Bonds Stabilizing Protein Structure, Levels of Organization in Proteins, Denaturation, Introduction to Simple and Conjugate Proteins
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
THE THICKNESSES of HEMOGLOBIN and BOVINE SERUM ALBUMIN MOLECULES AS UNIMOLECULAR LA YERS AD- SORBED ONTO FILMS of BARIUM STEARATE* by ALBERT A
518 BIOCHEMISTRY: A. A. FISK PROC. N. A. S. THE THICKNESSES OF HEMOGLOBIN AND BOVINE SERUM ALBUMIN MOLECULES AS UNIMOLECULAR LA YERS AD- SORBED ONTO FILMS OF BARIUM STEARATE* By ALBERT A. FIsKt GATES AND CRELLIN LABORATORIES OF CHEMISTRY, CALIFORNIA INSTITUTE OF TECHNOLOGY, PASADENA 4, CALIFORNIAt Communicated by Linus Pauling, July 17, 1950 The following work, which describes a method of measuring one dimen- sion of some protein molecules, is based on the determination of the apparent thickness of a unimolecular layer of globular protein molecules adsorbed from solution onto a metallic slide covered with an optical gauge of barium stearate. Langmuirl' 2 and Rothen3 have published a few results obtained by such a technique, but have not exploited the method thoroughly. A complete set of experimental data has been obtained by Clowes4 on insulin and protamine. He studied the effects of pH and time of exposure on the thickness of layers of protamine and insulin adsorbed onto slides covered with barium stearate and conditioned with uranyl acetate. He found that the pH was responsible for large variations in the thickness of the adsorbed layers and that the thickness of insulin layers adsorbed onto a protamine base was dependent on the concentration of the insulin. Since Clowes found thicknesses as high as 100 A. for protamine and 400 A. for insulin, he was without doubt usually dealing with multi- layers. Experimental.-The apparent thickness of a protein layer is measured with an optical instrument called the ellipsometer by Rothen,5-7 who has given a complete description of its design and optics and has calculated its sensitivity as 0.3 A. -
Flowering Buds of Globular Proteins: Transpiring Simplicity of Protein Organization
Comparative and Functional Genomics Comp Funct Genom 2002; 3: 525–534. Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.223 Conference Review Flowering buds of globular proteins: transpiring simplicity of protein organization Igor N. Berezovsky1 and Edward N. Trifonov2* 1 Department of Structural Biology, The Weizmann Institute of Science, PO Box 26, Rehovot 76100, Israel 2 Genome Diversity Centre, Institute of Evolution, University of Haifa, Haifa 31905, Israel *Correspondence to: Abstract Edward N. Trifonov, Genome Diversity Centre, Institute of Structural and functional complexity of proteins is dramatically reduced to a simple Evolution, University of Haifa, linear picture when the laws of polymer physics are considered. A basic unit of the Haifa 31905, Israel. protein structure is a nearly standard closed loop of 25–35 amino acid residues, and E-mail: every globular protein is built of consecutively connected closed loops. The physical [email protected] necessity of the closed loops had been apparently imposed on the early stages of protein evolution. Indeed, the most frequent prototype sequence motifs in prokaryotic proteins have the same sequence size, and their high match representatives are found as closed loops in crystallized proteins. Thus, the linear organization of the closed loop elements is a quintessence of protein evolution, structure and folding. Copyright 2002 John Wiley & Sons, Ltd. Received: 31 August 2002 Keywords: loop closure; prototype elements; protein structure; protein folding; Accepted: 14 October 2002 protein evolution; protein design; protein classification Introduction and the probability of the loop ends occurring in the vicinity of one another. The loop closure fortified One fundamental property of the polypeptide chain by the interactions between amino acid residues at is its ability to return to itself with the formation the ends of the loops provides an important degree of closed loops. -
Amino Acid Building Block Models – in Brief
Amino Acid Building Block Models – In Brief Key Teaching Points for Amino Acid Building Block Models© Overall Student Learning Objective: What Dictates How a Protein Folds? Amino acids are the building blocks of proteins. All amino acids have an identical core structure consisting of an alpha-carbon, carboxyl group, amino group and R-group (sidechain). A linear chain of amino acids is a polypeptide. The primary sequence of a protein is the linear sequence of amino acids in a polypeptide. Proteins are made up of amino acid monomers linked together by peptide bonds. Peptide bond formation between amino acids results in the release of water (dehydration synthesis or condensation reaction). The protein backbone is characterized by the “N-C-C-N-C-C. .” pattern. The “ends” of the protein can be identified by the N-terminus (amino group) end and the C-terminus (carboxyl group) end. For a more complete lesson guide, please visit: http://www.3dmoleculardesigns.com/3DMD-Files/AABB/ContentsandAssembly.pdf Amino Acid Core Structure Build an amino acid according to the diagram to the right: 1. Identify the alpha carbon, amino group, carboxyl group and R-group (sidechain representation) in the structure you have constructed. Two amino acids can be chemically linked by a reaction called “condensation” or “dehydration synthesis” to form a dipeptide bond linking the two amino acids. A chain of amino acid units (monomers) linked together by peptide bonds is called a polypeptide. General Dipeptide Structure Construct a model of a dipeptide using the amino acid models previously built. 2. What are the products of the condensation reaction (dehydration synthesis)? 3. -
