DOCSLIB.ORG

Regulation of Translesion DNA Synthesis: Posttranslational

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Regulation of Translesion DNA Synthesis: Posttranslational DNA Repair 29 (2015) 166–179 Contents lists available at ScienceDirect DNA Repair j ournal homepage: www.elsevier.com/locate/dnarepair Regulation of translesion DNA synthesis: Posttranslational modification of lysine residues in key proteins a,∗ b Justyna McIntyre , Roger Woodgate a Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland b Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA a r a t i b s c t l e i n f o r a c t Article history: Posttranslational modification of proteins often controls various aspects of their cellular function. Indeed, Received 27 October 2014 over the past decade or so, it has been discovered that posttranslational modification of lysine residues Received in revised form 9 February 2015 plays a major role in regulating translesion DNA synthesis (TLS) and perhaps the most appreciated lysine Accepted 10 February 2015 modification is that of ubiquitination. Much of the recent interest in ubiquitination stems from the fact Available online 18 February 2015 that proliferating cell nuclear antigen (PCNA) was previously shown to be specifically ubiquitinated at K164 and that such ubiquitination plays a key role in regulating TLS. In addition, TLS polymerases them- Keywords: selves are now known to be ubiquitinated. In the case of human polymerase ␩, ubiquitination at four Translesion synthesis Ubiquitin lysine residues in its C-terminus appears to regulate its ability to interact with PCNA and modulate TLS. Within the past few years, advances in global proteomic research have revealed that many proteins Y-family polymerase PCNA involved in TLS are, in fact, subject to a previously underappreciated number of lysine modifications. In this review, we will summarize the known lysine modifications of several key proteins involved in TLS; PCNA and Y-family polymerases ␩, ␫, ␬ and Rev1 and we will discuss the potential regulatory effects of such modification in controlling TLS in vivo. © 2015 Published by Elsevier B.V. 1. Introduction e.g. SUMOylation, ISGylation, neddylation, FATylation and other lysine modifications such as acetylation, methylation, butyrylation, Posttranslational modifications (PTMs) of proteins by attach- crotonylation, glycation, malonylation, phosphoglycerylation, pro- ing different functional groups to amino acids widens the target pionylation, succinylation, myristoylation [1–4]. protein’s range of function and provides additional mechanisms Eukaryotic cells have evolved a plethora of mechanisms in order by which the modified protein can be regulated. For example, to protect genome stability by removing DNA lesions, or preventing PTMs can control a protein’s activity by influencing its ability to their conversion into permanent mutations [5]. Importantly, due interact with protein-partners, alter its enzymatic activity, sub- to partially overlapping functions of some of these pathways, or cellular localization, and change the stability of the protein. Of time and conditional cellular requirements, their actions need to all the experimentally identified PTMs in mammals, serine phos- be precisely controlled. Recent studies in the DNA repair field have phorylation is the most frequent modification followed by lysine, accumulated evidence of an ever expanding role of ubiquitination which represents over 15% of all experimentally identified amino in regulating diverse DNA repair mechanisms and pathways acid modifications (calculation based on data from [1]). Lysine involved in genomic stability maintenance (reviewed in [6]). can be modified in a variety of ways including, but not limited Ubiquitin- and ubiquitin-like-dependent signaling processes have to: ubiquitination, ubiquitin-like protein (UBL) modification an important function in controlling cellular responses to DNA damage by navigating through the range of DNA damage repair, or tolerance mechanisms (reviewed in [6–10]). The majority of DNA lesions are repaired by one of the specialized DNA repair pathways; Abbreviations: TLS, translesion synthesis; PCNA, proliferating cell nuclear anti- gen; pol, polymerase; PIP, PCNA-interacting peptide; RIR, Rev1-interacting region; however the repair processes can be slow and incomplete and as a UBM, ubiquitin binding motif; UBZ, ubiquitin binding zinc motif; pol␫, DNA poly- consequence a number of DNA lesions remain in the template DNA. ␩ merase iota; pol , DNA polymerase eta; pol␬, DNA polymerase kappa; UBL, This causes a severe problem, especially during the S-phase of the ubiquitin-like protein; PTM, posttranslational modification; PRR, post replication cell cycle, when DNA is replicated, because efficient and accurate DNA repair. ∗ classical DNA polymerases are blocked at DNA lesions. At this Corresponding author. Tel.: +48 22 5921115. E-mail address: [email protected] (J. McIntyre). critical juncture, distinct mechanisms are required to temporarily http://dx.doi.org/10.1016/j.dnarep.2015.02.011 1568-7864/© 2015 Published by Elsevier B.V. J. McIntyre, R. Woodgate / DNA Repair 29 (2015) 166–179 167 tolerate cellular DNA damage, thereby avoiding the permanent E4s [34,35]. Ubiquitination can be reversed through the activity block to the replication fork and the threat of cell cycle arrest. Lesion of de-ubiquitinating enzymes (DUBs), which primarily disassem- tolerance can be achieved in two different ways; one via a damage ble polyubiquitin chains before protein degradation, but will also avoidance pathway using the information from the undamaged cleave off a single ubiquitin moiety, or a polyubiquitin chain to sister chromatid as a template for replication of the damaged regulate protein functionality [36]. DNA region, or via translesion synthesis (TLS), which employs specialized DNA polymerases to synthesize past the lesion. 2.2. Ubiquitin-like posttranslational modification Over the past dozen years, it has become evident that modifica- tion of lysine residues through the covalent linkage of ubiquitin, or Besides ubiquitin, at least 10 different ubiquitin-like proteins ubiquitin-like proteins, plays a central role in controlling both DNA (UBLs) exist in mammals (reviewed in [37,38]) with SUMO, NEDD8 damage avoidance mechanisms and TLS. This review will attempt and ISG15 being the best known. UBL modifiers, similar to ubiqui- to summarize the known sites and cellular effects of ubiquitin- tin, form an isopeptide bond between their C-terminal glycine and ation of several key proteins involved in TLS. We will recap the lysine residues of the substrate [38]. UBLs often have low sequence individually discovered and experimentally confirmed sites of ubi- homology, but share a similar three-dimensional structure [38]. quitination and ubiquitin-like modifications of TLS proteins and Posttranslational modification with UBL proteins can alter cellular combine them with recent data derived from multiple proteome- function, stability, interactions with protein partners, or subcellu- wide approaches that reveal a hitherto underappreciated extent of lar localization of the target protein [37,39]. Protein modification lysine ubiquitination of many of the TLS proteins. by UBLs follows the same three-step cascade similar to ubiquit- ination in that it is catalyzed by sets of analogous activation (E1), conjugation (E2s) and ligation (E3s) enzymes and can be reversed 2. Types of lysine modifications by deconjugating enzymes [40]. SUMO (Small Ubiquitin-like MOdifier) is the most studied UBL 2.1. Ubiquitination modifier and is expressed in all eukaryotes, mainly as a sin- gle variant. However in human cells there are four different In eukaryotic cells, ubiquitination is involved in the regulation paralogs (SUMO1–4), representing various homology, expression of almost all cellular processes, including cell division, membrane levels and substrate preferences. Many proteins interacting with a transport, signal transduction, DNA repair, endocytosis, inflamma- SUMOlyated substrate possess specific SIM domains (from SUMO- tory signaling, apoptosis, etc. [11–14]. It has been estimated that interaction motif) [41]. SUMOylation of a target protein can roughly 10% of human genes encode for proteins involved in ubiqui- influence the protein degradation, signal transduction, localiza- tin metabolism [15]. The malfunction of ubiquitination processes tion, transcription activation, cell cycle, chromatin organization, and ubiquitin-mediated proteolysis has been implicated in various DNA repair and other functions (reviewed in [42]). Dysfunction of pathologies, including neurodegenerative disorders, inflammatory SUMOylation can lead to neurodegenerative diseases, heart defects, diseases and cancers [16–19]. Due to their important cellular diabetes or cancer [42–45]. functions, ubiquitination pathways are significant targets for ther- One ubiquitin-like molecule, ISG15 (the interferon-stimulated apeutics [20,21]. gene 15), has a primary sequence that consists of two domains Protein ubiquitination is a dynamic and reversible process with significant similarity to ubiquitin [46]. Interestingly, ISGyla- where a three-step enzymatic cascade conjugates a small, regu- tion shares some of the E2 and E3 enzymes used in ubiquitination latory protein, ubiquitin, to a specific lysine residue in a target and ISGylated proteins can also be targeted for degradation by the protein [22]. Initially, one of the ubiquitin-activating enzymes (E1s) 20S proteasome [47,48]. ISG15 is only found in vertebrates. Type forms
