The Classification of Chemical Compounds Should Preferably Be Of
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NATURE Facts and Theories Tn Protein Chemistry*
No. 3606, DEC. 10, 1938 NATURE 1023 Facts and Theories tn Protein Chemistry* JN the last decade, many investigations of an Viscosity measurements on anisotropic proteins exact nature have been made on the proteins may be correlated with the axial ratios of the in solution and in the solid phase. Unfortunately, corresponding molecular ellipsoids of rotation by by a dissipation of the available research energy means of equations proposed independently by among a wide variety of proteins and by a signal Kuhn, Burgers and Polson. From the axial ratio absence of co-operation among the researchers the molecular frictional coefficient may be cal themselves, less significant advances have been culated, and this in turn supplies the necessary made in the elucidation of fundamental principles information for calculating molecular weights from than would otherwise have been the case. It was diffusion data. Molecular weights thus obtained a happy inspiration, therefore, which brought from viscosity and diffusion data agree with the together most of the authorities on protein ultracentrifuge values only when Polson's equa chemistry in Europe at the Royal Society on tion, which has a purely empirical basis, is used. November 17 to compare their experiences and Studies on the peptic digestion of egg albumin discuss each other's difficulties. by Tiselius show that the decomposition products Prof. The Svedberg (Uppsala) opened the con have a much lower electrophoretic mobility than ference with a vigorous and notably wide survey the uncharged protein. This supports the view of recent developments in the physical chemistry that the constituent units of a protein particle are of the proteins. -
The Contributions of George Beadle and Edward Tatum
| PERSPECTIVES Biochemical Genetics and Molecular Biology: The Contributions of George Beadle and Edward Tatum Bernard S. Strauss1 Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637 KEYWORDS George Beadle; Edward Tatum; Boris Ephrussi; gene action; history It will concern us particularly to take note of those cases in Genetics in the Early 1940s which men not only solved a problem but had to alter their mentality in the process, or at least discovered afterwards By the end of the 1930s, geneticists had developed a sophis- that the solution involved a change in their mental approach ticated, self-contained science. In particular, they were able (Butterfield 1962). to predict the patterns of inheritance of a variety of charac- teristics, most morphological in nature, in a variety of or- EVENTY-FIVE years ago, George Beadle and Edward ganisms although the favorites at the time were clearly Tatum published their method for producing nutritional S Drosophila andcorn(Zea mays). These characteristics were mutants in Neurospora crassa. Their study signaled the start of determined by mysterious entities known as “genes,” known a new era in experimental biology, but its significance is to be located at particular positions on the chromosomes. generally misunderstood today. The importance of the work Furthermore, a variety of peculiar patterns of inheritance is usually summarized as providing support for the “one gene– could be accounted for by alteration in chromosome struc- one enzyme” hypothesis, but its major value actually lay both ture and number with predictions as to inheritance pattern in providing a general methodology for the investigation of being quantitative and statistical. -
New Website Details Linus Pauling's Breakthroughs in Protein Structure 18 March 2013
