The Function of FK506-Binding Protein 13 in Protein Quality Control Protects Plasma Cells from Endoplasmic Reticulum Stress- Edited By: Associated Apoptosis Harry W
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Prokaryotic Ubiquitin-Like Protein Remains Intrinsically Disordered When Covalently Attached to Proteasomal Target Proteins Jonas Barandun1,2, Fred F
Barandun et al. BMC Structural Biology (2017) 17:1 DOI 10.1186/s12900-017-0072-1 RESEARCH ARTICLE Open Access Prokaryotic ubiquitin-like protein remains intrinsically disordered when covalently attached to proteasomal target proteins Jonas Barandun1,2, Fred F. Damberger1, Cyrille L. Delley1, Juerg Laederach1, Frédéric H. T. Allain1 and Eilika Weber-Ban1* Abstract Background: The post-translational modification pathway referred to as pupylation marks proteins for proteasomal degradation in Mycobacterium tuberculosis and other actinobacteria by covalently attaching the small protein Pup (prokaryotic ubiquitin-like protein) to target lysine residues. In contrast to the functionally analogous eukaryotic ubiquitin, Pup is intrinsically disordered in its free form. Its unfolded state allows Pup to adopt different structures upon interaction with different binding partners like the Pup ligase PafA and the proteasomal ATPase Mpa. While the disordered behavior of free Pup has been well characterized, it remained unknown whether Pup adopts a distinct structure when attached to a substrate. Results: Using a combination of NMR experiments and biochemical analysis we demonstrate that Pup remains unstructured when ligated to two well-established pupylation substrates targeted for proteasomal degradation in Mycobacterium tuberculosis, malonyl transacylase (FabD) and ketopantoyl hydroxylmethyltransferase (PanB). Isotopically labeled Pup was linked to FabD and PanB by in vitro pupylation to generate homogeneously pupylated substrates suitable for NMR analysis. The single target lysine of PanB was identified by a combination of mass spectroscopy and mutational analysis. Chemical shift comparison between Pup in its free form and ligated to substrate reveals intrinsic disorder of Pup in the conjugate. Conclusion: When linked to the proteasomal substrates FabD and PanB, Pup is unstructured and retains the ability to interact with its different binding partners. -
Yichen – Structure and Allostery of the Chaperonin Groel. Allosteric
Literature Lunch 5-1-13 Yichen – J Mol Biol. 2013 May 13;425(9):1476-87. doi: 10.1016/j.jmb.2012.11.028. Epub 2012 Nov 24. Structure and Allostery of the Chaperonin GroEL. Saibil HR, Fenton WA, Clare DK, Horwich AL. Source Crystallography and Institute of Structural and Molecular Biology, Birkbeck College London, Malet Street, London WC1E 7HX, UK. Abstract Chaperonins are intricate allosteric machines formed of two back-to-back, stacked rings of subunits presenting end cavities lined with hydrophobic binding sites for nonnative polypeptides. Once bound, substrates are subjected to forceful, concerted movements that result in their ejection from the binding surface and simultaneous encapsulation inside a hydrophilic chamber that favors their folding. Here, we review the allosteric machine movements that are choreographed by ATP binding, which triggers concerted tilting and twisting of subunit domains. These movements distort the ring of hydrophobic binding sites and split it apart, potentially unfolding the multiply bound substrate. Then, GroES binding is accompanied by a 100° twist of the binding domains that removes the hydrophobic sites from the cavity lining and forms the folding chamber. ATP hydrolysis is not needed for a single round of binding and encapsulation but is necessary to allow the next round of ATP binding in the opposite ring. It is this remote ATP binding that triggers dismantling of the folding chamber and release of the encapsulated substrate, whether folded or not. The basis for these ordered actions is an elegant system of nested cooperativity of the ATPase machinery. ATP binds to a ring with positive cooperativity, and movements of the interlinked subunit domains are concerted. -
1519038862M28translationand
