101
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Srivastava R, Li Z, Russo G, Tang J, Bi R, Muppirala U, Chudalayandi S, Severin A, He M, Vaitkevicius SI, Lawrence-Dill CJ, Liu P, Stapleton AE, Bassham DC, Brandizzi F, Howell SH. Response to Persistent ER Stress in Plants: A Multiphasic Process That Transitions Cells from Prosurvival Activities to Cell Death. THE PLANT CELL 2018; 30:1220-1242. [PMID: 29802214 PMCID: PMC6048783 DOI: 10.1105/tpc.18.00153] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 05/09/2023]
Abstract
The unfolded protein response (UPR) is a highly conserved response that protects plants from adverse environmental conditions. The UPR is elicited by endoplasmic reticulum (ER) stress, in which unfolded and misfolded proteins accumulate within the ER. Here, we induced the UPR in maize (Zea mays) seedlings to characterize the molecular events that occur over time during persistent ER stress. We found that a multiphasic program of gene expression was interwoven among other cellular events, including the induction of autophagy. One of the earliest phases involved the degradation by regulated IRE1-dependent RNA degradation (RIDD) of RNA transcripts derived from a family of peroxidase genes. RIDD resulted from the activation of the promiscuous ribonuclease activity of ZmIRE1 that attacks the mRNAs of secreted proteins. This was followed by an upsurge in expression of the canonical UPR genes indirectly driven by ZmIRE1 due to its splicing of Zmbzip60 mRNA to make an active transcription factor that directly upregulates many of the UPR genes. At the peak of UPR gene expression, a global wave of RNA processing led to the production of many aberrant UPR gene transcripts, likely tempering the ER stress response. During later stages of ER stress, ZmIRE1's activity declined, as did the expression of survival modulating genes, Bax inhibitor1 and Bcl-2-associated athanogene7, amid a rising tide of cell death. Thus, in response to persistent ER stress, maize seedlings embark on a course of gene expression and cellular events progressing from adaptive responses to cell death.
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Affiliation(s)
- Renu Srivastava
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
| | - Zhaoxia Li
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
| | - Giulia Russo
- MSU-DOE Plant Research Laboratories, Department of Plant Biology, East Lansing, Michigan 48824
| | - Jie Tang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Ran Bi
- Department of Statistics, Iowa State University, Ames, Iowa 50011
| | - Usha Muppirala
- Genome Informatics Facility, Iowa State University, Ames, Iowa 50011
| | | | - Andrew Severin
- Genome Informatics Facility, Iowa State University, Ames, Iowa 50011
| | - Mingze He
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Samuel I Vaitkevicius
- MSU-DOE Plant Research Laboratories, Department of Plant Biology, East Lansing, Michigan 48824
| | - Carolyn J Lawrence-Dill
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, Iowa 50011
| | - Ann E Stapleton
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina 28403
| | - Diane C Bassham
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Federica Brandizzi
- MSU-DOE Plant Research Laboratories, Department of Plant Biology, East Lansing, Michigan 48824
| | - Stephen H Howell
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
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102
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Yano H, Bonifazi A, Xu M, Guthrie DA, Schneck SN, Abramyan AM, Fant AD, Hong WC, Newman AH, Shi L. Pharmacological profiling of sigma 1 receptor ligands by novel receptor homomer assays. Neuropharmacology 2018; 133:264-275. [PMID: 29407216 PMCID: PMC5858991 DOI: 10.1016/j.neuropharm.2018.01.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/06/2018] [Accepted: 01/29/2018] [Indexed: 12/20/2022]
Abstract
The sigma 1 receptor (σ1R) is a structurally unique transmembrane protein that functions as a molecular chaperone in the endoplasmic reticulum (ER), and has been implicated in cancer, neuropathic pain, and psychostimulant abuse. Despite physiological and pharmacological significance, mechanistic underpinnings of structure-function relationships of σ1R are poorly understood, and molecular interactions of selective ligands with σ1R have not been elucidated. The recent crystallographic determination of σ1R as a homo-trimer provides the foundation for mechanistic elucidation at the molecular level. Here we report novel bioluminescence resonance energy transfer (BRET) assays that enable analyses of ligand-induced multimerization of σ1R and its interaction with BiP. Haloperidol, PD144418, and 4-PPBP enhanced σ1R homomer BRET signals in a dose dependent manner, suggesting their significant effects in stabilizing σ1R multimerization, whereas (+)-pentazocine and several other ligands do not. In non-denaturing gels, (+)-pentazocine significantly decreased whereas haloperidol increased the fraction of σ1R multimers, consistent with the results from the homomer BRET assay. Further, BRET assays examining heteromeric σ1R-BiP interaction revealed that (+)-pentazocine and haloperidol induced opposite trends of signals. From molecular modeling and simulations of σ1R in complex with the tested ligands, we identified initial clues that may lead to the differed responses of σ1R upon binding of structurally diverse ligands. By combining multiple in vitro pharmacological and in silico molecular biophysical methods, we propose a novel integrative approach to analyze σ1R-ligand binding and its impact on interaction of σ1R with client proteins.