New website details Linus Pauling's breakthroughs in protein structure 18 March 2013 The Oregon State University Libraries Special The proteins story was not without its drama, and Collections & Archives Research Center has readers will learn of Pauling's sometimes caustic added to its series of documentary history websites confrontations with Dorothy Wrinch, whose cyclol on the life of Linus Pauling with its newest addition, theory of protein structure was a source of intense "Linus Pauling and the Structure of Proteins: A objection for Pauling and his colleague, Carl Documentary History." Niemann. The website also delves into the fruitful collaboration enjoyed between Pauling and his The website (scarc.library.oregonstate.edu/ … Caltech co-worker, Robert Corey and explores the /proteins/index.html) is filled with rarely-seen controversy surrounding his interactions with photographs and letters and behind-the-scenes another associate, Herman Branson. tales of controversy and collaboration. Many more discoveries lie in waiting for those This is the sixth website in the Special Collections interested in the history of molecular biology: the & Archives Research Center's series focusing on invention of the ultracentrifuge by Theodor specific aspects of Pauling's remarkable life and Svedberg; Pauling's long dalliance with a theory of career. The proteins site is organized around a antibodies; his critical concept of biological narrative written by Pauling biographer Thomas specificity; and the contested notion of coiled-coils, Hager and incorporates more than 400 letters, an episode that pit Pauling against Francis Crick. manuscripts, published papers, photographs and audio-visual snippets in telling its story. Linus Pauling and the Structure of Proteins constitutes a major addition to the Pauling-related Pauling (1901-1994) remains the only individual to resources available online. -
A Deeply Glimpse Into Protein Fold Recognition
International Journal of Sciences Research Article (ISSN 2305-3925) Volume 2, Issue June 2013 http://www.ijSciences.com A Deep Glimpse into Protein Fold Recognition Ahmed Sharaf Eldin1, Taysir Hassan A. Soliman2, Mohammed Ebrahim Marie3, Marwa Mohamed M. Ghareeb4 1Information Systems Department, Faculty of Computers and Information, Helwan University, Cairo, Egypt 2Supervisor of Information Systems Department, Faculty of Computers and Information, Assiut University, Assiut, Egypt 3Information Systems Department, Faculty of Computers and Information, Helwan University, Cairo, Egypt 4Assistant Lecturer, Information Systems Department, Modern Academy, Cairo, Egypt Abstract: The rapid growth in genomic and proteomic data causes a lot of challenges that are raised up and need powerful solutions. It is worth noting that UniProtKB/TrEMBL database Release 28-Nov-2012 contains 28,395,832 protein sequence entries, while the number of stored protein structures in Protein Data Bank (PDB, 4- 12-2012) is 65,643. Thus, the need of extracting structural information through computational analysis of protein sequences has become very important, especially, the prediction of the fold of a query protein from its primary sequence has become very challenging. The traditional computational methods are not powerful enough to address theses challenges. Researchers have examined the use of a lot of techniques such as neural networks, Monte Carlo, support vector machine and data mining techniques. This paper puts a spot on this growing field and covers the main approaches and perspectives to handle this problem. Keywords: Protein fold recognition, Neural network, Evolutionary algorithms, Meta Servers. research has been conducted towards this goal in the I. INTRODUCTION late years. Especially, the prediction of the fold of a Proteins transport oxygen to cells, prevent harmful query protein from its primary sequence has become infections, convert chemical energy into mechanical very challenging. -
Alpha Helical Mimics, Their Uses and Methods for Their
(19) TZZ_¥_T (11) EP 1 737 884 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C07K 7/50 (2006.01) A61K 38/12 (2006.01) 19.10.2016 Bulletin 2016/42 A61P 35/00 (2006.01) A61P 25/00 (2006.01) A61P 25/08 (2006.01) A61P 25/32 (2006.01) (21) Application number: 05714272.1 (86) International application number: (22) Date of filing: 21.03.2005 PCT/AU2005/000400 (87) International publication number: WO 2005/090388 (29.09.2005 Gazette 2005/39) (54) ALPHA HELICAL MIMICS, THEIR USES AND METHODS FOR THEIR PRODUCTION ALPHA-HELIX-MIMETIKA, DEREN ANWENDUNGEN UND VERFAHREN ZU DEREN HERSTELLUNG ALPHA-MIMETIQUES HELICOIDALES, LEURS UTILISATIONS ET LEURS PROCEDES DE PRODUCTION (84) Designated Contracting States: • CONDON ET AL: "The Bioactive Conformation of AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Human Parathyroid Hormone. Structural HU IE