Load more

Recommended publications
  • Understanding and Exploiting Post-Translational Modifications for Plant Disease Resistance
    biomolecules Review Understanding and Exploiting Post-Translational Modifications for Plant Disease Resistance Catherine Gough and Ari Sadanandom * Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK; [email protected] * Correspondence: [email protected]; Tel.: +44-1913341263 Abstract: Plants are constantly threatened by pathogens, so have evolved complex defence signalling networks to overcome pathogen attacks. Post-translational modifications (PTMs) are fundamental to plant immunity, allowing rapid and dynamic responses at the appropriate time. PTM regulation is essential; pathogen effectors often disrupt PTMs in an attempt to evade immune responses. Here, we cover the mechanisms of disease resistance to pathogens, and how growth is balanced with defence, with a focus on the essential roles of PTMs. Alteration of defence-related PTMs has the potential to fine-tune molecular interactions to produce disease-resistant crops, without trade-offs in growth and fitness. Keywords: post-translational modifications; plant immunity; phosphorylation; ubiquitination; SUMOylation; defence Citation: Gough, C.; Sadanandom, A. 1. Introduction Understanding and Exploiting Plant growth and survival are constantly threatened by biotic stress, including plant Post-Translational Modifications for pathogens consisting of viruses, bacteria, fungi, and chromista. In the context of agriculture, Plant Disease Resistance. Biomolecules crop yield losses due to pathogens are estimated to be around 20% worldwide in staple 2021, 11, 1122. https://doi.org/ crops [1]. The spread of pests and diseases into new environments is increasing: more 10.3390/biom11081122 extreme weather events associated with climate change create favourable environments for food- and water-borne pathogens [2,3]. Academic Editors: Giovanna Serino The significant estimates of crop losses from pathogens highlight the need to de- and Daisuke Todaka velop crops with disease-resistance traits against current and emerging pathogens.
    [Show full text]
  • Ginkgolic Acid, a Sumoylation Inhibitor, Promotes Adipocyte
    www.nature.com/scientificreports OPEN Ginkgolic acid, a sumoylation inhibitor, promotes adipocyte commitment but suppresses Received: 25 October 2017 Accepted: 15 January 2018 adipocyte terminal diferentiation Published: xx xx xxxx of mouse bone marrow stromal cells Huadie Liu1,2, Jianshuang Li2, Di Lu2, Jie Li1,2, Minmin Liu 3, Yuanzheng He4, Bart O. Williams2, Jiada Li1 & Tao Yang 2 Sumoylation is a post-translational modifcation process having an important infuence in mesenchymal stem cell (MSC) diferentiation. Thus, sumoylation-modulating chemicals might be used to control MSC diferentiation for skeletal tissue engineering. In this work, we studied how the diferentiation of mouse bone marrow stromal cells (mBMSCs) is afected by ginkgolic acid (GA), a potent sumoylation inhibitor also reported to inhibit histone acetylation transferase (HAT). Our results show that GA promoted the diferentiation of mBMSCs into adipocytes when cultured in osteogenic medium. Moreover, mBMSCs pre-treated with GA showed enhanced pre-adipogenic gene expression and were more efciently diferentiated into adipocytes when subsequently cultured in the adipogenic medium. However, when GA was added at a later stage of adipogenesis, adipocyte maturation was markedly inhibited, with a dramatic down-regulation of multiple lipogenesis genes. Moreover, we found that the efects of garcinol, a HAT inhibitor, difered from those of GA in regulating adipocyte commitment and adipocyte maturation of mBMSCs, implying that the GA function in adipogenesis is likely through its activity as a sumoylation inhibitor, not as a HAT inhibitor. Overall, our studies revealed an unprecedented role of GA in MSC diferentiation and provide new mechanistic insights into the use of GA in clinical applications.