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Affiliation(s)
- Hideaki Yano
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA.
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Min Xu
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Daryl A Guthrie
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Stephanie N Schneck
- Department of Pharmaceutical Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Ara M Abramyan
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Andrew D Fant
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - W Conrad Hong
- Department of Pharmaceutical Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Amy H Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA.
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103
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Gurusinghe KRDSNS, Mishra A, Mishra S. Glucose-regulated protein 78 substrate-binding domain alters its conformation upon EGCG inhibitor binding to nucleotide-binding domain: Molecular dynamics studies. Sci Rep 2018; 8:5487. [PMID: 29615633 PMCID: PMC5882873 DOI: 10.1038/s41598-018-22905-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 03/01/2018] [Indexed: 12/13/2022] Open
Abstract
Glucose-regulated protein 78 (GRP78), is overexpressed in glioblastoma, other tumors and during viral and bacterial infections, and so, it is postulated to be a key drug target. EGCG, an ATP-competitive natural inhibitor, inhibits GRP78 effect in glioblastoma. Structural basis of its action on GRP78 nucleotide-binding domain and selectivity has been investigated. We were interested in exploring the large-scale conformational movements travelling to substrate-binding domain via linker region. Conformational effects of EGCG inhibitor as well as ATP on full length GRP78 protein were studied using powerful MD simulations. Binding of EGCG decreases mobility of residues in SBDα lid region as compared to ATP-bound state and similar to apo state. The decreased mobility may prevent its opening and closing over SBDβ. This hindrance to SBDα subdomain movement, in turn, may reduce the binding of substrate peptide to SBDβ. EGCG binding folds the protein stably as opposed to ATP binding. Several results from EGCG binding simulations are similar to that of the apo state. Key insights from these results reveal that after EGCG binding upon competitive inhibition with ATP, GRP78 conformation may revert to that of inactive, apo state. Further, SBD may adopt a semi-open conformation unable to facilitate association of substrates.
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Affiliation(s)
| | - Aanchal Mishra
- Ronin Institute for Independent Scholarship, Montclair, NJ, USA.,Osmania University, Hyderabad, Telangana, India
| | - Seema Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.
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104
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O'Donnell JP, Marsh HM, Sondermann H, Sevier CS. Disrupted Hydrogen-Bond Network and Impaired ATPase Activity in an Hsc70 Cysteine Mutant. Biochemistry 2018; 57:1073-1086. [PMID: 29300467 DOI: 10.1021/acs.biochem.7b01005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The ATPase domain of members of the 70 kDa heat shock protein (Hsp70) family shows a high degree of sequence, structural, and functional homology across species. A broadly conserved residue within the Hsp70 ATPase domain that captured our attention is an unpaired cysteine, positioned proximal to the site of nucleotide binding. Prior studies of several Hsp70 family members show this cysteine is not required for Hsp70 ATPase activity, yet select amino acid replacements of the cysteine can dramatically alter ATP hydrolysis. Moreover, post-translational modification of the cysteine has been reported to limit ATP hydrolysis for several Hsp70s. To better understand the underlying mechanism for how perturbation of this noncatalytic residue modulates Hsp70 function, we determined the structure for a cysteine-to-tryptophan mutation in the constitutively expressed, mammalian Hsp70 family member Hsc70. Our work reveals that the steric hindrance produced by a cysteine-to-tryptophan mutation disrupts the hydrogen-bond network within the active site, resulting in a loss of proper catalytic magnesium coordination. We propose that a similarly altered active site is likely observed upon post-translational oxidation. We speculate that the subtle changes we detect in the hydrogen-bonding network may relate to the previously reported observation that cysteine oxidation can influence Hsp70 interdomain communication.
