Biochemistry Enzyme Ionizable Groups
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Side-Chain Liquid Crystal Polymers (SCLCP): Methods and Materials. an Overview
Materials 2009, 2, 95-128; doi:10.3390/ma2010095 OPEN ACCESS materials ISSN 1996-1944 www.mdpi.com/journal/materials Review Side-chain Liquid Crystal Polymers (SCLCP): Methods and Materials. An Overview Tomasz Ganicz * and Włodzimierz Stańczyk Centre of Molecular and Macromolecular Studies, Polish Academy of Science, Sienkiewicza 112, 90- 363 Łódź, Poland; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel. +48-42-684-71-13; Fax: +48-42-684-71-26 Received: 5 February 2009; in revised form: 3 March 2009 / Accepted: 9 March 2009 / Published: 11 March 2009 Abstract: This review focuses on recent developments in the chemistry of side chain liquid crystal polymers. It concentrates on current trends in synthetic methods and novel, well defined structures, supramolecular arrangements, properties, and applications. The review covers literature published in this century, apart from some areas, such as dendritic and elastomeric systems, which have been recently reviewed. Keywords: Liquid crystals, side chain polymers, polymer modification, polymer synthesis, self-assembly. 1. Introduction Over thirty years ago the work of Finkelmann and Ringsdorf [1,2] gave important momentum to synthesis of side chain liquid crystal polymers (SCLCPs), materials which combine the anisotropy of liquid crystalline mesogens with the mechanical properties of polymers. Although there were some earlier attempts [2], their approach of decoupling the motions of a polymer main chain from a mesogen, thus allowed side chain moieties to build up long range ordering (Figure 1). They were able to synthesize polymers with nematic, smectic and cholesteric phases via free radical polymerization of methacryloyl type monomers [3]. -
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. -
The Role of Side-Chain Branch Position on Thermal Property of Poly-3-Alkylthiophenes
Polymer Chemistry The Role of Side-chain Branch Position on Thermal Property of Poly-3-alkylthiophenes Journal: Polymer Chemistry Manuscript ID PY-ART-07-2019-001026.R2 Article Type: Paper Date Submitted by the 02-Oct-2019 Author: Complete List of Authors: Gu, Xiaodan; University of Southern Mississippi, School of Polymer Science and Engineering Cao, Zhiqiang; University of Southern Mississippi, School of Polymer Science and Engineering Galuska, Luke; University of Southern Mississippi, School of Polymer Science and Engineering Qian, Zhiyuan; University of Southern Mississippi, School of Polymer Science and Engineering Zhang, Song; University of Southern Mississippi, School of Polymer Science and Engineering Huang, Lifeng; University of Southern Mississippi, School of Polymers and High Performance Materials Prine, Nathaniel; University of Southern Mississippi, School of Polymer Science and Engineering Li, Tianyu; Oak Ridge National Laboratory; University of Tennessee Knoxville He, Youjun; Oak Ridge National Laboratory Hong, Kunlun; Oak Ridge National Laboratory, Center for Nanophase Materials Science; Oak Ridge National Laboratory, Center for Nanophase Materials Science Page 1 of 13 PleasePolymer do not Chemistryadjust margins ARTICLE The Role of Side-chain Branch Position on Thermal Property of Poly-3-alkylthiophenes Received 00th January 20xx, a a a a a a Accepted 00th January 20xx Zhiqiang Cao, Luke Galuska, Zhiyuan Qian, Song Zhang, Lifeng Huang, Nathaniel Prine, Tianyu Li,b, c Youjun He,b Kunlun Hong,*b, c and Xiaodan Gu*a DOI: 10.1039/x0xx00000x Thermomechanical properties of conjugated polymers (CPs) are greatly influenced by both their microstructures and backbone structures. In the present work, to investigate the effect of side-chain branch position on the backbone’s mobility and molecular packing structure, four poly (3-alkylthiophene-2, 5-diyl) derivatives (P3ATs) with different side chains, either branched and linear, were synthesized by a quasi-living Kumada catalyst transfer polymerization (KCTP) method. -
Thermal Decomposition of the Amino Acids Glycine, Cysteine, Aspartic Acid, Asparagine, Glutamic Acid, Glutamine, Arginine and Histidine
