The Solubility of Amino Acids in Various Solvent Systems
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Insights Into the Molecular Basis for Substrate Binding and Specificity of the Wild-Type L-Arginine/Agmatine Antiporter Adic
Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC Hüseyin Ilgüa,b,1, Jean-Marc Jeckelmanna,b,1, Vytautas Gapsysc, Zöhre Ucuruma,b, Bert L. de Grootc, and Dimitrios Fotiadisa,b,2 aInstitute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland; bSwiss National Centre of Competence in Research TransCure, University of Bern, CH-3012 Bern, Switzerland; and cComputational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, D-37077 Goettingen, Germany Edited by Christopher Miller, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, and approved July 26, 2016 (received for review April 4, 2016) Pathogenic enterobacteria need to survive the extreme acidity of Arg-bound states (10). The two outward-open, substrate-free the stomach to successfully colonize the human gut. Enteric bacteria structures are at the reasonable and moderate resolutions of 3.2 Å circumvent the gastric acid barrier by activating extreme acid- (8) and 3.6 Å (9), respectively, and the only ones available of wild- resistance responses, such as the arginine-dependent acid resistance type AdiC (AdiC-wt). The two other structures are with bound system. In this response, L-arginine is decarboxylated to agmatine, Arg and at 3-Å resolution, and could only be obtained as a result thereby consuming one proton from the cytoplasm. In Escherichia of the introduction of specific point mutations: AdiC-N22A (10) coli,theL-arginine/agmatine antiporter AdiC facilitates the export and AdiC-N101A (11). The N101A mutation results in a defective of agmatine in exchange of L-arginine, thus providing substrates for AdiC protein unable to bind Arg and with a dramatically de- further removal of protons from the cytoplasm and balancing the creased turnover rate compared with wild-type (11). -
Separation of Isomers <Emphasis Type="Italic">L </Emphasis>-Alanine and Sarcosine in Urine by Electrospra
SHORT COMMUNICATION Separation of Isomers L-Alanine and Sarcosine in Urine by Electrospray Ionization and Tandem Differential Mobility Analysis-Mass Spectrometry Pablo Martínez-Lozanoa and Juan Rusb a Institute for Biomedical Technologies-National Research Council, Milan, Italy b SEADM, Valladolid, Spain Sarcosine, an isomer of L-alanine, has been proposed as a prostate cancer progression biomarker [1]. Both compounds are detected in urine, where the measured sarcosine/alanine ratio has been found to be higher in prostate biopsy-positive group versus controls. We present here preliminary evidence showing that urine samples spiked with sarcosine/alanine can be partially resolved in 3 min via tandem differential mobility analysis-mass spectrometry (DMA-MS). Based on the calibration curves obtained for two mobility peaks, we finally estimate their concentration ratio in urine. (J Am Soc Mass Spectrom 2010, 21, 1129–1132) © 2010 American Society for Mass Spectrometry rostate cancer is a leading cause of death among the tive-ion mode at the DMA entrance slit. Our nanospray male population. Sarcosine, an isomer of alanine, parameters were: capillary 360 m o.d., 50 m i.d., length Pwas recently proposed as a prostate cancer progres- 22 cm, driving pressure 75 mbar, and 3.8 kV. The ions sion biomarker [1]. In particular, the sarcosine/alanine entered the separation region propelled by an electric field ratio was found to be significantly higher in urine derived and against a counterflow gas (0.2 L/min). Sheath gas from biopsy-positive prostate cancer patients compared flow was kept constant, and the classification voltage was with biopsy-negative controls. -
Workshop 1 – Biochemistry (Chem 160)
Workshop 1 – Biochemistry (Chem 160) 1. Draw the following peptide at pH = 7 and make sure to include the overall charge, label the N- and C-terminus, the peptide bond and the -carbon. AVDKY Give the overall charge of the peptide at pH = 3 and 12. 2. Draw a titration curve for Arg, make sure to label the different points. Determine the pI for Arg. 3. Nonpolar solute + water = solution a. What is the S of the universe, system and surroundings? The S of the universe would decrease this is why it is not spontaneous, the S of the system would increase but to a lesser extent to which the S of the surrounding would decrease S universe = S system + S surroundings 4. What is the hydrophobic effect and explain why it is thermodynamically favorable. The hydrophobic effect is when hydrophobic molecules tend to clump together burying them and placing hydrophilic molecules on the outside. The reason this is thermodynamically favorable is because it frees caged water molecules when burying clumping the hydrophobic molecules together. 