Paper No. : 15 Molecular Cell Biology Module : 28 Translation and Post-translation Modifications in Eukaryotes Development Team Principal Investigator : Prof. Neeta Sehgal Department of Zoology, University of Delhi Co-Principal Investigator : Prof. D.K. Singh Department of Zoology, University of Delhi Paper Coordinator : Prof. Kuldeep K. Sharma Department of Zoology, University of Jammu Content Writer : Dr. Renu Solanki, Deen Dayal Upadhyaya College Dr. Sudhida Gautam, Hansraj College, University of Delhi Mr. Kiran K. Salam, Hindu College, University of Delhi Content Reviewer : Prof. Rup Lal Department of Zoology, University of Delhi 1 Molecular Genetics ZOOLOGY Translation and Post-translation Modifications in Eukaryotes Description of Module Subject Name ZOOLOGY Paper Name Molecular Cell Biology; Zool 015 Module Name/Title Cell regulatory mechanisms Module Id M28: Translation and Post-translation Modifications in Eukaryotes Keywords Genome, Proteome diversity, post-translational modifications, glycosylation, phosphorylation, methylation Contents 1. Learning Objectives 2. Introduction 3. Purpose of post translational modifications 4. Post translational modifications 4.1. Phosphorylation, the addition of a phosphate group 4.2. Methylation, the addition of a methyl group 4.3. Glycosylation, the addition of sugar groups 4.4. Disulfide bonds, the formation of covalent bonds between 2 cysteine amino acids 4.5. Proteolysis/ Proteolytic Cleavage 4.6. Subunit binding to form a multisubunit protein 4.7. S-nitrosylation 4.8. Lipidation 4.9. Acetylation 4.10. Ubiquitylation 4.11. SUMOlytion 4.12. Vitamin C-Dependent Modifications 4.13. Vitamin K-Dependent Modifications 4.14. Selenoproteins 4.15. Myristoylation 5. Chaperones: Role in PTM and mechanism 6. Role of PTMs in diseases 7. Detecting and Quantifying Post-Translational Modifications 8. -
SUMO and Ubiquitin in the Nucleus: Different Functions, Similar Mechanisms?
Downloaded from genesdev.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW SUMO and ubiquitin in the nucleus: different functions, similar mechanisms? Grace Gill1 Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA The small ubiquitin-related modifier SUMO posttrans- tin, SUMO modification regulates protein localization lationally modifies many proteins with roles in diverse and activity. processes including regulation of transcription, chroma- This review focuses on recent advances in our under- tin structure, and DNA repair. Similar to nonproteolytic standing of SUMO function and regulation, drawing on a roles of ubiquitin, SUMO modification regulates protein limited set of examples relating to gene expression, chro- localization and activity. Some proteins can be modified matin structure, and DNA repair. Comparison of SUMO by SUMO and ubiquitin, but with distinct functional and ubiquitin activities in the nucleus reveals interest- consequences. It is possible that the effects of ubiquiti- ing differences in function and suggests surprising simi- nation and SUMOylation are both largely due to binding larities in mechanism. Thus, for example, modification of proteins bearing specific interaction domains. Both of transcription factors and histones by ubiquitin is gen- modifications are reversible, and in some cases dynamic erally associated with increased gene expression whereas cycles of modification may be required for activity. Stud- modification of transcription factors and histones by ies of SUMO and ubiquitin in the nucleus are yielding SUMO is generally associated with decreased gene ex- new insights into regulation of gene expression, genome pression. In some cases, SUMO and ubiquitin may di- maintenance, and signal transduction. -
Loss of Conserved Ubiquitylation Sites in Conserved Proteins During Human Evolution
INTERNATIONAL JOURNAL OF MOleCular meDICine 42: 2203-2212, 2018 Loss of conserved ubiquitylation sites in conserved proteins during human evolution DONGBIN PARK, CHUL JUN GOH, HYEIN KIM, JI SEOK LEE and YOONSOO HAHN Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea Received January 30, 2018; Accepted July 6, 2018 DOI: 10.3892/ijmm.2018.3772 Abstract. Ubiquitylation of lysine residues in proteins serves Introduction a pivotal role in the efficient removal of misfolded or unused proteins and in the control of various regulatory pathways Ubiquitylation, in which the highly conserved 76‑residue poly- by monitoring protein activity that may lead to protein peptide ubiquitin is covalently attached to a lysine residue of degradation. The loss of ubiquitylated lysines may affect substrate proteins, mediates the targeted destruction of ubiq- the ubiquitin‑mediated regulatory network and result in the uitylated proteins by the ubiquitin‑proteasome system (1‑4). emergence of novel phenotypes. The present study analyzed The ubiquitin‑mediated protein degradation pathway serves a mouse ubiquitylation data and orthologous proteins from crucial role in the efficient and specific removal of misfolded 62 mammals to identify 193 conserved ubiquitylation sites from proteins and certain key regulatory proteins (5,6). Ubiquitin 169 proteins that were lost in the Euarchonta lineage leading and other ubiquitin‑like proteins, including autophagy‑related to humans. A total of 8 proteins, including betaine homo- protein 8, Ubiquitin‑like -
