall P. Niedz USDA, Agricultural Research Service, U.S. Horticultural Research Laboratory, 2001 South Rock Road, Ft. Pierce, FL 34945-3030, USA Correspondence should be addressed to Terence J. Evens, [email protected] Received 29 February 2008; Revised 17 April 2008; Accepted 5 May 2008 Ion-specific effects underlie a vast array of physicochemical and biological phenomena ranging from human physiology to biotechnology to ecology. These effects have traditionally been quantified by measuring the response of interest in a series of salt solutions at multiple concentrations; pH has consistently been shown to be of primary concern. However, salt-based approaches violate critical tenets of proper experimental design and introduce confounding errors that make it impossible to quantify ion- specific effects. For example, pH is a variable dependent on the type and concentration of ions in a solution, but is typically treated as an independent factor, thus confounding experiments designed to determine ion-specific effects. We examined the relevancy of ion-specific effects research in relation to these concepts and demonstrated how these ideas impact protein precipitation and enzyme activity. Based on these results, we present a conceptual and experimental framework of general applicability for proper quantification of ion-specific effects. Copyright © 2008 T. J. Evens and R. P. Niedz. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. -
Biochemistry 06 Salt Fractionation of Proteins
. 1 Biochemical Techniques Biochemistry 06 Salt Fractionation of Proteins Description of Module Subject Name Biochemistry Paper Name 12 Biochemical Techniques Module Name/Title 06 Salt Fractionation of Proteins 2 Biochemical Techniques Biochemistry 06 Salt Fractionation of Proteins 1. Objectives Understanding the concept of protein fractionation Understanding protein fractionation with salt 2. Concept Map 3. Description 3.1 Protein purification Protein purification is vital for the characterization of protein structure, function and interactions, for example conformational alterations, substrate specificities, specific activities as well as interaction with other ligands. Further, for applications in the food and pharmaceutical industry, a high level of protein purity is 3 Biochemical Techniques Biochemistry 06 Salt Fractionation of Proteins essential and the desired protein must be purified over a number of steps. This is thus achieved through methods of protein purification. Purification is a multistep procedure. The various steps in the purification process are aimed removing non- protein components and impurities to finally separating out the desired protein in its pure form. 3.2 Fractionation of proteins The first step in purifying intracellular proteins is preparing a crude extract. The extract will contain a complex mixture of proteins from cell cytoplasm, and additional components such as macromolecules, cofactors and nutrients. The debris are removed by centrifugation and supernatant (crude protein extract) recovered. Crude preparations of extracellular proteins may be obtained by removing cells by centrifugation. The extract can be subjected to treatments that separate proteins into different fractions based on several properties such as size, charge etc. This process is known as fractionation. Fractionation helps in the removal of any other contaminating material and also in the enrichment of the desired protein fraction.