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Affiliation(s)
- John P O'Donnell
- Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Heather M Marsh
- Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Holger Sondermann
- Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Carolyn S Sevier
- Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
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105
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Kouznetsova VL, Hu H, Teigen K, Zanetti M, Tsigelny IF. Cripto stabilizes GRP78 on the cell membrane. Protein Sci 2017; 27:653-661. [PMID: 29226519 DOI: 10.1002/pro.3358] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/16/2017] [Accepted: 12/05/2017] [Indexed: 01/19/2023]
Abstract
The ER resident chaperone molecule GRP78 has been shown to translocate to the cell surface where it associates with Cripto and signals cell growth, playing a still partially understood role in tumorigenesis. Consequently, a better understanding of GRP78 topology and structure at the surface of cancer cells represents an important step in the development of a new class of therapeutics. Here, we used a set of programs for creation of a complex containing GRP78 and Cripto proteins. We elucidated possible interactions of GRP78, Cripto, and their complex with the membrane. Using molecular dynamics simulations, we demonstrated that Cripto binding to GRP78 completely changes the dynamics of its behavior on the membrane, not allowing GRP78 to disconnect from it, thus enabling GRP78 tumorigenic functions.
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Affiliation(s)
- Valentina L Kouznetsova
- The Moores Cancer Center, University of California at San Diego, La Jolla, California.,San Diego Supercomputer Center, University of California at San Diego, La Jolla, California
| | - Hannah Hu
- REHS program, San Diego Supercomputer Center, University of California at San Diego, La Jolla, California
| | - Knut Teigen
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Maurizio Zanetti
- The Moores Cancer Center, University of California at San Diego, La Jolla, California
| | - Igor F Tsigelny
- The Moores Cancer Center, University of California at San Diego, La Jolla, California.,San Diego Supercomputer Center, University of California at San Diego, La Jolla, California.,Department of Neurosciences, University of California at San Diego, La Jolla, California.,CureMatch Inc., San Diego, California
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106
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Wang SH, Yu J. Structure-based design for binding peptides in anti-cancer therapy. Biomaterials 2017; 156:1-15. [PMID: 29182932 DOI: 10.1016/j.biomaterials.2017.11.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/30/2017] [Accepted: 11/21/2017] [Indexed: 12/18/2022]
Abstract
The conventional anticancer therapeutics usually lack cancer specificity, leading to damage of normal tissues that patients find hard to tolerate. Ideally, anticancer therapeutics carrying payloads of drugs equipped with cancer targeting peptides can act like "guided missiles" with the capacity of targeted delivery toward many types of cancers. Peptides are amenable for conjugation to nano drugs for functionalization, thereby improving drug delivery and cellular uptake in cancer-targeting therapies. Peptide drugs are often more difficult to design through molecular docking and in silico analysis than small molecules, because peptide structures are more flexible, possess intricate molecular conformations, and undergo complex interactions. In this review, the development and application of strategies for structure-based design of cancer-targeting peptides against GRP78 are discussed. This Review also covers topics related to peptide pharmacokinetics and targeting delivery, including molecular docking studies, features that provide advantages for in vivo use, and properties that influence the cancer-targeting ability. Some advanced technologies and special peptides that can overcome the pharmacokinetic challenges have also been included.
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Affiliation(s)
- Sheng-Hung Wang
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, Chang Gung University, Taoyuan 333, Taiwan
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, Chang Gung University, Taoyuan 333, Taiwan; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
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107
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Conformation transitions of the polypeptide-binding pocket support an active substrate release from Hsp70s. Nat Commun 2017; 8:1201. [PMID: 29084938 PMCID: PMC5662698 DOI: 10.1038/s41467-017-01310-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/07/2017] [Indexed: 12/21/2022] Open
Abstract
Cellular protein homeostasis depends on heat shock proteins 70 kDa (Hsp70s), a class of ubiquitous and highly conserved molecular chaperone. Key to the chaperone activity is an ATP-induced allosteric regulation of polypeptide substrate binding and release. To illuminate the molecular mechanism of this allosteric coupling, here we present a novel crystal structure of an intact human BiP, an essential Hsp70 in ER, in an ATP-bound state. Strikingly, the polypeptide-binding pocket is completely closed, seemingly excluding any substrate binding. Our FRET, biochemical and EPR analysis suggests that this fully closed conformation is the major conformation for the ATP-bound state in solution, providing evidence for an active release of bound polypeptide substrates following ATP binding. The Hsp40 co-chaperone converts this fully closed conformation to an open conformation to initiate productive substrate binding. Taken together, this study provided a mechanistic understanding of the dynamic nature of the polypeptide-binding pocket in the Hsp70 chaperone cycle. Hsp70s are highly conserved molecular chaperones that play multiple essential roles in maintaining cellular protein homeostasis. Here, the authors provide structural evidence for active substrate release by Hsp70s upon ATP binding and provide insight into the molecular mechanism of ATP-driven Hsp70 chaperone activity.