Proteasomes: Unfoldase-Assisted Protein Degradation Machines
Biol. Chem. 2020; 401(1): 183–199 Review Parijat Majumder and Wolfgang Baumeister* Proteasomes: unfoldase-assisted protein degradation machines https://doi.org/10.1515/hsz-2019-0344 housekeeping functions such as cell cycle control, signal Received August 13, 2019; accepted October 2, 2019; previously transduction, transcription, DNA repair and translation published online October 29, 2019 (Alves dos Santos et al., 2001; Goldberg, 2007; Bader and Steller, 2009; Koepp, 2014). Consequently, any disrup- Abstract: Proteasomes are the principal molecular tion of selective protein degradation pathways leads to a machines for the regulated degradation of intracellular broad array of pathological states, including cancer, neu- proteins. These self-compartmentalized macromolecu- rodegeneration, immune-related disorders, cardiomyo- lar assemblies selectively degrade misfolded, mistrans- pathies, liver and gastrointestinal disorders, and ageing lated, damaged or otherwise unwanted proteins, and (Dahlmann, 2007; Motegi et al., 2009; Dantuma and Bott, play a pivotal role in the maintenance of cellular proteo- 2014; Schmidt and Finley, 2014). stasis, in stress response, and numerous other processes In eukaryotes, two major pathways have been identi- of vital importance. Whereas the molecular architecture fied for the selective removal of unwanted proteins – the of the proteasome core particle (CP) is universally con- ubiquitin-proteasome-system (UPS), and the autophagy- served, the unfoldase modules vary in overall structure, lysosome pathway (Ciechanover, 2005; Dikic, 2017). UPS subunit complexity, and regulatory principles. Proteas- constitutes the principal degradation route for intracel- omal unfoldases are AAA+ ATPases (ATPases associated lular proteins, whereas cellular organelles, cell-surface with a variety of cellular activities) that unfold protein proteins, and invading pathogens are mostly degraded substrates, and translocate them into the CP for degra- via autophagy. -
Mdm2-Mediated Ubiquitylation: P53 and Beyond
Cell Death and Differentiation (2010) 17, 93–102 & 2010 Macmillan Publishers Limited All rights reserved 1350-9047/10 $32.00 www.nature.com/cdd Review Mdm2-mediated ubiquitylation: p53 and beyond J-C Marine*,1 and G Lozano2 The really interesting genes (RING)-finger-containing oncoprotein, Mdm2, is a promising drug target for cancer therapy. A key Mdm2 function is to promote ubiquitylation and proteasomal-dependent degradation of the tumor suppressor protein p53. Recent reports provide novel important insights into Mdm2-mediated regulation of p53 and how the physical and functional interactions between these two proteins are regulated. Moreover, a p53-independent role of Mdm2 has recently been confirmed by genetic data. These advances and their potential implications for the development of new cancer therapeutic strategies form the focus of this review. Cell Death and Differentiation (2010) 17, 93–102; doi:10.1038/cdd.2009.68; published online 5 June 2009 Mdm2 is a key regulator of a variety of fundamental cellular has also emerged from recent genetic studies. These processes and a very promising drug target for cancer advances and their potential implications for the development therapy. It belongs to a large family of (really interesting of new cancer therapeutic strategies form the focus of this gene) RING-finger-containing proteins and, as most of its review. For a more detailed discussion of Mdm2 and its other members, Mdm2 functions mainly, if not exclusively, as various functions an interested reader should also consult an E3 ligase.1 It targets various substrates for mono- and/or references9–12. poly-ubiquitylation thereby regulating their activities; for instance by controlling their localization, and/or levels by The p53–Mdm2 Regulatory Feedback Loop proteasome-dependent degradation. -
The HSP70 Chaperone Machinery: J Proteins As Drivers of Functional Specificity