5. Urea dissolves very readily in water, but the solution becomes very cold as the urea dissolves. How is this possible? Urea dissolves in water because when dissolving there is a net increase in entropy of the universe. The heat exchange, getting colder only reflects the enthalpy (H) component of the total energy change. The entropy change is high enough to offset the enthalpy component and to add up to an overall -G 6. A mutation that changes an alanine residue in the interior of a protein to valine is found to lead to a loss of activity. -
Beta Alanine
PERFORMANCE ENHANCERS FACTS AND BOTTOM LINE BETA ALANINE What is it? B-alanine is a naturally occurring amino acid (a non-essential amino acid) not used by the body to make muscle tissue. Rather, research has shown that B-alanine works by increasing the muscle content of an important compound – carnosine. In fact, the production of carnosine is limited by the availability of B-alanine. Carnosine is highly concentrated in muscle tissue where its role is primarily to soak up hydrogen ions. Does it work? B-alanine is one of the few dietary supplements that actually have good scientific evidence that it can possibly enhance performance. How does it work? When you exercise intensely the body produces hydrogen ions. The longer you exercise the more hydrogen ions you produce and this reduces the pH level in your muscles. Muscles work best in a very specific pH range and when the pH drops below that level then muscular performance also starts to decrease. Anything that helps to prevent or delay that drop in pH will help delay muscle fatigue. This is where B-alanine has proven to be very helpful. Beta-alanine increases the levels of carnosine in your slow and fast twitch muscle fibers and carnosine is a buffer that basically soaks up hydrogen ions and so reduces the drop in pH. By keeping your hydrogen ion levels lower, B-alanine allows you to train harder and longer. The bottom line is that B-alanine works by increasing the hydrogen ion buffering abilities of your muscles. What benefits does it offer? B-alanine has been shown to increase muscle strength, increase muscle mass, increase anaerobic endurance, increase aerobic endurance and increase exercise capacity. -
Targeting Glycine Reuptake in Alcohol Seeking and Relapse
JPET Fast Forward. Published on January 24, 2018 as DOI: 10.1124/jpet.117.244822 This article has not been copyedited and formatted. The final version may differ from this version. TITLE PAGE Targeting Glycine Reuptake in Alcohol Seeking and Relapse Valentina Vengeliene, Martin Roßmanith, Tatiane T. Takahashi, Daniela Alberati, Berthold Behl, Anton Bespalov, Rainer Spanagel Downloaded from The primary laboratory of origin: Institute of Psychopharmacology, Central Institute of jpet.aspetjournals.org Mental Health, Faculty of Medicine Mannheim, Heidelberg University, Germany; at ASPET Journals on September 30, 2021 VV, MR, TTT, RS: Institute of Psychopharmacology, Central Institute of Mental Health, Faculty of Medicine Mannheim, Heidelberg University, Germany; DA: Roche Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, CH-4070 Basel, Switzerland; BB, AB: Department of Neuroscience Research, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen, Germany; AB: Department of Psychopharmacology, Pavlov Medical University, St Petersburg, Russia JPET #244822 JPET Fast Forward. Published on January 24, 2018 as DOI: 10.1124/jpet.117.244822 This article has not been copyedited and formatted. The final version may differ from this version. RUNNING TITLE GlyT1 in Alcohol Seeking and Relapse Corresponding author with complete address: Valentina Vengeliene, Institute of Psychopharmacology, Central Institute of Mental Health (CIMH), J5, 68159 Mannheim, Germany Email: [email protected], phone: +49-621-17036261; fax: +49-621- Downloaded from 17036255 jpet.aspetjournals.org The number of text pages: 33 Number of tables: 0 Number of figures: 6 Number of references: 44 at ASPET Journals on September 30, 2021 Number of words in the Abstract: 153 Number of words in the Introduction: 729 Number of words in the Discussion: 999 A recommended section assignment to guide the listing in the table of content: Drug Discovery and Translational Medicine 2 JPET #244822 JPET Fast Forward. -