    [Show full text]
  • Sumoylation and Phosphorylation Cross-Talk in Hepatocellular Carcinoma
    Review Article SUMOylation and phosphorylation cross-talk in hepatocellular carcinoma Maria Lauda Tomasi, Komal Ramani Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA Contributions: (I) Conception and design: All authors; (II) Administrative support: All authors; (III) provision of study materials or patients: All authors; (IV) Collection and assembly of data: All authors; (V) Data analysis and interpretation: All authors; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. Correspondence to: Maria Lauda Tomasi, PhD; Komal Ramani, PhD. Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA. Email: [email protected]; [email protected]. Abstract: Hepatocellular carcinoma (HCC) is a primary malignancy of the liver and occurs predominantly in patients with underlying chronic liver disease and cirrhosis. The large spectrum of protein post- translational modification (PTM) includes numerous critical signaling events that occur during neoplastic transformation. PTMs occur to nearly all proteins and increase the functional diversity of proteins. We have reviewed the role of two major PTMs, SUMOylation and phosphorylation, in the altered signaling of key players in HCC. SUMOylation is a PTM that involves addition of a small ubiquitin-like modifiers (SUMO) group to proteins. It is known to regulate protein stability, protein-protein interactions, trafficking and transcriptional activity. The major pathways that are regulated by SUMOylation and may influence HCC are regulation of transcription, cell growth pathways associated with B-cell lymphoma 2 (Bcl-2) and methionine adenosyltransferases (MAT), oxidative stress pathways [nuclear erythroid 2-related factor 2 (Nrf2)], tumor suppressor pathways (p53), hypoxia-inducible signaling [hypoxia-inducible factor-1 (HIF-1)], glucose and lipid metabolism, nuclear factor kappa B (NF-κB) and β-Catenin signaling.
    [Show full text]
  • The Cycle of Protein Engineering: Bioinformatics Design of Two Dimeric Proteins and Computational Design of a Small Globular Domain
    The Cycle of Protein Engineering: Bioinformatics Design of Two Dimeric Proteins and Computational Design of a Small Globular Domain DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Venuka Durani, M.Sc. Graduate Program in Chemistry The Ohio State University 2012 Dissertation Committee: Thomas J. Magliery, Advisor Ross E. Dalbey Karin Musier-Forsyth William C. Ray Copyright by Venuka Durani 2012 Abstract The protein folding problem is an ongoing challenge, and even though there have been significant advances in our understanding of proteins, accurately predicting the effect of amino acid mutations on the structure and stability of a protein remains a challenge. This makes the task of engineering proteins to suit our purposes labor intensive as significant trial and error is involved. In this thesis, we have explored possibilities of better understanding and if possible improving some bioinformatics and computational methods to study proteins and also to engineer them. A significant portion of this thesis is based on bioinformatics approaches involving consensus and correlation analyses of multiple sequence alignments. We have illustrated how consensus and correlation metrics can be calculated and analyzed to explore various aspects of protein structure. Proteins triosephosphate isomerase and Cu, Zn superoxide dismutase were studied using these approaches and we found that a significant amount of information about a protein fold is encoded at the consensus level; however, the effect of amino acid correlations, while subtle, is significant nonetheless and some of the failures of consensus approach can be attributed to broken amino acid correlations.
    [Show full text]
  • Heat Shock Protein 27 Is Involved in SUMO-2&Sol
    Oncogene (2009) 28, 3332–3344 & 2009 Macmillan Publishers Limited All rights reserved 0950-9232/09 $32.00 www.nature.com/onc ORIGINAL ARTICLE Heat shock protein 27 is involved in SUMO-2/3 modification of heat shock factor 1 and thereby modulates the transcription factor activity M Brunet Simioni1,2, A De Thonel1,2, A Hammann1,2, AL Joly1,2, G Bossis3,4,5, E Fourmaux1, A Bouchot1, J Landry6, M Piechaczyk3,4,5 and C Garrido1,2,7 1INSERM U866, Dijon, France; 2Faculty of Medicine and Pharmacy, University of Burgundy, Dijon, Burgundy, France; 3Institut de Ge´ne´tique Mole´culaire UMR 5535 CNRS, Montpellier cedex 5, France; 4Universite´ Montpellier 2, Montpellier cedex 5, France; 5Universite´ Montpellier 1, Montpellier cedex 2, France; 6Centre de Recherche en Cance´rologie et De´partement de Me´decine, Universite´ Laval, Quebec City, Que´bec, Canada and 7CHU Dijon BP1542, Dijon, France Heat shock protein 27 (HSP27) accumulates in stressed otherwise lethal conditions. This stress response is cells and helps them to survive adverse conditions. We have universal and is very well conserved through evolution. already shown that HSP27 has a function in the Two of the most stress-inducible HSPs are HSP70 and ubiquitination process that is modulated by its oligomeriza- HSP27. Although HSP70 is an ATP-dependent chaper- tion/phosphorylation status. Here, we show that HSP27 is one induced early after stress and is involved in the also involved in protein sumoylation, a ubiquitination- correct folding of proteins, HSP27 is a late inducible related process. HSP27 increases the number of cell HSP whose main chaperone activity is to inhibit protein proteins modified by small ubiquitin-like modifier aggregation in an ATP-independent manner (Garrido (SUMO)-2/3 but this effect shows some selectivity as it et al., 2006).