REVIEWS The HSP70 chaperone machinery: J proteins as drivers of functional specificity Harm H. Kampinga* and Elizabeth A. Craig‡ Abstract | Heat shock 70 kDa proteins (HSP70s) are ubiquitous molecular chaperones that function in a myriad of biological processes, modulating polypeptide folding, degradation and translocation across membranes, and protein–protein interactions. This multitude of roles is not easily reconciled with the universality of the activity of HSP70s in ATP-dependent client protein-binding and release cycles. Much of the functional diversity of the HSP70s is driven by a diverse class of cofactors: J proteins. Often, multiple J proteins function with a single HSP70. Some target HSP70 activity to clients at precise locations in cells and others bind client proteins directly, thereby delivering specific clients to HSP70 and directly determining their fate. In their native cellular environment, polypeptides are participates in such diverse cellular functions. Their constantly at risk of attaining conformations that pre- functional diversity is remarkable considering that vent them from functioning properly and/or cause them within and across species, HSP70s have high sequence to aggregate into large, potentially cytotoxic complexes. identity. They share a single biochemical activity: an Molecular chaperones guide the conformation of proteins ATP-dependent client-binding and release cycle com- throughout their lifetime, preventing their aggregation bined with client protein recognition, which is typi- by protecting interactive surfaces against non-productive cally rather promiscuous. This apparent conundrum interactions. Through such inter actions, molecular chap- is resolved by the fact that HSP70s do not work alone, erones aid in the folding of nascent proteins as they are but rather as ‘HSP70 machines’, collaborating with synthesized by ribosomes, drive protein transport across and being regulated by several cofactors. -
Ubiquitin-Dependent Folding of the Wnt Signaling Coreceptor LRP6
RESEARCH ARTICLE Ubiquitin-dependent folding of the Wnt signaling coreceptor LRP6 Elsa Perrody1†, Laurence Abrami1†, Michal Feldman1, Beatrice Kunz1, Sylvie Urbe´ 2, F Gisou van der Goot1* 1Global Health Institute, Ecole Polytechnique Fe´de´rale de Lausanne, Lausanne, Switzerland; 2Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom Abstract Many membrane proteins fold inefficiently and require the help of enzymes and chaperones. Here we reveal a novel folding assistance system that operates on membrane proteins from the cytosolic side of the endoplasmic reticulum (ER). We show that folding of the Wnt signaling coreceptor LRP6 is promoted by ubiquitination of a specific lysine, retaining it in the ER while avoiding degradation. Subsequent ER exit requires removal of ubiquitin from this lysine by the deubiquitinating enzyme USP19. This ubiquitination-deubiquitination is conceptually reminiscent of the glucosylation-deglucosylation occurring in the ER lumen during the calnexin/ calreticulin folding cycle. To avoid infinite futile cycles, folded LRP6 molecules undergo palmitoylation and ER export, while unsuccessfully folded proteins are, with time, polyubiquitinated on other lysines and targeted to degradation. This ubiquitin-dependent folding system also controls the proteostasis of other membrane proteins as CFTR and anthrax toxin receptor 2, two poor folders involved in severe human diseases. DOI: 10.7554/eLife.19083.001 *For correspondence: gisou. [email protected] Introduction † These authors contributed While protein folding may be extremely efficient, the presence of multiple domains, in soluble or equally to this work membrane proteins, greatly reduces the efficacy of the overall process. Thus, a set of enzymes and Competing interests: The chaperones assist folding and ensure that a sufficient number of active molecules reach their final authors declare that no destination (Brodsky and Skach, 2011; Ellgaard et al., 2016). -
Heat Shock Protein 70 (HSP70) Induction: Chaperonotherapy for Neuroprotection After Brain Injury
