COVID-19: the Disease, the Immunological Challenges, the Treatment with Pharmaceuticals and Low-Dose Ionizing Radiation
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Nucleotide Base Coding and Am1ino Acid Replacemients in Proteins* by Emil L
VOL. 48, 1962 BIOCHEMISTRY: E. L. SAIITH 677 18 Britten, R. J., and R. B. Roberts, Science, 131, 32 (1960). '9 Crestfield, A. M., K. C. Smith, and F. WV. Allen, J. Biol. Chem., 216, 185 (1955). 20 Gamow, G., Nature, 173, 318 (1954). 21 Brenner, S., these PROCEEDINGS, 43, 687 (1957). 22 Nirenberg, M. WV., J. H. Matthaei, and 0. WV. Jones, unpublished data. 23 Crick, F. H. C., L. Barnett, S. Brenner, and R. J. Watts-Tobin, Nature, 192, 1227 (1961). 24 Levene, P. A., and R. S. Tipson, J. Biol. Ch-nn., 111, 313 (1935). 25 Gierer, A., and K. W. Mundry, Nature, 182, 1437 (1958). 2' Tsugita, A., and H. Fraenkel-Conrat, J. Mllot. Biol., in press. 27 Tsugita, A., and H. Fraenkel-Conrat, personal communication. 28 Wittmann, H. G., Naturwissenschaften, 48, 729 (1961). 29 Freese, E., in Structure and Function of Genetic Elements, Brookhaven Symposia in Biology, no. 12 (1959), p. 63. NUCLEOTIDE BASE CODING AND AM1INO ACID REPLACEMIENTS IN PROTEINS* BY EMIL L. SMITHt LABORATORY FOR STUDY OF HEREDITARY AND METABOLIC DISORDERS AND THE DEPARTMENTS OF BIOLOGICAL CHEMISTRY AND MEDICINE, UNIVERSITY OF UTAH COLLEGE OF MEDICINE Communicated by Severo Ochoa, February 14, 1962 The problem of which bases of messenger or template RNA' specify the coding of amino acids in proteins has been largely elucidated by the use of synthetic polyri- bonucleotides.2-7 For these triplet nucleotide compositions (Table 1), it is of in- terest to examine some of the presently known cases of amino acid substitutions in polypeptides or proteins of known structure. -
Evolutionary and Functional Lessons from Human-Specific Amino-Acid
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.09.086009; this version posted May 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Evolutionary and Functional Lessons from Human-Specific Amino- Acid Substitution Matrices Tair Shauli1, Nadav Brandes1, Michal Linial 2 1The Rachel and Selim Benin School of Computer Science and Engineering, 2Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel Corresponding Author: Michal Linial Email: [email protected] ORCID: (M.L.) 0000-0002-9357-4526 Abstract The characterization of human genetic variation in coding regions is fundamental to our understanding of protein function, structure, and evolution. Amino-acid (AA) substitution matrices such as BLOSUM (BLOcks SUbstitution Matrix) and PAM (Point Accepted Mutations) encapsulate the stochastic nature of such proteomic variation and are used in studying protein families and evolutionary processes. However, these matrices were constructed from protein sequences spanning long evolutionary distances and are not designed to reflect polymorphism within species. To accurately represent proteomic variation within the human population, we constructed a set of human-centric substitution matrices derived from genetic variations by analyzing the frequencies of >4.8M single nucleotide variants (SNVs). These human-specific matrices expose short-term evolutionary trends at both codon and AA resolution and therefore present an evolutionary perspective that differs from that implicated in the traditional matrices. Specifically, our matrices consider the directionality of variants, and uncover a set of AA pairs that exhibit a strong tendency to substitute in a specific direction. -
Rational Drug Design of Peptide-Based Therapies for Sickle Cell Disease