Proteasome System of Protein Degradation and Processing
ISSN 0006-2979, Biochemistry (Moscow), 2009, Vol. 74, No. 13, pp. 1411-1442. © Pleiades Publishing, Ltd., 2009. Original Russian Text © A. V. Sorokin, E. R. Kim, L. P. Ovchinnikov, 2009, published in Uspekhi Biologicheskoi Khimii, 2009, Vol. 49, pp. 3-76. REVIEW Proteasome System of Protein Degradation and Processing A. V. Sorokin*, E. R. Kim, and L. P. Ovchinnikov Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; E-mail: [email protected]; [email protected] Received February 5, 2009 Abstract—In eukaryotic cells, degradation of most intracellular proteins is realized by proteasomes. The substrates for pro- teolysis are selected by the fact that the gate to the proteolytic chamber of the proteasome is usually closed, and only pro- teins carrying a special “label” can get into it. A polyubiquitin chain plays the role of the “label”: degradation affects pro- teins conjugated with a ubiquitin (Ub) chain that consists at minimum of four molecules. Upon entering the proteasome channel, the polypeptide chain of the protein unfolds and stretches along it, being hydrolyzed to short peptides. Ubiquitin per se does not get into the proteasome, but, after destruction of the “labeled” molecule, it is released and labels another molecule. This process has been named “Ub-dependent protein degradation”. In this review we systematize current data on the Ub–proteasome system, describe in detail proteasome structure, the ubiquitination system, and the classical ATP/Ub- dependent mechanism of protein degradation, as well as try to focus readers’ attention on the existence of alternative mech- anisms of proteasomal degradation and processing of proteins. -
Introduction to Proteins and Amino Acids Introduction
Introduction to Proteins and Amino Acids Introduction • Twenty percent of the human body is made up of proteins. Proteins are the large, complex molecules that are critical for normal functioning of cells. • They are essential for the structure, function, and regulation of the body’s tissues and organs. • Proteins are made up of smaller units called amino acids, which are building blocks of proteins. They are attached to one another by peptide bonds forming a long chain of proteins. Amino acid structure and its classification • An amino acid contains both a carboxylic group and an amino group. Amino acids that have an amino group bonded directly to the alpha-carbon are referred to as alpha amino acids. • Every alpha amino acid has a carbon atom, called an alpha carbon, Cα ; bonded to a carboxylic acid, –COOH group; an amino, –NH2 group; a hydrogen atom; and an R group that is unique for every amino acid. Classification of amino acids • There are 20 amino acids. Based on the nature of their ‘R’ group, they are classified based on their polarity as: Classification based on essentiality: Essential amino acids are the amino acids which you need through your diet because your body cannot make them. Whereas non essential amino acids are the amino acids which are not an essential part of your diet because they can be synthesized by your body. Essential Non essential Histidine Alanine Isoleucine Arginine Leucine Aspargine Methionine Aspartate Phenyl alanine Cystine Threonine Glutamic acid Tryptophan Glycine Valine Ornithine Proline Serine Tyrosine Peptide bonds • Amino acids are linked together by ‘amide groups’ called peptide bonds. -
1 Epitomic Analysis of the Specificity of Conformation-Dependent, Anti-AЯ
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.05.238105; this version posted November 19, 2020. 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. Epitomic analysis of the specificity of conformation-dependent, anti-Aß amyloid monoclonal antibodies. Jorge Mauricio Reyes-Ruiz1, Rie Nakajima2, Ibtisam Baghallab3, Luki Goldschmidt4, Justyna Sosna1, Phuong Nguyen Mai Ho1, Taha Kumosani3, Philip L. Felgner2, and Charles Glabe1* 1Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 29697- 3900 3900 2Vaccine Research and Development Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA. 3Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah - Saudi Arabia 4Institute for Protein Design, Department of Biochemistry, University of Washington, NanoES 396, Seattle, WA 98195-7370 *Corresponding author: Charles Glabe Email: [email protected] Running title: Epitomic analysis of anti-Aß antibodies Keywords: Bioinformatics, Alzheimer Disease, Amyloid antibodies, Discontinuous epitopes, Epitope mapping, Phage display, Immunotherapy 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.05.238105; this version posted November 19, 2020. 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. Abstract arrangement, the segments -