    [Show full text]
  • Review Sumoylation Regulates Diverse Biological Processes
    Cell. Mol. Life Sci. 64 (2007) 3017 – 3033 1420-682X/07/233017-17 Cellular and Molecular Life Sciences DOI 10.1007/s00018-007-7137-4 Birkhuser Verlag, Basel, 2007 Review Sumoylation regulates diverse biological processes J. Zhao Center for Cell Biology and Cancer Research, Albany Medical College, 47 New Scotland Avenue, MC-165, Albany, New York 12208 (USA) Fax: +1 518 262 5669; e-mail: [email protected] Received 19 March 2007; received after version 16 July 2007; accepted 1 August 2007 Online First 4 September 2007 Abstract. Ten years after its discovery, the small turn affect gene expression, genomic and chromoso- ubiquitin-like protein modifier (SUMO) has emerged mal stability and integrity, and signal transduction. as a key regulator of proteins. While early studies Sumoylation is counter-balanced by desumoylation, indicated that sumoylation takes place mainly in the and well-balanced sumoylation is essential for normal nucleus, an increasing number of non-nuclear sub- cellular behaviors. Loss of the balance has been strates have recently been identified, suggesting a associated with a number of diseases. This paper wider stage for sumoylation in the cell. Unlike reviews recent progress in the study of SUMO path- ubiquitylation, which primarily targets a substrate ways, substrates, and cellular functions and highlights for degradation, sumoylation regulates a substrates important findings that have accelerated advances in functions mainly by altering the intracellular local- this study field and link sumoylation to human ization, protein-protein interactions or other types of diseases. post-translational modifications. These changes in Keywords. SUMO, sumoylation cycle, desumoylation, gene expression, genomic and chromosomal integrity, signal transduction, loss-of-function of SUMO pathway, SUMO-associated disease.
    [Show full text]
  • Protein Denaturation Catalyzed by AAA+ Unfolding Machines and Proteases
    Assaying the kinetics of protein denaturation catalyzed by AAA+ unfolding machines and proteases Vladimir Baytshtoka, Tania A. Bakera,b, and Robert T. Sauera,1 aDepartment of Biology and bHoward Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139 Contributed by Robert T. Sauer, March 24, 2015 (sent for review February 14, 2015; reviewed by James U. Bowie and Andreas Matouschek) ATP-dependent molecular machines of the AAA+ superfamily un- subunits of an oligomer could either free subunits to carry out fold or remodel proteins in all cells. For example, AAA+ ClpX and other functions blocked in the multimer, as in the RepA example, ClpA hexamers collaborate with the self-compartmentalized ClpP or lead to disassembly of a dead-end complex, as in the case of peptidase to unfold and degrade specific proteins in bacteria and MuA tetramers bound to translocated DNA. some eukaryotic organelles. Although degradation assays are Protein degradation is readily assayed by the disappearance of straightforward, robust methods to assay the kinetics of enzyme- intact substrate on SDS gels, by the appearance of acid-soluble catalyzed protein unfolding in the absence of proteolysis have been peptides, or by loss of native fluorescence for proteins such as lacking. Here, we describe a FRET-based assay in which enzymatic GFP. More limited methods, largely involving stable naturally unfolding converts a mixture of donor-labeled and acceptor-labeled fluorescent proteins or single-molecule optical trapping, are homodimers into heterodimers. In this assay, ClpX is a more efficient available to probe unfolding by AAA+ enzymes in the absence protein-unfolding machine than ClpA both kinetically and in terms of proteolysis but are generally poorly suited for determining of ATP consumed.