molecules Review Rational Drug Design of Peptide-Based Therapies for Sickle Cell Disease Olujide O. Olubiyi 1,2,* , Maryam O. Olagunju 1 and Birgit Strodel 1,3 1 Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany; [email protected] (M.O.O.); [email protected] (B.S.) 2 Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife 220282, Nigeria 3 Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany * Correspondence: [email protected] Academic Editor: Rainer Riedl Received: 30 September 2019; Accepted: 9 December 2019; Published: 12 December 2019 Abstract: Sickle cell disease (SCD) is a group of inherited disorders affecting red blood cells, which is caused by a single mutation that results in substitution of the amino acid valine for glutamic acid in the sixth position of the β-globin chain of hemoglobin. These mutant hemoglobin molecules, called hemoglobin S, can polymerize upon deoxygenation, causing erythrocytes to adopt a sickled form and to suffer hemolysis and vaso-occlusion. Until recently, only two drug therapies for SCD, which do not even fully address the manifestations of SCD, were approved by the United States (US) Food and Drug Administration. A third treatment was newly approved, while a monoclonal antibody preventing vaso-occlusive crises is also now available. The complex nature of SCD manifestations provides multiple critical points where drug discovery efforts can be and have been directed. These notwithstanding, the need for new therapeutic approaches remains high and one of the recent efforts includes developments aimed at inhibiting the polymerization of hemoglobin S. -
Synthetic Polynucleotides Andthe Amino Acid
VOL. 48, 1962 BIOCHEMISTRY: SPEYER ET AL. 63 14 Meselson, M., F. W. Stahl, and J. Vinograd, these PROCEEDINGS, 43, 581 (1957). 15 Szybalski, W., Experientia, 16, 164 (1960). 16 Zubay, G., Nature, 182, 1290 (1958); Stent, G., Adv. in Virus Res., 5, 95 (1958); Sinsheimer, R. L., J. Mol. Biol., 1, 218 (1959); Rich, A., Ann. N. Y. Acad. Sci., 81, 709 (1959). 17 Zalokar, M., Exp. Cell Res., 19, 559 (1960). SYNTHETIC POLYNUCLEOTIDES AND THE AMINO ACID CODE, I* BY JOSEPH F. SPEYER, PETER LENGYEL, CARLOS BASILIO, t AND SEVERO OCHOA DEPARTMENT OF BIOCHEMISTRY, NEW YORK UNIVERSITY SCHOOL OF MEDICINE Communicated November 21, 1961 Previous studies' on the incorporation of amino acids into acid-insoluble products by an Escherchia coli system, in the presence of synthetic polyribonucleotides, have been continued. This paper presents additional results with previously used and new copolymers containing uridylic2 and guanylic acid (UG); uridylic, adenylic, and cytidylic acid (UAC); uridylic, cytidylic, and guanylic acid (UCG); and uridy- lic, adenylic, and guanylic acid (UAG). Assuming a triplet code, code letters (although in an as yet unspecified sequence) can now be assigned to the following eleven amino acids: cysteine, histidine, isoleucine, leucine, lysine, phenylalanine, proline, serine, threonine, tyrosine, and valine. Preparations and Methods.-These were as previously described.' The following new polymers were prepared with polynucleotide phosphorylase. Poly UC (3: 1), from a mixture of UDP and CDP in molar ratio 3:1; poly UG (5:1), from UDP and GDP in molar ratio 5:1; poly UAC, from UDP, ADP, and CDP in molar ratio 6:1: 1; poly UCG and poly UAG, from mixtures of the appropriate nucleoside 5'-diphosphates in molar ratio of 6 of UDP to 1 of each of the other two. -
Nucleotide Base Coding and Am1ino Acid Replacemients in Proteins* by Emil L