Folding Units in Globular Proteins (Protein Folding/Domains/Folding Intermediates/Structural Hierarchy/Protein Structure) ARTHUR M
Proc. NatL Acad. Sci. USA Vol. 78, No. 7, pp. 4304-4308, July 1981 Biochemistry Folding units in globular proteins (protein folding/domains/folding intermediates/structural hierarchy/protein structure) ARTHUR M. LESK* AND GEORGE D. ROSE#T *Fairleigh Dickinson- University, Teaneck, New Jersey 07666; and tDepartment of Biologial Chemistry, The Milton S. Hershey Medical Center, The Pennsylvania State University, Hershey, Per'nsykania 17033 Communicated by Charles Tanford, April 20, 1981 ABSTRACT We presenta method toidentify all compact, con- (ii) Analysis of protein structures elucidated by x-ray crys- tiguous-chain, structural units in a globular protein from x-ray tallography showed that protein molecules can be dissected into coordinates. These units are then used to describe a complete set a succession of spatially compact pieces of graduated size (4). of hierarchic folding pathways for the molecule. Our analysis Each of these elements is formed from a contiguous stretch of shows that the larger units are combinations ofsmaller units, giv- the polypeptide chain. A related analysis was reported by Crip- ing rise to a structural hierarchy ranging from the whole protein pen (5). The spatial compartmentation oflinear segments, seen monomer through supersecondary structures down to individual in the final structure, is likely to be a helices and strands. It turns out that there is more than one way feature of intermediate to assemble the protein by self-association of its compact units. folding stages as well. Otherwise, mixing of chain segments However, the number ofpossible pathways is small-small enough occurring during intermediate stages would have to be followed to be exhaustively explored by a computer program. -
Proquest Dissertations
©Copyright 2011 Andrew M. Simms Mining Mountains of Data: Organizing All Atom Molecular Dynamics Protein Simulation Data into SQL and OLAP Cubes Andrew M. Simms A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2011 Program Authorized to Offer Degree: Medical Education and Biomedical Informatics UMI Number: 3472310 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI' Dissertation Publishing UMI 3472310 Copyright 2011 by ProQuest LLC. All rights reserved. This edition of the work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 University of Washington Graduate School This is to certify that I have examined this copy of a doctoral dissertation by Andrew M. Simms and have found that it is complete and satisfactory in all respects, and that any and all revisions required by the final examining committee have been made. Chair of the Supervisory Committee: Valerie Daggett' Reading Committee: ^J CtJ..JLA^~JL Valerie Daggett (sA^d^/^y ^PUl« IraP,. Kalet JMer Myler Date: ^'/^v-ZO/r*y. / In presenting this dissertation in partial fulfillment of the requirements for the doctoral degree at the University of Washington, I agree that the Library shall make its copies freely available for inspection. -
Methionine Aminopeptidase Emerging Role in Angiogenesis
Chapter 2 Methionine Aminopeptidase Emerging role in angiogenesis Joseph A. Vetro1, Benjamin Dummitt2, and Yie-Hwa Chang2 1Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Ave., Lawrence, KS 66047, USA. 2Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Health Sciences Center, 1402 S. Grand Blvd., St. Louis, MO 63104, USA. Abstract: Angiogenesis, the formation of new blood vessels from existing vasculature, is a key factor in a number of vascular-related pathologies such as the metastasis and growth of solid tumors. Thus, the inhibition of angiogenesis has great potential as a therapeutic modality in the treatment of cancer and other vascular-related diseases. Recent evidence suggests that the inhibition of mammalian methionine aminopeptidase type 2 (MetAP2) catalytic activity in vascular endothelial cells plays an essential role in the pharmacological activity of the most potent small molecule angiogenesis inhibitors discovered to date, the fumagillin class. Methionine aminopeptidase (MetAP, EC 3.4.11.18) catalyzes the non-processive, co-translational hydrolysis of initiator N-terminal methionine when the second residue of the nascent polypeptide is small and uncharged. Initiator Met removal is a ubiquitous and essential modification. Indirect evidence suggests that removal of initiator Met by MetAP is important for the normal function of many proteins involved in DNA repair, signal transduction, cell transformation, secretory vesicle trafficking, and viral capsid assembly and infection. Currently, much effort is focused on understanding the essential nature of methionine aminopeptidase activity and elucidating the role of methionine aminopeptidase type 2 catalytic activity in angiogenesis. In this chapter, we give an overview of the MetAP proteins, outline the importance of initiator Met hydrolysis, and discuss the possible mechanism(s) through which MetAP2 inhibition by the fumagillin class of angiogenesis inhibitors leads to cytostatic growth arrest in vascular endothelial cells. -