    [Show full text]
  • Asca (Yeca) Is a Molecular Chaperone Involved in Sec-Dependent Protein Translocation
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.21.215244; this version posted July 22, 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-ND 4.0 International license. 1 1 AscA (YecA) is a molecular chaperone involved in Sec-dependent protein translocation 2 in Escherichia coli 3 4 Running title: AscA is a Sec chaperone 5 6 Tamar Cranford Smith1, Max Wynne1, Cailean Carter, Chen Jiang, Mohammed Jamshad, 7 Mathew T. Milner, Yousra Djouider, Emily Hutchinson, Peter A. Lund, Ian Henderson2 and 8 Damon Huber* 9 10 Institute for Microbiology and Infection; University of Birmingham; Edgbaston, 11 Birmingham, UK 12 13 1These authors contributed equally to this work 14 15 2Current address: Institute for Molecular Bioscience; University of Queensland; Brisbane, 16 Australia 17 18 *To whom correspondence should be addressed: [email protected] 19 20 Keywords: protein translocation, Sec pathway, molecular chaperone, SecB, metal binding 21 domain 22 23 ABSTRACT. 24 Proteins that are translocated across the cytoplasmic membrane by Sec 25 machinery must be in an unfolded conformation in order to pass through the protein- bioRxiv preprint doi: https://doi.org/10.1101/2020.07.21.215244; this version posted July 22, 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-ND 4.0 International license.
    [Show full text]
  • High Yield Expression of Proteins in E. Coli for NMR Studies
    Advances in Bioscience and Biotechnology, 2013, 4, 751-767 ABB http://dx.doi.org/10.4236/abb.2013.46099 Published Online June 2013 (http://www.scirp.org/journal/abb/) High yield expression of proteins in E. coli for NMR studies Somnath Mondal1,2, Divya Shet1, Chinmayi Prasanna 1, Hanudatta S. Atreya1,2* 1NMR Research Centre, Indian Institute of Science, Bangalore, India 2Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India Email: *[email protected] Received 1 April 2013; revised 12 May 2013; accepted 25 May 2013 Copyright © 2013 Somnath Mondal et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT increase in size of the molecules the sensitivity of NMR experiments decrease and hence isotopic enrichment helps In recent years, high yield expression of proteins in E. to alleviate to some extent the deleterious effects of large coli has witnessed rapid progress with developments size. of new methodologies and technologies. An important Isotope labeling implies the replacement of 12C, 14N or advancement has been the development of novel re- 1H atoms of the backbone or side-chain of proteins by combinant cloning approaches and protocols to ex- 13C, 15N or 2H, respectively, either uniformly through- press heterologous proteins for Nuclear Magnetic Re- out the protein (i.e., independent of the amino acid type) sonance (NMR) studies and for isotopic enrichment. or in a selective manner (i.e., amino acid type dependent) Isotope labeling in NMR is necessary for rapid acqui- [2].
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 9.221,882 B2 Skerra Et Al
    USOO922.1882B2 (12) United States Patent (10) Patent No.: US 9.221,882 B2 Skerra et al. (45) Date of Patent: Dec. 29, 2015 (54) BIOSYNTHETIC PROLINE/ALANINE WO WO 2007/103,515 A2 9, 2007 RANDOMCOL POLYPEPTDES AND THEIR WO WO 2008, 145400 A2 12/2008 USES WO WO 2010/091122 A1 8, 2010 (75) Inventors: Arne Skerra, Freising (DE); Uli Binder, OTHER PUBLICATIONS Freising (DE); Martin Schlapschy, Rudinger, Peptide Hormones, JA Parsons, Ed., 1976, pp. 1-7.* Freising (DE) SIGMA, 2004, pp. 1-2.* Berendsen, A Glimpae of the Holy Grail?, Science, 1998, 282, pp. (73) Assignees: Technische Universitat Munchen, 642-643. Munich (DE); XL-Protein GmbH, Ngo et al. Computational Complexity, Protein Structure Protection, Freising (DE) and the Levinthal Paradox, 1994, pp. 491-494.* (*) Notice: Subject to any disclaimer, the term of this Bradley et al., Limits of Cooperativity in a Structurally Modular patent is extended or adjusted under 35 Protein: Response of the Notch Ankyrin Domain to Analogous Alanine Substitutions in Each Repeat, J. Mol. BIoL (2002) 324. U.S.C. 154(b) by 0 days. 373-386. Voet et al. Biochemistry, John Wiley & Sons Inc., 1995, pp. 235 (21) Appl. No.: 13/697,569 241.* UniProt Protein Database, Very large tegument protein, UL36, pro (22) PCT Filed: May 20, 2011 tein accession Q7T5D9, accessed on Nov. 25, 2014.* International Search Report received in the parent application PCT/ (86). PCT No.: PCT/EP2011/0583.07 EP2011/0583.07, dated Oct. 7, 2011. “Cell Therapeutics Inc.'s Polyglutamate (PG) Technology High S371 (c)(1), lighted at International Polymer Therapeutics Meeting; Novel Recombinant Technology Extends PG Platform to G-CSF.” PR (2), (4) Date: Nov.