VOL. 48, 1962 BIOCHEMISTRY: E. L. SAIITH 677 18 Britten, R. J., and R. B. Roberts, Science, 131, 32 (1960). '9 Crestfield, A. M., K. C. Smith, and F. WV. Allen, J. Biol. Chem., 216, 185 (1955). 20 Gamow, G., Nature, 173, 318 (1954). 21 Brenner, S., these PROCEEDINGS, 43, 687 (1957). 22 Nirenberg, M. WV., J. H. Matthaei, and 0. WV. Jones, unpublished data. 23 Crick, F. H. C., L. Barnett, S. Brenner, and R. J. Watts-Tobin, Nature, 192, 1227 (1961). 24 Levene, P. A., and R. S. Tipson, J. Biol. Ch-nn., 111, 313 (1935). 25 Gierer, A., and K. W. Mundry, Nature, 182, 1437 (1958). 2' Tsugita, A., and H. Fraenkel-Conrat, J. Mllot. Biol., in press. 27 Tsugita, A., and H. Fraenkel-Conrat, personal communication. 28 Wittmann, H. G., Naturwissenschaften, 48, 729 (1961). 29 Freese, E., in Structure and Function of Genetic Elements, Brookhaven Symposia in Biology, no. 12 (1959), p. 63. NUCLEOTIDE BASE CODING AND AM1INO ACID REPLACEMIENTS IN PROTEINS* BY EMIL L. SMITHt LABORATORY FOR STUDY OF HEREDITARY AND METABOLIC DISORDERS AND THE DEPARTMENTS OF BIOLOGICAL CHEMISTRY AND MEDICINE, UNIVERSITY OF UTAH COLLEGE OF MEDICINE Communicated by Severo Ochoa, February 14, 1962 The problem of which bases of messenger or template RNA' specify the coding of amino acids in proteins has been largely elucidated by the use of synthetic polyri- bonucleotides.2-7 For these triplet nucleotide compositions (Table 1), it is of in- terest to examine some of the presently known cases of amino acid substitutions in polypeptides or proteins of known structure. -
Beyond Mistranslation: Expanding the Role of Aminoacyl-Trna Synthetases Towards the Maintenance of Cellular Viability DISSERTATI
Beyond Mistranslation: Expanding the Role of Aminoacyl-tRNA Synthetases towards the Maintenance of Cellular Viability DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Kyle Phillip Mohler Graduate Program in Microbiology The Ohio State University 2017 Dissertation Committee: Professor Michael Ibba, Advisor Professor Juan Alfonzo Professor Irina Artsimovitch Professor Kelly Wrighton Copyrighted by Kyle Phillip Mohler 2017 Abstract When the sequence of amino acids in a newly synthesized protein is not the same as the genetically encoded sequence, a gene is said to have been mistranslated. Alterations in protein sequence resulting from errors in genome maintenance and expression occur with low frequency. The next step in gene expression, protein synthesis, offers the greatest opportunity for errors, with mistranslation events routinely occurring at a frequency of ~1 per 10,000 mRNA codons translated. The translation of genetic information into functional proteins is a multistep process. Aminoacyl-tRNA synthetases (aaRSs) provide the cell with substrates for protein synthesis by correctly pairing amino acids with their cognate tRNAs. Aminoacylation occurs in a two-step reaction. First, cognate amino acid is activated within the catalytic domain to form an aminoacyl-adenylate (aa-AMP). The activated amino acid is then transferred to the 3’ OH of the terminal adenosine on the tRNA acceptor stem of its cognate tRNA, forming an aminoacyl-tRNA (aa-tRNA). Phenylalanyl-tRNA synthetase (PheRS), for example, is responsible for pairing phenylalanine (Phe) with tRNAPhe. Mispaired aa-tRNA species occasionally arise due to a lack of adequate amino acid discrimination within the PheRS active site, resulting in the synthesis of misacylated Tyr- tRNAPhe. -
Investigation of Mutations in Nuclear Genes That Affect the Atp Synthase Russell Dsouza Wayne State University
Wayne State University Wayne State University Dissertations 1-1-2016 Investigation Of Mutations In Nuclear Genes That Affect The Atp Synthase Russell Dsouza Wayne State University, Follow this and additional works at: https://digitalcommons.wayne.edu/oa_dissertations Part of the Biochemistry Commons, and the Molecular Biology Commons Recommended Citation Dsouza, Russell, "Investigation Of Mutations In Nuclear Genes That Affect The tA p Synthase" (2016). Wayne State University Dissertations. 