IS IT LI LT LU MC NL PL PT RO SE SI SK TR Evidence for the Extended Helix Postulate" J.AM.CHEM.SOC., vol. 122, 2000, pages (30) Priority: 19.03.2004 AU 2004901447 3007-3014, XP002496104 • BRACKEN CLAY ET AL: "Synthesis and nuclear (43) Date of publication of application: magnetic resonance structure determination of 03.01.2007 Bulletin 2007/01 an alpha-helical, bicyclic, lactam-bridged hexapeptide" JOURNAL OF THE AMERICAN (73) Proprietor: THE UNIVERSITY OF QUEENSLAND CHEMICAL SOCIETY, vol. 116, no. 14, 1994, St Lucia, pages 6431-6432, XP002496089 ISSN: 0002-7863 Queensland 4072 (AU) • BOUVIERM ET AL: "PROBING THE FUNCTIONAL CONFORMATION OF NEUROPEPTIDE Y (72) Inventors: THROUGH THE DESIGN AND STUDY OF CYCLIC • FAIRLIE, David, P. -
Energy of Formation of Cyclol Molecules
242 NATURE AUGUST 8, 1936 The implications of the calculation for the process dehydration will render the protein excessively liable of linkage (2) are explored in the accompanying letter to opening into chain forlllS, unless restrained by side by my colleague, F. C. Frank. chains or deprived of catalysts necessary for trans D. M. WRINCH. formation. Mildly dehydrating conditions should be Mathematical Institute, most effective because water is a catalyst for trans Oxford. formation as well as a stabilizer of one form. So long as the rings only occasionally open they can 1 D. M. Wrinch, NATURE, 137, 411 (1936). 'See, for example, J. W. Baker, "Tautomerism" (1934), p. 38. re-form in the same configuration, but as soon as ' The figures of Pauling and Sherman given in J. Chem. Phys., the opening becomes too frequent this will cease to 1, 606 (1933), calculated on the basis of the value of 208 kilogram calories for the heat of dissociation of N,, have been modified to take be the case and they will then re-form in altered account of the revised value of 169 kilogram calories (see Mulliken, structures, derived more directly from open chains. Phys. Rev., 46. 144 (1934) ; Herzberg and Sponer, Z. phys. Chem., B, 28, 1, though this modification Is without effect on these calculations. This conforms with all observations on the processes • J. Biol. Chem., 109, 325, 329 (1935). of degeneration and denaturation, including Astbury's 7 X-ray studies of these processes6 • • Thus what seems at first to be a destructive obstacle to the theory WRINCH 1 recently proposed that in monolayers may be capable not only of reconciliation with it, or globular molecules of proteins, polypeptide chains but even of enhancing its effectiveness. -
Modeling and Predicting Super-Secondary Structures of Transmembrane Beta-Barrel Proteins Thuong Van Du Tran
Modeling and predicting super-secondary structures of transmembrane beta-barrel proteins Thuong van Du Tran To cite this version: Thuong van Du Tran. Modeling and predicting super-secondary structures of transmembrane beta-barrel proteins. Bioinformatics [q-bio.QM]. Ecole Polytechnique X, 2011. English. NNT : 2011EPXX0104. pastel-00711285 HAL Id: pastel-00711285 https://pastel.archives-ouvertes.fr/pastel-00711285 Submitted on 23 Jun 2012 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. THESE` pr´esent´ee pour obtenir le grade de DOCTEUR DE L’ECOLE´ POLYTECHNIQUE Sp´ecialit´e: INFORMATIQUE par Thuong Van Du TRAN Titre de la th`ese: Modeling and Predicting Super-secondary Structures of Transmembrane β-barrel Proteins Soutenue le 7 d´ecembre 2011 devant le jury compos´ede: MM. Laurent MOUCHARD Rapporteurs Mikhail A. ROYTBERG MM. Gregory KUCHEROV Examinateurs Mireille REGNIER M. Jean-Marc STEYAERT Directeur Laboratoire d’Informatique UMR X-CNRS 7161 Ecole´ Polytechnique, 91128 Plaiseau CEDEX, FRANCE Composed with LATEX !c Thuong Van Du Tran. All rights reserved. Contents Introduction 1 1Fundamentalreviewofproteins 5 1.1 Introduction................................... 5 1.2 Proteins..................................... 5 1.2.1 Aminoacids............................... 5 1.2.2 Properties of amino acids . -
Final List of NGF Publications (2001-2007)