bioRxiv preprint doi: https://doi.org/10.1101/119123; this version posted March 22, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Thermal decomposition of the amino acids glycine, cysteine, aspartic acid, asparagine, glutamic acid, glutamine, arginine and histidine Ingrid M. Weiss*, Christina Muth, Robert Drumm & Helmut O.K. Kirchner INM-Leibniz Institute for New Materials, Campus D2 2, D-66123 Saarbruecken Germany *Present address: Universität Stuttgart, Institut für Biomaterialien und biomolekulare Systeme, Pfaffenwaldring 57, D-70569 Stuttgart, Germany Abstract Calorimetry, thermogravimetry and mass spectrometry were used to follow the thermal decomposition of the eight amino acids G, C, D, N, E, Q, R and H between 185°C and 280°C. Endothermic heats of decomposition between 72 and 151 kJ/mol are needed to form 12 to 70 % volatile products. This process is neither melting nor sublimation. With exception of cysteine they emit mainly H2O, some NH3 and no CO2. Cysteine produces CO2 and little else. The reactions are described by polynomials, AA → a (NH3) + b (H2O) + c (CO2) + d (H2S) + e (residue), with integer or half integer coefficients. The solid monomolecular residues are rich in peptide bonds. 1. Motivation Amino acids might have been synthesized under prebiological conditions on earth or deposited on earth from interstellar space, where they have been found [Follmann and Brownson, 2009]. Robustness of amino acids against extreme conditions is required for early occurrence, but little is known about their nonbiological thermal destruction. There is hope that one might learn something about the molecules needed in synthesis from the products found in decomposition. -
Improved Prediction of Protein Side-Chain Conformations with SCWRL4 Georgii G
proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improved prediction of protein side-chain conformations with SCWRL4 Georgii G. Krivov,1,2 Maxim V. Shapovalov,1 and Roland L. Dunbrack Jr.1* 1 Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111 2 Department of Applied Mathematics, Moscow Engineering Physics Institute (MEPhI), Kashirskoe Shosse 31, Moscow 115409, Russian Federation INTRODUCTION ABSTRACT The side-chain conformation prediction problem is an integral Determination of side-chain conformations is an component of protein structure determination, protein structure important step in protein structure prediction and protein design. Many such methods have prediction, and protein design. In single-site mutants and in closely been presented, although only a small number related proteins, the backbone often changes little and structure pre- 1 are in widespread use. SCWRL is one such diction can be accomplished by accurate side-chain prediction. In method, and the SCWRL3 program (2003) has docking of ligands and other proteins, taking into account changes remained popular because of its speed, accuracy, in side-chain conformation is often critical to accurate structure pre- and ease-of-use for the purpose of homology dictions of complexes.2–4 Even in methods that take account of modeling. However, higher accuracy at compara- changes in backbone conformation, one step in the process is recal- ble speed is desirable. This has been achieved in culation of side-chain conformation or ‘‘repacking.’’5 Because many a new program SCWRL4 through: (1) a new backbone conformations may be sampled in model refinements, backbone-dependent rotamer library based on side-chain prediction must also be very fast. -
Mendelian Randomization Study on Amino Acid Metabolism Suggests Tyrosine As Causal Trait for Type 2 Diabetes
nutrients Article Mendelian Randomization Study on Amino Acid Metabolism Suggests Tyrosine as Causal Trait for Type 2 Diabetes Susanne Jäger 1,2,* , Rafael Cuadrat 1,2, Clemens Wittenbecher 1,2,3, Anna Floegel 4, Per Hoffmann 5,6, Cornelia Prehn 7 , Jerzy Adamski 2,7,8,9 , Tobias Pischon 10,11,12 and Matthias B. Schulze 1,2,13 1 Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; [email protected] (R.C.); [email protected] (C.W.); [email protected] (M.B.S.) 2 German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; [email protected] 3 Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA 4 Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany; fl[email protected] 5 Human Genomics Research Group, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland; per.hoff[email protected] 6 Institute of Human Genetics, Division of Genomics, Life & Brain Research Centre, University Hospital of Bonn, 53105 Bonn, Germany 7 Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; [email protected] 8 Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany 9 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, -