1526. https://digitalcommons.wayne.edu/oa_dissertations/1526 This Open Access Dissertation is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Dissertations by an authorized administrator of DigitalCommons@WayneState. INVESTIGATION OF MUTATIONS IN NUCLEAR GENES THAT AFFECT THE ATP SYNTHASE by RUSSELL L. D’SOUZA DISSERTATION Submitted to the Graduate School of Wayne State University, Detroit, Michigan in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY 2016 MAJOR: BIOCHEMISTRY & MOLECULAR BIOLOGY Approved By: Advisor Date © COPYRIGHT BY RUSSELL L. D’SOUZA 2016 All Rights Reserved DEDICATION I dedicate my dissertation work to my family. My deepest gratitude to my parents, Raymond and Emma D’Souza, whose constant support has helped me pursue my dreams. My brother Reuben, who has always been there by my side. I also dedicate this thesis to my wife, Jayshree Bhakta, who has always been there for me during the difficult times at graduate school. I will always appreciate all that she’s done for me and for all the encouragement. She’s been the best cheerleader in my life. Finally, a special thanks to my best friend Joe D. -
Of the Same Glycine Residue by Arginine and Glutamic Acid Residues
VOL. 48, 1962 GENETICS: HENNING AND YANOFSKY 1497 of their data with ours indicates that the phenomenon described herein is most likely due to the combination of ma-i + and ry+ subunits. We have also observed reactivation of "inactive" xanthine dehydrogenase of wild-type Drosophila. II Forrest, H. S., E. W. Hanly, and J. M. Lagowski, Genetics, 56, 1455 (1961). 12Horowitz, N., personal communication. 13 Hadorn, E., and I. Schwink, Nature, 177, 940 (1956); Glassman, E., Dros. Inform. Service, 31, 121 (1957). '4Glassman, E., and W. Pinkerton, Science, 131, 1810 (1960). AMINO ACID REPLACEMENTS ASSOCIATED WITH REVERSION AND RECOMBINA TION WITHIN THE A GENE* BY ULF HENNINGt AND CHARLES YANOFSKY DEPARTMENT OF BIOLOGICAL SCIENCES, STANFORD UNIVERSITY, STANFORD, CALIFORNIA Communicated by V. C. Twitty, July 26, 1962 Studies with the A protein of the tryptophan synthetase of Escherichia coli have established that mutationally altered sites that are located at or near the same position in the A gene lead to amino acid substitutions in the same tryptic peptide of the A protein." 2 It has also been shown that two mutants, strains A23 and A46, with alterations extremely close to one another on the genetic map, form A proteins that are distinguishable from the wild-type A protein by the replacement of the same glycine residue by arginine and glutamic acid residues, respectively.1 2 It was concluded from these findings that the mutational alteration characteristic of each of the mutants involved a different nucleotide in the same amino acid coding unit in the A gene. 1 2 Mutants A23 and A46 revert spontaneously to tryptophan independence. -
(12) United States Patent (10) Patent No.: US 7,338,790 B2 Thierbach Et Al
US007338790B2 (12) United States Patent (10) Patent No.: US 7,338,790 B2 Thierbach et al. (45) Date of Patent: Mar. 4, 2008 (54) ALLELES OF THE GND GENE FROM 2004/0063181 A1 4/2004 Duncan et al. CORYNEFORM BACTERIA 2006, O246554 A1 11/2006 Thierbach et al. (75) Inventors: Georg Thierbach, Bielefeld (DE): Brigitte Bathe, Salzkotten (DE); Natalie Schischka, Bielefeld (DE) FOREIGN PATENT DOCUMENTS (73) Assignee: Degussa AG, Intellectual Property EP 1 462516 A1 9, 2004 Management, Hanau (DE) WO WOO 1/71012 A1 9, 2001 (*) Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S.C. 154(b) by 0 days. OTHER PUBLICATIONS (21) Appl. No.: 11/227,138 Yousuke Nishio, et al., “Comparative Complete Genome Sequence Analysis of the Amino Acid Replacements Responsible for the (22) Filed: Sep. 16, 2005 Thermostability of Corynebacterium efficiens”. Genome Research, XP-002995065, 2003, pp. 1572-1579 and 2 pages of DATABASE (65) Prior Publication Data UniProt, AN Q8FTI1, XP-002375536, Mar. 1, 2003. US 2006/0246554 A1 Nov. 2, 2006 A. M. Cerdeno-Tarraga, et al., “The complete genome sequence and analysis of Corynebacterium diphteriae NCTC 13129. Nucleic Related U.S. Application Data Acids Research, vol. 31, No. 22, XP-002375534, Nov. 15, 2003, pp. 6516-6523 and 2 pages of DATABASE UniProt, AN Q6NHC5, (60) Provisional application No. 60/646,482, filed on Jan. XP-002375537, Jul. 5, 2004. 25, 2005. U.S. Appl. No. 1 1/227,138, filed Sep. 16, 2005, Thierbach et al. (30) Foreign Application Priority Data U.S. -