Final List of NGF Publications (2001-2007) (1) Abahuni N, Gispert S, Bauer P, Riess O, Krüger R, Becker T, Auburger G. Mitochondrial translation initiation factor 3 gene polymorphism associated with Parkinson's disease. Neurosci Lett. 2007 Mar 6;414(2):126-9. (2) Abarca C, Albrecht U, Spanagel R. Cocaine sensitization and reward are influenced by circadian genes and rhythm. Proc. Natl. Acad. Sci. USA 2002; 99, 9026-9030 (3) Abdelaziz AI, Segaric J, Bartsch H, Petzhold D, Schlegel WP, Kott M, Seefeldt I, Klose J, Bader M, Haase H, Morano I. Functional characterization of the human atrial essential myosin light chain (hALC-1) in a transgenic rat model. J Mol Med. 2004 Apr;82(4):265-74. (4) Abdollahi A, Hahnfeldt P, Maercker C, Grone HJ, Debus J, Ansorge W, Folkman J, Hlatky L, Huber PE. Endostatin's antiangiogenic signaling network. Mol Cell. 2004 Mar 12;13(5):649-63. (5) Abe K, Fuchs H, Lisse T, Hans W, de Angelis MH. New ENU-induced semidominant mutation, Ali18, causes inflammatory arthritis, dermatitis, and osteoporosis in the mouse. Mamm Genome. 2006 Sep 8; [Epub ahead of print] (6) Abe M, Westermann F, Nakagawara A, Takato T, Schwab M, Ushijima T. Marked and independent prognostic significance of the CpG island methylator phenotype in neuroblastomas. Cancer Lett. 2007 Mar 18;247(2):253- 258. (7) Abeysinghe SS, Chuzhanova N, Krawczak M, Ball EV, Cooper DN. Translocation and gross deletion breakpoints in human inherited disease and cancer I. Nucleotide composition and recombination-associated motifs. Hum Mutat. 2003; 22:229-244 (8) Abeysinghe SS, Stenson PD, Krawczak M, Cooper DN. -
A Tri-Gram Based Feature Extraction Technique Using Linear Probabilities of Position Specific Scoring Matrix for Protein Fold Recognition
A Tri-Gram Based Feature Extraction Technique Using Linear Probabilities of Position Specific Scoring Matrix for Protein Fold Recognition Author Paliwal, Kuldip K, Sharma, Alok, Lyons, James, Dehzangi, Abdollah Published 2014 Journal Title IEEE Transactions on NanoBioscience DOI https://doi.org/10.1109/TNB.2013.2296050 Copyright Statement © 2014 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. Downloaded from http://hdl.handle.net/10072/67288 Griffith Research Online https://research-repository.griffith.edu.au A Tri-gram Based Feature Extraction Technique Using Linear Probabilities of Position Specific Scoring Matrix for Protein Fold Recognition Kuldip K. Paliwal, Member, IEEE, Alok Sharma, Member, IEEE, James Lyons, Abdollah Dhezangi, Member, IEEE protein structure in a reasonable amount of time. Abstract— In biological sciences, the deciphering of a three The prime objective of protein fold recognition is to find the dimensional structure of a protein sequence is considered to be an fold of a protein sequence. Assigning of protein fold to a important and challenging task. The identification of protein folds protein sequence is a transitional stage in the recognition of from primary protein sequences is an intermediate step in three dimensional structure of a protein. The protein fold discovering the three dimensional structure of a protein. This can be done by utilizing feature extraction technique to accurately recognition broadly covers feature extraction task and extract all the relevant information followed by employing a classification task. -
Proteins of Escherichia Coli Come in Sizes That Are Multiples Of
Proc. Natl. Acad. Sci. USA Vol. 83, pp. 1198-1202, March 1986 Biochemistry Proteins of Escherichia coli come in sizes that are multiples of 14 kDa: Domain concepts and evolutionary implications (distribution of protein sizes/HeLa cell proteins/distribution of gene lengths/protein structure/chromatin structure) MICHAEL A. SAVAGEAU Department of Microbiology and Immunology, The University of Michigan, Ann Arbor, MI 48109 Communicated by J. L. Oncley, October 10, 1985 ABSTRACT Initial attempts to correlate the distribution different proteins (polypeptide chains) have been isolated on of gene density (number of gene loci per unit length on the O'Farrell gels and associated with a region of the genome linkage map) with the distribution of lengths of coding se- containing their coding sequence. When the frequency dis- quences have led to the observation that 46% of approximately tribution of molecular masses for these proteins is plotted, 1000 sampled proteins in Escherichia coli have molecular one finds the expected skewed distribution (1). masses of n x 14,000 ± 2500 daltons (n = 1, 2, ...). This Further analysis with more refined class sizes for molec- clustering around multiples of 14,000 contrasts with the 36% ular mass shows that although the "envelope" of this one would expect in these ranges if the sizes were uniformly distribution is nearly lognormal, there is a pronounced "fine distributed. The entire distribution is well fit by a sum of structure" (Fig. 1). A class size of 2 kDa was chosen for this normal or lognormal distributions located at multiples of distribution because it smooths out random variations on the 14,000, which suggests that the percentage of E. -