H-Tyrosine-Glycine-Phenylalanine-Glycine-Glycine-OH for the Treatment of Chronic Idiopathic Myelofibrosis
European Medicines Agency Pre-authorisation Evaluation of Medicines for Human Use Document Date: London, 5 October 2009 Doc.Ref.: EMEA/COMP/1579/2003 Rev.1 Please note that this product was withdrawn from the Community Register of designated Orphan Medicinal Products in March 2009 on request of the Sponsor. Committee for Orphan Medicinal Products Public summary of positive opinion for orphan designation of H-Tyrosine-Glycine-Phenylalanine-Glycine-Glycine-OH for the treatment of chronic idiopathic myelofibrosis On 20 October 2003, orphan designation (EU/3/03/167) was granted by the European Commission to Abiogen Pharma S.p.A, Italy, for H-Tyrosine-Glycine-Phenylalanine-Glycine-Glycine-OH for the treatment of chronic idiopathic myelofibrosis. What is chronic idiopathic myelofibrosis? Chronic idiopathic myelofibrosis is a disease in which cancer cells are found in the blood and in the bone marrow. The bone marrow is the spongy tissue inside the large bones in the body. Normally the bone marrow makes cells called “blasts” that mature into several different types of blood cells that have specific functions in the body. These include red cells, white cells and platelets. Red blood cells carry oxygen and other materials to all tissues of the body. White blood cells fight infection. Platelets make the blood clot. When myelofibrosis develops, the bone marrow produces large number of abnormal blood cells. In chronic idiopathic myelofibrosis the abnormal population of cells produce substances that alter the growth media of bone marrow and makes bone marrow very dense and rigid. As the abnormal bone marrow environment is no more adequate for the cells, some migrate to other sites where proliferation and maturation take place. -
Relative Reaction Rates of the Amino Acids Cysteine, Methionine, and Histidine with Analogs of the Anti-Cancer Drug Cisplatin Cynthia A
Western Kentucky University TopSCHOLAR® Honors College Capstone Experience/Thesis Honors College at WKU Projects 5-11-2015 Relative Reaction Rates of the Amino Acids Cysteine, Methionine, and Histidine with Analogs of the Anti-Cancer Drug Cisplatin Cynthia A. Tope Western Kentucky University, [email protected] Follow this and additional works at: http://digitalcommons.wku.edu/stu_hon_theses Part of the Medicinal-Pharmaceutical Chemistry Commons Recommended Citation Tope, Cynthia A., "Relative Reaction Rates of the Amino Acids Cysteine, Methionine, and Histidine with Analogs of the Anti-Cancer Drug Cisplatin" (2015). Honors College Capstone Experience/Thesis Projects. Paper 571. http://digitalcommons.wku.edu/stu_hon_theses/571 This Thesis is brought to you for free and open access by TopSCHOLAR®. It has been accepted for inclusion in Honors College Capstone Experience/ Thesis Projects by an authorized administrator of TopSCHOLAR®. For more information, please contact [email protected]. RELATIVE REACTION RATES OF THE AMINO ACIDS CYSTEINE, METHIONINE, AND HISTIDINE WITH ANALOGS OF THE ANTI-CANCER DRUG CISPLATIN A Capstone Experience/Thesis Project Presented in Partial Fulfillment of the Requirements for the Degree Bachelor of Science with Honors College Graduate Distinction at Western Kentucky University By: Cynthia A. Tope ***** Western Kentucky University 2015 CE/T Committee: Approved by: Professor Kevin Williams, Advisor _________________________ Professor Darwin Dahl Advisor Professor Lee Ann Smith Department of Chemistry Copyright: Cynthia A. Tope 2015 ABSTRACT We are studying the reaction of analogs of the anticancer drug cisplatin with amino acids that differ in size and shape. The reaction of cisplatin with proteins likely precedes reaction with DNA in the body, forming a variety of products that may be toxic to the human body. -
Molecule Based on Evans Blue Confers Superior Pharmacokinetics and Transforms Drugs to Theranostic Agents