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108
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Broadening the functionality of a J-protein/Hsp70 molecular chaperone system. PLoS Genet 2017; 13:e1007084. [PMID: 29084221 PMCID: PMC5679652 DOI: 10.1371/journal.pgen.1007084] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/09/2017] [Accepted: 10/18/2017] [Indexed: 12/21/2022] Open
Abstract
By binding to a multitude of polypeptide substrates, Hsp70-based molecular chaperone systems perform a range of cellular functions. All J-protein co-chaperones play the essential role, via action of their J-domains, of stimulating the ATPase activity of Hsp70, thereby stabilizing its interaction with substrate. In addition, J-proteins drive the functional diversity of Hsp70 chaperone systems through action of regions outside their J-domains. Targeting to specific locations within a cellular compartment and binding of specific substrates for delivery to Hsp70 have been identified as modes of J-protein specialization. To better understand J-protein specialization, we concentrated on Saccharomyces cerevisiae SIS1, which encodes an essential J-protein of the cytosol/nucleus. We selected suppressors that allowed cells lacking SIS1 to form colonies. Substitutions changing single residues in Ydj1, a J-protein, which, like Sis1, partners with Hsp70 Ssa1, were isolated. These gain-of-function substitutions were located at the end of the J-domain, suggesting that suppression was connected to interaction with its partner Hsp70, rather than substrate binding or subcellular localization. Reasoning that, if YDJ1 suppressors affect Ssa1 function, substitutions in Hsp70 itself might also be able to overcome the cellular requirement for Sis1, we carried out a selection for SSA1 suppressor mutations. Suppressing substitutions were isolated that altered sites in Ssa1 affecting the cycle of substrate interaction. Together, our results point to a third, additional means by which J-proteins can drive Hsp70's ability to function in a wide range of cellular processes-modulating the Hsp70-substrate interaction cycle.
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109
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Preissler S, Rohland L, Yan Y, Chen R, Read RJ, Ron D. AMPylation targets the rate-limiting step of BiP's ATPase cycle for its functional inactivation. eLife 2017; 6:29428. [PMID: 29064368 PMCID: PMC5667935 DOI: 10.7554/elife.29428] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/22/2017] [Indexed: 12/21/2022] Open
Abstract
The endoplasmic reticulum (ER)-localized Hsp70 chaperone BiP contributes to protein folding homeostasis by engaging unfolded client proteins in a process that is tightly coupled to ATP binding and hydrolysis. The inverse correlation between BiP AMPylation and the burden of unfolded ER proteins suggests a post-translational mechanism for adjusting BiP's activity to changing levels of ER stress, but the underlying molecular details are unexplored. We present biochemical and crystallographic studies indicating that irrespective of the identity of the bound nucleotide AMPylation biases BiP towards a conformation normally attained by the ATP-bound chaperone. AMPylation does not affect the interaction between BiP and J-protein co-factors but appears to allosterically impair J protein-stimulated ATP-hydrolysis, resulting in the inability of modified BiP to attain high affinity for its substrates. These findings suggest a molecular mechanism by which AMPylation serves as a switch to inactivate BiP, limiting its interactions with substrates whilst conserving ATP.
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Affiliation(s)
- Steffen Preissler
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Lukas Rohland
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Yahui Yan
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Ruming Chen
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Randy J Read
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - David Ron
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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110
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Wieteska L, Shahidi S, Zhuravleva A. Allosteric fine-tuning of the conformational equilibrium poises the chaperone BiP for post-translational regulation. eLife 2017; 6:29430. [PMID: 29064369 PMCID: PMC5655141 DOI: 10.7554/elife.29430] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/01/2017] [Indexed: 12/12/2022] Open
Abstract
BiP is the only Hsp70 chaperone in the endoplasmic reticulum (ER) and similar to other Hsp70s, its activity relies on nucleotide- and substrate-controllable docking and undocking of its nucleotide-binding domain (NBD) and substrate-binding domain (SBD). However, little is known of specific features of the BiP conformational landscape that tune BiP to its unique tasks and the ER environment. We present methyl NMR analysis of the BiP chaperone cycle that reveals surprising conformational heterogeneity of ATP-bound BiP that distinguishes BiP from its bacterial homologue DnaK. This unusual poise enables gradual post-translational regulation of the BiP chaperone cycle and its chaperone activity by subtle local perturbations at SBD allosteric 'hotspots'. In particular, BiP inactivation by AMPylation of its SBD does not disturb Hsp70 inter-domain allostery and preserves BiP structure. Instead it relies on a redistribution of the BiP conformational ensemble and stabilization the domain-docked conformation in presence of ADP and ATP.