Simple Proteins Conjugated Proteins Enzymes
Ministry of Health of Ukraine Zaporizhzhia State Medical University Biochemistry & Laboratory Diagnostics Department Simple proteins Conjugated proteins Enzymes A manual for study of submodule 1 on Biochemistry for second-year students of International Faculty specialty: 7.12010001 ―General medicine‖ Zaporizhzhia-2015 This manual is recommended as additional one for independent work of students at home and in class for submodule 1 of Biochemistry at 2-d year study at specialty 7.12010001 ―General Medicine‖. Editors: Dr.Hab. professor Aleksandrova K.V. PhD, associate professor Krisanova N.V. PhD, assistant Levich S.V. Rewiewers Head of Department of Organic and Bioorganic Chemistry ZSMU, Dr.Hab. professor Kovalenko S. I. Head of Department of Biology, Parasitology and Genetics ZSMU, Dr.Hab. associate professor Pryhod’ko O. B. 2 Вступ Наведений навчально-методичний посібник пропонується викладачами кафедри біохімії та лабораторної діагностики для використання у самостійній роботі англомовних іноземних студентів медичного факультету ЗДМУ з метою підготовки до змістового модулю 1 з біохімії. Цей навчальний посібник містить все необхідне для вивчення базових питань зi змістового модулю 1 «Прості та складні білки. Ферменти» відповідно робочої програми з дисципліни «Біохімія» для студентів 2-го курсу медичного факультету вищих навчальних медичних закладів III-IV рівнів акредитації в Україні. Автори INTRODUCTION This methodological manual is recommended for students to use like additional materials in preparation for practical classes on Biochemistry for submodule 1. The plan to work with it: 1) to prepare theoretical questions for topic using literature sources, summaries of lectures and this textbook; 2) to make testing control yourself; 3) to be ready to answer teacher about principles of methods used for the determination of proposed biochemical indexes and about their clinical significance. -
Amino ACIDS PROTEINS
Taras Shevchenko National University of Kyiv The Institute of Biology and Medicine METHODICAL POINTING from the course “Biological and bioorganic chemistry” (part 3. Amino acids and proteins) for the studens of a 1 course with English of educating Compiler – the candidate of biological sciences, the associate professor Synelnyk Tatyana Borysivna Readers: It is ratified to printing by meeting of scientific advice of The Institute of Biology and Medicine (“____”________________ 2018, protocol №____) Kyiv-2018 2 CONTENT 3.1. General information …………………………………………………….. 3 3.2. Nomenclature and classification of α-amino acids ……………. 4 3.3. Amphoteric and stereochemical properties of amino acids. Chiral carbon atom……………………………………………………………… 8 3.4. Isoelectric point of amino acid . Titration curves ……………… 9 3.4.1. The typical titration curve of amino acids with uncharged radical…………………………………………………………. 10 3.4.2. The titration curves of amino acids with charged radical ……………………………………………………………………….. 11 3.5. Chemical properties of amino acids and some methods for amino acids determination and separation…………………………….. 14 3.6. Peptide bond formation. Peptides. …………………………………. 15 3.7. Proteins. The levels of protein molecules organization ……… 16 3.7.1. Primary protein structure ……………………………………. 17 3.7.2. The secondary structure of proteins: types …………….. 18 3.7.3. Super secondary structure …………………………………… 22 3.7.4. Tertiary Structure of proteins ……………………………… 23 3.7.5. Domain structure of proteins ……………………………… 26 3.7.6. Quaternary Structure of proteins ………………………… 26 3.8. Methods of extraction and purification of proteins ………….. 28 3.8.1. Methods of extraction of proteins from cells or tissues in the dissolved state. ………………………………………………….. 28 3.8.2. Methods of separating a mixture of proteins 29 3.9.