Poly(L-Alanine) As a Universal Reference Material for Understanding Protein Energies and Structures TERESA HEAD-GORDON, FRANK H
Proc. Nati. Acad. Sci. USA Vol. 89, pp. 11513-11517, December 1992 Biophysics Poly(L-alanine) as a universal reference material for understanding protein energies and structures TERESA HEAD-GORDON, FRANK H. STILLINGER, MARGARET H. WRIGHT, AND DAVID M. GAY AT&T Bell Laboratories, Murray Hill, NJ 07974 Contributed by Frank H. Stillinger, June 17, 1992 ABSTRACT We present a proposition, the "poly(L- alanine) hypothesis," which asserts that the native backbone geometry for any polypeptide or protein of M residues has a closely mimicking, mechanically stable, image in poly(L- POLY-L-ALANINE alanine) of the same number of residues. Using a molecular co mechanics force field to represent the relevant potential energy a: hypersurfaces, we have carried out calculations over a wide z range of M values to show that poly(L-alanine) possesses the w structural versatility necessary to satisfy the proposition. These w include poly(L-alanine) representatives of minima correspond- U- ing to secondary and supersecondary structures, as well as PROTEIN poly(L-alanine) images for tertiary structures of the naturally occurring proteins bovine pancreatic trypsin inhibitor, crambin, ribonuclease A, and superoxide dismutase. The suc- cessful validation of the hypothesis presented in this paper BACKBONE COORDINATES indicates that poly(L-alanine) will serve as a good reference FIG. 1. Topographic basis ofthe poly(L-alanine) hypothesis. Free material in thermodynamic perturbation theory and calcula- energy hypersurfaces are compared for a given protein and for tions aimed at evaluating relative free energies for competing poly(L-alanine) with the same number of residues. candidate tertiary structures in real polypeptides and proteins. -
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. -
101 Lime Solvent
Sure Klean® CLEANING & PROTECTIVE TREATMENTS 101 Lime Solvent Sure Klean® 101 Lime Solvent is a concentrated acidic cleaner for dark-colored brick and tile REGULATORY COMPLIANCE surfaces which are not subject to metallic oxidation. VOC Compliance Safely removes excess mortar and construction dirt. Sure Klean® 101 Lime Solvent is compliant with all national, state and district VOC regulations. ADVANTAGES • Removes construction dirt and excess mortar with TYPICAL TECHNICAL DATA simple cold water rinse. Clear, brown liquid • Removes efflorescence from new brick and new FORM Pungent odor stone construction. SPECIFIC GRAVITY 1.12 • Safer than muriatic acid on colored mortar and dark-colored new masonry surfaces. pH 0.50 @ 1:6 dilution • Proven effective since 1954. WT/GAL 9.39 lbs Limitations ACTIVE CONTENT not applicable • Not generally effective in removal of atmospheric TOTAL SOLIDS not applicable stains and black carbon found on older masonry VOC CONTENT not applicable surfaces. Use the appropriate Sure Klean® FLASH POINT not applicable restoration cleaner to remove atmospheric staining from older masonry surfaces. FREEZE POINT <–22° F (<–30° C) • Not for use on polished natural stone. SHELF LIFE 3 years in tightly sealed, • Not for use on treated low-E glass; acrylic and unopened container polycarbonate sheet glazing; and glazing with surface-applied reflective, metallic or other synthetic coatings and films. SAFETY INFORMATION Always read full label and SDS for precautionary instructions before use. Use appropriate safety equipment and job site controls during application and handling. 24-Hour Emergency Information: INFOTRAC at 800-535-5053 Product Data Sheet • Page 1 of 4 • Item #10010 – 102715 • ©2015 PROSOCO, Inc. -
Amino Acid Chemistry
Handout 4 Amino Acid and Protein Chemistry ANSC 619 PHYSIOLOGICAL CHEMISTRY OF LIVESTOCK SPECIES Amino Acid Chemistry I. Chemistry of amino acids A. General amino acid structure + HN3- 1. All amino acids are carboxylic acids, i.e., they have a –COOH group at the #1 carbon. 2. All amino acids contain an amino group at the #2 carbon (may amino acids have a second amino group). 3. All amino acids are zwitterions – they contain both positive and negative charges at physiological pH. II. Essential and nonessential amino acids A. Nonessential amino acids: can make the carbon skeleton 1. From glycolysis. 2. From the TCA cycle. B. Nonessential if it can be made from an essential amino acid. 1. Amino acid "sparing". 