    [Show full text]
  • SUMO Proteases Are Extremely Efficient at Cleaving Fusion Proteins
    SUMO Gene Fusion Technology NEW METHODS FOR ENHANCING PROTEIN EXPRESSION AND PURIFICATION IN PROKARYOTES Applications to Express and Purify Drug Targets, Therapeutics, Vaccines and Industrial Proteins and Peptides White Paper October 2004 Contact Person: John Hall [email protected] [email protected] 610.644.8845 x23 (phone) 610.644.8616 (fax) LifeSensors Inc. 271 Great Valley Parkway Malvern, PA 19355 This document is the property of LifeSensors Inc. The proprietary ideas mentioned in the document are the subject of patent filings. This document may not be copied or distributed to others except to the relevant staff of your company. If you are not the intended recipient, you are hereby notified that any disclosure, copy or distribution of this information, or taking of any action in reliance on the contents of this transmission is strictly prohibited. Copyright © 2003 LifeSensors Inc. LifeSensors Inc From Genomics to Proteomics “Nobel” Ubiquitin In 2004, the Nobel Prize in chemistry was awarded to Drs. Aaron Ciechanover, Avram Hershko, and Irwin Rose for their contributions towards the discovery of the ubiquitin pathway, which regulates protein degradation. We would like to thank them and others, including Drs. Alex Varshavsky, Keith Wilkinson, and Arthur Haas, for their seminal work in this fascinating field. The following technology is based on their life’s work. Nobel Prize Winners in Chemistry Introduction Aaron Ciechanover, Avram Hershko, and Irwin Rose Expression and purification of tractable quantities of active and properly folded protein is a major bottleneck in structural and functional genomics. Difficulties include poor protein expression as well as insoluble and/or improperly folded protein.
    [Show full text]
  • Global Analysis of SUMO-Binding Proteins Identifies Sumoylation As a Key Regulator of the INO80 Chromatin Remodeling Complex
    MCP Papers in Press. Published on March 2, 2017 as Manuscript M116.063719 Global Analysis of SUMO-Binding Proteins Identifies SUMOylation as a Key Regulator of the INO80 Chromatin Remodeling Complex Eric Coxa,b,c, Woochang Hwangd, Ijeoma Uzomac, Jianfei Hud, Catherine M. Guzzoe, Junseop Jeongc,f, Michael J. Matunise, Jiang Qiand*, Heng Zhuc,f* and Seth Blackshawb,f,g,h* From the aBiochemistry, Cellular and Molecular Biology Graduate Program, bSolomon H. Snyder Department of Neuroscience, cDepartment of Pharmacology and Molecular Sciences, dWilmer Eye Institute, fCenter for Human Systems Biology, gInstitute for Cell Engineering, hDepartment of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, eDepartment of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland *To whom correspondence should be addressed at [email protected] (S.B), [email protected] (H.Z.), and [email protected] (J.Q.) ABSTRACT SUMOylation is a critical regulator of a broad range of cellular processes, and is thought to do so in part by modulation of protein interaction. To comprehensively identify human proteins whose interaction is modulated by SUMOylation, we developed an in vitro binding assay using human proteome microarrays to identify targets of SUMO1 and SUMO2. We then integrated these results with protein SUMOylation and protein-protein interaction data to perform network motif analysis. We focused on a single network motif we termed a SUMOmodPPI (SUMO-modulated Protein-Protein Interaction) that included the INO80 chromatin remodeling complex subunits TFPT and INO80E. We validated the SUMO-binding activity of INO80E, and showed that TFPT is a SUMO substrate both in vitro and in vivo.
    [Show full text]