Novel “Add-On” Molecule Based on Evans Blue Confers Superior Pharmacokinetics and Transforms Drugs to Theranostic Agents Haojun Chen*1,2, Orit Jacobson*2, Gang Niu2, Ido D. Weiss3, Dale O. Kiesewetter2, Yi Liu2, Ying Ma2, Hua Wu1, and Xiaoyuan Chen2 1Department of Nuclear Medicine, Xiamen Cancer Hospital of the First Affiliated Hospital of Xiamen University, Xiamen, China; 2Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland; and 3Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland One of the major design considerations for a drug is its The goal of drug development is to achieve high activity and pharmacokinetics in the blood. A drug with a short half-life in specificity for a desired biologic target. However, many potential the blood is less available at a target organ. Such a limitation pharmaceuticals that meet these criteria fail as therapeutics because dictates treatment with either high doses or more frequent doses, of unfavorable pharmacokinetics, in particular, rapid blood clearance, both of which may increase the likelihood of undesirable side effects. To address the need for additional methods to improve which prevents the achievement of therapeutic concentrations. For the blood half-life of drugs and molecular imaging agents, we some drugs, the administration of large or frequently repeated doses developed an “add-on” molecule that contains 3 groups: a trun- is required to achieve and maintain therapeutic levels (1) but can, in cated Evans blue dye molecule that binds to albumin with a low turn, increase the probability of undesired side effects. -
A Review of Dietary (Phyto)Nutrients for Glutathione Support
nutrients Review A Review of Dietary (Phyto)Nutrients for Glutathione Support Deanna M. Minich 1,* and Benjamin I. Brown 2 1 Human Nutrition and Functional Medicine Graduate Program, University of Western States, 2900 NE 132nd Ave, Portland, OR 97230, USA 2 BCNH College of Nutrition and Health, 116–118 Finchley Road, London NW3 5HT, UK * Correspondence: [email protected] Received: 8 July 2019; Accepted: 23 August 2019; Published: 3 September 2019 Abstract: Glutathione is a tripeptide that plays a pivotal role in critical physiological processes resulting in effects relevant to diverse disease pathophysiology such as maintenance of redox balance, reduction of oxidative stress, enhancement of metabolic detoxification, and regulation of immune system function. The diverse roles of glutathione in physiology are relevant to a considerable body of evidence suggesting that glutathione status may be an important biomarker and treatment target in various chronic, age-related diseases. Yet, proper personalized balance in the individual is key as well as a better understanding of antioxidants and redox balance. Optimizing glutathione levels has been proposed as a strategy for health promotion and disease prevention, although clear, causal relationships between glutathione status and disease risk or treatment remain to be clarified. Nonetheless, human clinical research suggests that nutritional interventions, including amino acids, vitamins, minerals, phytochemicals, and foods can have important effects on circulating glutathione which may translate to clinical benefit. Importantly, genetic variation is a modifier of glutathione status and influences response to nutritional factors that impact glutathione levels. This narrative review explores clinical evidence for nutritional strategies that could be used to improve glutathione status. -
L -Glutamic Acid (G1251)
L-Glutamic acid Product Number G 1251 Store at Room Temperature Product Description Precautions and Disclaimer Molecular Formula: C5H9NO4 For Laboratory Use Only. Not for drug, household or Molecular Weight: 147.1 other uses. CAS Number: 56-86-0 pI: 3.081 Preparation Instructions 1 pKa: 2.10 (α-COOH), 9.47 (α-NH2), 4.07 (ϕ-COOH) This product is soluble in 1 M HCl (100 mg/ml), with 2 Specific Rotation: D +31.4 ° (6 N HCl, 22.4 °C) heat as needed, yielding a clear, colorless solution. Synonyms: (S)-2-aminoglutaric acid, (S)-2- The solubility in water at 25 °C has been reported to aminopentanedioic acid, 1-aminopropane-1,3- be 8.6 mg/ml.2 dicarboxylic acid, Glu2 Storage/Stability L-Glutamic acid is one of the two amino acids that Aqueous glutamic acid solutions will form contains a carboxylic acid group in its side chains. pyrrolidonecarboxylic acid slowly at room temperature Glutamic acid is commonly referred to as "glutamate", and more rapidly at 100 °C.9 because its carboxylic acid side chain will be deprotonated and thus negatively charged in its References anionic form at physiological pH. In amino acid 1. Molecular Biology LabFax, Brown, T. A., ed., BIOS metabolism, glutamate is formed from the transfer of Scientific Publishers Ltd. (Oxford, UK: 1991), p. amino groups from amino acids to α-ketoglutarate. It 29. thus acts as an intermediary between ammonia and 2. The Merck Index, 12th ed., Entry# 4477. the amino acids in vivo. Glutamate is converted to 3. Biochemistry, 3rd ed., Stryer, L., W. -
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).