Introduction 1.1 Post-Translational Modifications
Chapter I: Introduction 1.1 Post-translational modifications Post-translational modifications (PTMs) are responsible for dynamic regulation of protein structure and function (Jensen et al., 2006). One example of the function of post-translational modifications in the dynamic regulation of protein structure and function is signal transduction; post-translational modification of key regulatory proteins in signal transduction pathways controls cellular proliferation, metabolism, gene expression, cytoskeletal organization and apoptosis (Jensen et al., 2006). Post-translational modifications not only change the mass of the protein, they are also often responsible for changes in charge, structure and conformation. This leads to changes in the biological activity of proteins like enzymes, the binding affinity of proteins to receptors and other protein-protein interactions (Hoffmann et al., 2008) (Murray et al., 1998). For example, the interaction of the cytokine TGF-beta with its receptor complex results in the phosphorylation of SMAD family proteins which activates these proteins to regulate target gene expression (Massague et al., 2000). Post-translational modified amino acid residues can act as binding sites on proteins for a specific recognition domain on other proteins. For example, phosphorylated tyrosine residues can bind to SH2 or PTB domains (Pawson et al., 1997). Depending on the type of PTM they can be very abundant and have a large number of target proteins, whereas other PTM`s have only a few target proteins. Moreover, some PTM`s are connected with several different residues and not only with one residue. For example multi-site phosphorylation that primarily targets Serine, Threonine and Tyrosine residues is a crucial mechanism for the regulation of protein localization and functional activity (Cohen et al., 2000). -
Peptides & Proteins
Peptides & Proteins (thanks to Hans Börner) 1 Proteins & Peptides Proteuos: Proteus (Gr. mythological figure who could change form) proteuo: „"first, ref. the basic constituents of all living cells” peptos: „Cooked referring to digestion” Proteins essential for: Structure, metabolism & cell functions 2 Bacterium Proteins (15 weight%) 50% (without water) • Construction materials Collagen Spider silk proteins 3 Proteins Structural proteins structural role & mechanical support "cell skeleton“: complex network of protein filaments. muscle contraction results from action of large protein assemblies Myosin und Myogen. Other organic material (hair and bone) are also based on proteins. Collagen is found in all multi cellular animals, occurring in almost every tissue. • It is the most abundant vertebrate protein • approximately a quarter of mammalian protein is collagen 4 Proteins Storage Various ions, small molecules and other metabolites are stored by complexation with proteins • hemoglobin stores oxygen (free O2 in the blood would be toxic) • iron is stored by ferritin Transport Proteins are involved in the transportation of particles ranging from electrons to macromolecules. • Iron is transported by transferrin • Oxygen via hemoglobin. • Some proteins form pores in cellular membranes through which ions pass; the transport of proteins themselves across membranes also depends on other proteins. Beside: Regulation, enzymes, defense, functional properties 5 Our universal container system: Albumines 6 zones: IA, IB, IIA, IIB, IIIA, IIIB; IIB and -
CATALOG Hands On, Minds On! New Products
...where molecules become real TM CATALOG Hands On, Minds On! New Products Flu Fight: Immunity & Infection Panorama© Page 15 NEW Durable Plastic! Synapse Construction Kit© Page 19 Antibody and Antigen Models Page 17 Insulin Model Page 9 Our Customers’ Favorite Products Water Kit© Page 3 Flow of Genetic Information Kit© Page 13 DNA Discovery Kit© Page 11 Enzymes in Action Kit© Page 8 Amino Acid Starter Kit© Page 7 Phospholipid & Membrane Transport Kit© Page 5 David Goodsell Cellular Landscapes Page 14 3dmoleculardesigns.com Made in the U.S.A. ...where molecules become real TM 2018 Product by Category Water and Membrane Science Olympiad Protein Modeling Event © © Water Kit and NaCl Lattice .................................................................... 3 Pre-Build Kit and Practice Kit ............................................................... 23 Channel Mini Models: Sodium Channel, Aquaporin Channel, Potassium Channel and Potassium Project-Based Learning Activities © Channel with Scorpion Toxin ............................................................... 4 Neurotransmitters Module: The Beery Twins’ Story © © Phospholipid & Membrane Transport Kit and Human Sepiapterin Reductase mRNA Gene Map and Mini © Phospholipid Modeling Set ................................................................ 5 Model and Dopamine and Serotonin Biosynthesis Models ... 18 © Molecules of Life Collection ................................................................... 12 Water Tattoos .………………………………………….........................………….... 21 Kits ©