Incorporating Nonproteinogenic Amino Acids Into Azurin and Cua Azurin
! ! ! ! ! "#$%&'(!)*+!#$,+-!$.!/+)0,!%&'1&'(!,&(0'1-!&'!23"#+1$4&'-5! 0 &'2$#"$#0)&'(!'$'"#$)+&'$(+'&2!0/&'$!02&1-!&')$!063#&'!0'1!23 !063#&'! ! ! ! ! ! ! %7! ! 8+9&'!/:!2,0#8! ! ! ! ! ! ! ! 1&--+#)0)&$'! ! -;<=>??@A!>B!CDE?>DF!G;FG>FF=@B?!HG!?I@!E@J;>E@=@B?K! GHE!?I@!1HL?HE!HG!"I>FHKHCIM!>B!%>HLI@=>K?EM! >B!?I@!(EDA;D?@!2HFF@N@!HG!?I@! 3B>O@EK>?M!HG!&FF>BH>K!D?!3E<DBDP2ID=CD>NBQ!RSTS! ! ! ! 3E<DBDQ!&FF>BH>K! ! ! ! 1HL?HEDF!2H==>??@@5! ! ! "EHG@KKHE!7>!,;Q!2ID>E!DBA!2HP1>E@L?HE!HG!#@K@DELI! ! ! "EHG@KKHE!U>FGE@A!ODB!A@E!1HBVQ!2HP1>E@L?HE!HG!#@K@DELI! ! "EHG@KKHE!0B?HBM!2EHG?K! ! "EHG@KKHE!+E>V!WDVH<KKHB! ABSTRACT Metalloproteins play important roles in biological systems since metal-binding sites are found in ~ 1/3 of structurally characterized proteins and in ~ 1/2 of all proteins. Despite progress, the role of many metal-binding sites remains poorly understood. Furthermore, their detailed geometric and electronic structure has yet to be fully elucidated. Site-directed mutagenesis using natural amino acids has continued to be the primary method of probing of metal-binding sites. However, it has become increasingly evident that site-directed mutagenesis, though powerful, cannot address the precise role of the metal ligands without changing multiple factors because of limited number of natural amino acids that allows isostructural substitutions. The relative paucity of functional group availability within the proteinogenic amino acids also limits ability to fine tune and expand protein’s activity. -
Eight Novel Mutations of the Androgen Receptor Gene in Patients with Androgen Insensitivity Syndrome
J Hum Genet (2001) 46:560–565 © Jpn Soc Hum Genet and Springer-Verlag 2001 ORIGINAL ARTICLE Bertha Chávez · Juan Pablo Méndez Alfredo Ulloa-Aguirre · Fernando Larrea · Felipe Vilchis Eight novel mutations of the androgen receptor gene in patients with androgen insensitivity syndrome Received: May 7, 2001 / Accepted: June 28, 2001 Abstract Androgen insensitivity syndrome (AIS) is an Introduction X-linked genetic disorder of male sexual differentiation caused by mutations in the androgen receptor (AR) gene. A reliable genotype–phenotype correlation in these patients Androgen insensitivity syndrome (AIS) is an X-linked does not exist as yet. Here we report the molecular studies hereditary disorder that leads to male pseudohermaphro- performed on eight individuals with AIS. Exon-specific ditism with variable phenotypes. This defective response polymerase chain reaction (PCR), single-strand conforma- results from the impairment of androgen receptor (AR) tion polymorphism, and sequencing analyses, were per- function in activating androgen responsive genes in target formed in exons 2 to 8 of the AR gene. In one case, total cells (McPhaul et al. 1993). The phenotype in 46,XY af- cellular RNA was extracted from genital skin fibroblasts fected individuals varies depending on the extent of the and reverse transcriptase-PCR was performed. Six different AR defect, ranging from subjects with complete androgen point mutations leading to amino acid substitutions (P682T, insensitivity syndrome (CAIS) where a female phenotype is Q711E, G743E, F827V, H874R, D879Y), one splice- observed, to patients with genital ambiguity who present junction mutation (gÆc at ϩ5, exon 6/intron 6), and a mis- with partial androgen insensitivity syndrome (PAIS).