2. May still be essential under some conditions. C. Essential amino acids 1. Branched chain amino acids (isoleucine, leucine and valine) 2. Lysine 3. Methionine 4. Phenyalanine 5. Threonine 6. Tryptophan 1 Handout 4 Amino Acid and Protein Chemistry D. Essential during rapid growth or for optimal health 1. Arginine 2. Histidine E. Nonessential amino acids 1. Alanine (from pyruvate) 2. Aspartate, asparagine (from oxaloacetate) 3. Cysteine (from serine and methionine) 4. Glutamate, glutamine (from α-ketoglutarate) 5. Glycine (from serine) 6. Proline (from glutamate) 7. Serine (from 3-phosphoglycerate) 8. Tyrosine (from phenylalanine) E. Nonessential and not required for protein synthesis 1. Hydroxyproline (made postranslationally from proline) 2. Hydroxylysine (made postranslationally from lysine) III. Acidic, basic, polar, and hydrophobic amino acids A. Acidic amino acids: amino acids that can donate a hydrogen ion (proton) and thereby decrease pH in an aqueous solution 1. -
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. -
Solvent Effects on the Thermodynamic Functions of Dissociation of Anilines and Phenols
University of Wollongong Research Online University of Wollongong Thesis Collection 1954-2016 University of Wollongong Thesis Collections 1982 Solvent effects on the thermodynamic functions of dissociation of anilines and phenols Barkat A. Khawaja University of Wollongong Follow this and additional works at: https://ro.uow.edu.au/theses University of Wollongong Copyright Warning You may print or download ONE copy of this document for the purpose of your own research or study. The University does not authorise you to copy, communicate or otherwise make available electronically to any other person any copyright material contained on this site. You are reminded of the following: This work is copyright. Apart from any use permitted under the Copyright Act 1968, no part of this work may be reproduced by any process, nor may any other exclusive right be exercised, without the permission of the author. Copyright owners are entitled to take legal action against persons who infringe their copyright. A reproduction of material that is protected by copyright may be a copyright infringement. A court may impose penalties and award damages in relation to offences and infringements relating to copyright material. Higher penalties may apply, and higher damages may be awarded, for offences and infringements involving the conversion of material into digital or electronic form. Unless otherwise indicated, the views expressed in this thesis are those of the author and do not necessarily represent the views of the University of Wollongong. Recommended Citation Khawaja, Barkat A., Solvent effects on the thermodynamic functions of dissociation of anilines and phenols, Master of Science thesis, Department of Chemistry, University of Wollongong, 1982. -
Therapeutic Effect of Agmatine on Neurological Disease: Focus on Ion Channels and Receptors
Neurochemical Research (2019) 44:735–750 https://doi.org/10.1007/s11064-018-02712-1 REVIEW PAPER Therapeutic Effect of Agmatine on Neurological Disease: Focus on Ion Channels and Receptors Sumit Barua1 · Jong Youl Kim1 · Jae Young Kim1 · Jae Hwan Kim4 · Jong Eun Lee1,2,3 Received: 15 October 2018 / Revised: 19 December 2018 / Accepted: 24 December 2018 / Published online: 4 January 2019 © Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract The central nervous system (CNS) is the most injury-prone part of the mammalian body. Any acute or chronic, central or peripheral neurological disorder is related to abnormal biochemical and electrical signals in the brain cells. As a result, ion channels and receptors that are abundant in the nervous system and control the electrical and biochemical environment of the CNS play a vital role in neurological disease. The N-methyl-D-aspartate receptor, 2-amino-3-(5-methyl-3-oxo-1,2-oxazol-4-yl) propanoic acid receptor, kainate receptor, acetylcholine receptor, serotonin receptor, α2-adrenoreceptor, and acid-sensing ion channels are among the major channels and receptors known to be key components of pathophysiological events in the CNS. The primary amine agmatine, a neuromodulator synthesized in the brain by decarboxylation of L-arginine, can regu- late ion channel cascades and receptors that are related to the major CNS disorders. In our previous studies, we established that agmatine was related to the regulation of cell differentiation, nitric oxide synthesis, and murine brain endothelial cell migration, relief of chronic pain, cerebral edema, and apoptotic cell death in experimental CNS disorders.