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Affiliation(s)
- Lukasz Wieteska
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Saeid Shahidi
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Anastasia Zhuravleva
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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111
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Dowaidar M, Gestin M, Cerrato CP, Jafferali MH, Margus H, Kivistik PA, Ezzat K, Hallberg E, Pooga M, Hällbrink M, Langel Ü. Role of autophagy in cell-penetrating peptide transfection model. Sci Rep 2017; 7:12635. [PMID: 28974718 PMCID: PMC5626743 DOI: 10.1038/s41598-017-12747-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 09/15/2017] [Indexed: 01/01/2023] Open
Abstract
Cell-penetrating peptides (CPPs) uptake mechanism is still in need of more clarification to have a better understanding of their action in the mediation of oligonucleotide transfection. In this study, the effect on early events (1 h treatment) in transfection by PepFect14 (PF14), with or without oligonucleotide cargo on gene expression, in HeLa cells, have been investigated. The RNA expression profile was characterized by RNA sequencing and confirmed by qPCR analysis. The gene regulations were then related to the biological processes by the study of signaling pathways that showed the induction of autophagy-related genes in early transfection. A ligand library interfering with the detected intracellular pathways showed concentration-dependent effects on the transfection efficiency of splice correction oligonucleotide complexed with PepFect14, proving that the autophagy process is induced upon the uptake of complexes. Finally, the autophagy induction and colocalization with autophagosomes have been confirmed by confocal microscopy and transmission electron microscopy. We conclude that autophagy, an inherent cellular response process, is triggered by the cellular uptake of CPP-based transfection system. This finding opens novel possibilities to use autophagy modifiers in future gene therapy.
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Affiliation(s)
- Moataz Dowaidar
- Department of Neurochemistry, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Svante Arrhenius väg 16B, SE-10691, Stockholm, Sweden.
| | - Maxime Gestin
- Department of Neurochemistry, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Svante Arrhenius väg 16B, SE-10691, Stockholm, Sweden
| | - Carmine Pasquale Cerrato
- Department of Neurochemistry, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Svante Arrhenius väg 16B, SE-10691, Stockholm, Sweden
| | - Mohammed Hakim Jafferali
- Department of Neurochemistry, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Svante Arrhenius väg 16B, SE-10691, Stockholm, Sweden
| | - Helerin Margus
- Department of Developmental Biology, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010, Tartu, Estonia
| | | | - Kariem Ezzat
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Einar Hallberg
- Department of Neurochemistry, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Svante Arrhenius väg 16B, SE-10691, Stockholm, Sweden
| | - Margus Pooga
- Department of Developmental Biology, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010, Tartu, Estonia
- Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Nooruse, 50411, Tartu, Estonia
| | - Mattias Hällbrink
- Department of Neurochemistry, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Svante Arrhenius väg 16B, SE-10691, Stockholm, Sweden
| | - Ülo Langel
- Department of Neurochemistry, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Svante Arrhenius väg 16B, SE-10691, Stockholm, Sweden.
- Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Nooruse, 50411, Tartu, Estonia.