cells Review Heat Shock Protein 70 (HSP70) Induction: Chaperonotherapy for Neuroprotection after Brain Injury Jong Youl Kim 1, Sumit Barua 1, Mei Ying Huang 1,2, Joohyun Park 1,2, Midori A. Yenari 3,* and Jong Eun Lee 1,2,* 1 Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea; [email protected] (J.Y.K.); [email protected] (S.B.); [email protected] (M.Y.H.); [email protected] (J.P.) 2 BK21 Plus Project for Medical Science and Brain Research Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea 3 Department of Neurology, University of California, San Francisco & the San Francisco Veterans Affairs Medical Center, Neurology (127) VAMC 4150 Clement St., San Francisco, CA 94121, USA * Correspondence: [email protected] (M.A.Y.); [email protected] (J.E.L.); Tel.: +1-415-750-2011 (M.A.Y.); +82-2-2228-1646 (ext. 1659) (J.E.L.); Fax: +1-415-750-2273 (M.A.Y.); +82-2-365-0700 (J.E.L.) Received: 17 July 2020; Accepted: 26 August 2020; Published: 2 September 2020 Abstract: The 70 kDa heat shock protein (HSP70) is a stress-inducible protein that has been shown to protect the brain from various nervous system injuries. It allows cells to withstand potentially lethal insults through its chaperone functions. Its chaperone properties can assist in protein folding and prevent protein aggregation following several of these insults. Although its neuroprotective properties have been largely attributed to its chaperone functions, HSP70 may interact directly with proteins involved in cell death and inflammatory pathways following injury. -
HSP90 Interacts with the Fibronectin N-Terminal Domains and Increases Matrix Formation
cells Article HSP90 Interacts with the Fibronectin N-terminal Domains and Increases Matrix Formation Abir Chakraborty 1 , Natasha Marie-Eraine Boel 1 and Adrienne Lesley Edkins 1,2,* 1 Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; [email protected] (A.C.); [email protected] (N.M.-E.B.) 2 Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa * Correspondence: [email protected] Received: 20 December 2019; Accepted: 18 January 2020; Published: 22 January 2020 Abstract: Heat shock protein 90 (HSP90) is an evolutionarily conserved chaperone protein that controls the function and stability of a wide range of cellular client proteins. Fibronectin (FN) is an extracellular client protein of HSP90, and exogenous HSP90 or inhibitors of HSP90 alter the morphology of the extracellular matrix. Here, we further characterized the HSP90 and FN interaction. FN bound to the M domain of HSP90 and interacted with both the open and closed HSP90 conformations; and the interaction was reduced in the presence of sodium molybdate. HSP90 interacted with the N-terminal regions of FN, which are known to be important for matrix assembly. The highest affinity interaction was with the 30-kDa (heparin-binding) FN fragment, which also showed the greatest colocalization in cells and accommodated both HSP90 and heparin in the complex. The strength of interaction with HSP90 was influenced by the inherent stability of the FN fragments, together with the type of motif, where HSP90 preferentially bound the type-I FN repeat over the type-II repeat. Exogenous extracellular HSP90 led to increased incorporation of both full-length and 70-kDa fragments of FN into fibrils. -
Roles of Heat Shock Proteins in Apoptosis, Oxidative Stress, Human Inflammatory Diseases, and Cancer
pharmaceuticals Review Roles of Heat Shock Proteins in Apoptosis, Oxidative Stress, Human Inflammatory Diseases, and Cancer Paul Chukwudi Ikwegbue 1, Priscilla Masamba 1, Babatunji Emmanuel Oyinloye 1,2 ID and Abidemi Paul Kappo 1,* ID 1 Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa; [email protected] (P.C.I.); [email protected] (P.M.); [email protected] (B.E.O.) 2 Department of Biochemistry, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Nigeria * Correspondence: [email protected]; Tel.: +27-35-902-6780; Fax: +27-35-902-6567 Received: 23 October 2017; Accepted: 17 November 2017; Published: 23 December 2017 Abstract: Heat shock proteins (HSPs) play cytoprotective activities under pathological conditions through the initiation of protein folding, repair, refolding of misfolded peptides, and possible degradation of irreparable proteins. Excessive apoptosis, resulting from increased reactive oxygen species (ROS) cellular levels and subsequent amplified inflammatory reactions, is well known in the pathogenesis and progression of several human inflammatory diseases (HIDs) and cancer. Under normal physiological conditions, ROS levels and inflammatory reactions are kept in check for the cellular benefits of fighting off infectious agents through antioxidant mechanisms; however, this balance can be disrupted under pathological conditions, thus leading to oxidative stress and massive cellular destruction. Therefore, it becomes apparent that the interplay between oxidant-apoptosis-inflammation is critical in the dysfunction of the antioxidant system and, most importantly, in the progression of HIDs. Hence, there is a need to maintain careful balance between the oxidant-antioxidant inflammatory status in the human body.