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112
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Shah DD, Singh SM, Dzieciatkowska M, Mallela KMG. Biophysical analysis of the effect of chemical modification by 4-oxononenal on the structure, stability, and function of binding immunoglobulin protein (BiP). PLoS One 2017; 12:e0183975. [PMID: 28886061 PMCID: PMC5590874 DOI: 10.1371/journal.pone.0183975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/15/2017] [Indexed: 11/24/2022] Open
Abstract
Binding immunoglobulin protein (BiP) is a molecular chaperone important for the folding of numerous proteins, which include millions of immunoglobulins in human body. It also plays a key role in the unfolded protein response (UPR) in the endoplasmic reticulum. Free radical generation is a common phenomenon that occurs in cells under healthy as well as under stress conditions such as ageing, inflammation, alcohol consumption, and smoking. These free radicals attack the cell membranes and generate highly reactive lipid peroxidation products such as 4-oxononenal (4-ONE). BiP is a key protein that is modified by 4-ONE. In this study, we probed how such chemical modification affects the biophysical properties of BiP. Upon modification, BiP shows significant tertiary structural changes with no changes in its secondary structure. The protein loses its thermodynamic stability, particularly, that of the nucleotide binding domain (NBD) where ATP binds. In terms of function, the modified BiP completely loses its ATPase activity with decreased ATP binding affinity. However, modified BiP retains its immunoglobulin binding function and its chaperone activity of suppressing non-specific protein aggregation. These results indicate that 4-ONE modification can significantly affect the structure-function of key proteins such as BiP involved in cellular pathways, and provide a molecular basis for how chemical modifications can result in the failure of quality control mechanisms inside the cell.
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Affiliation(s)
- Dinen D Shah
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Surinder M Singh
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Monika Dzieciatkowska
- Biological Mass Spectrometry Facility, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Krishna M G Mallela
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America.,Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
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113
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N-glycosylation Triggers a Dual Selection Pressure in Eukaryotic Secretory Proteins. Sci Rep 2017; 7:8788. [PMID: 28821844 PMCID: PMC5562741 DOI: 10.1038/s41598-017-09173-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/07/2017] [Indexed: 01/08/2023] Open
Abstract
Nearly one third of the eukaryotic proteome traverses the secretory pathway and most of these proteins are N-glycosylated in the lumen of the endoplasmic reticulum. N-glycans fulfill multiple structural and biological functions, and are crucial for productive folding of many glycoproteins. N-glycosylation involves the attachment of an oligosaccharide to selected asparagine residues in the sequence N-X-S/T (X ≠ P), a motif known as an N-glycosylation’sequon’. Mutations that create novel sequons can cause disease due to the destabilizing effect of a bulky N-glycan. Thus, an analogous process must have occurred during evolution, whenever ancestrally cytosolic proteins were recruited to the secretory pathway. Here, we show that during evolution N-glycosylation triggered a dual selection pressure on secretory pathway proteins: while sequons were positively selected in solvent exposed regions, they were almost completely eliminated from buried sites. This process is one of the sharpest evolutionary signatures of secretory pathway proteins, and was therefore critical for the evolution of an efficient secretory pathway.
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114
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English CA, Sherman W, Meng W, Gierasch LM. The Hsp70 interdomain linker is a dynamic switch that enables allosteric communication between two structured domains. J Biol Chem 2017; 292:14765-14774. [PMID: 28754691 DOI: 10.1074/jbc.m117.789313] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/19/2017] [Indexed: 12/20/2022] Open
Abstract
Hsp70 molecular chaperones play key roles in cellular protein homeostasis by binding to exposed hydrophobic regions of incompletely folded or aggregated proteins. This crucial Hsp70 function relies on allosteric communication between two well-structured domains: an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD), which are tethered by an interdomain linker. ATP or ADP binding to the NBD alters the substrate-binding affinity of the SBD, triggering functionally essential cycles of substrate binding and release. The interdomain linker is a well-structured participant in the interdomain interface in ATP-bound Hsp70s. By contrast, in the ADP-bound state, exemplified by the Escherichia coli Hsp70 DnaK, the interdomain linker is flexible. Hsp70 interdomain linker sequences are highly conserved; moreover, mutations in this region compromise interdomain allostery. To better understand the role of this region in Hsp70 allostery, we used molecular dynamics simulations to explore the conformational landscape of the interdomain linker in ADP-bound DnaK and supported our simulations by strategic experimental data. We found that while the interdomain linker samples many conformations, it behaves as three relatively ordered segments connected by hinges. As a consequence, the distances and orientations between the NBD and SBD are limited. Additionally, the C-terminal region of the linker forms previously unreported, transient interactions with the SBD, and the predominant linker-docking site is available in only one allosteric state, that with high affinity for substrate. This preferential binding implicates the interdomain linker as a dynamic allosteric switch. The linker-binding site on the SBD is a potential target for small molecule modulators of the Hsp70 allosteric cycle.
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Affiliation(s)
| | - Woody Sherman
- From the Departments of Biochemistry and Molecular Biology and.,Schrödinger Inc., Cambridge, Massachusetts 02142.,Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 and
| | - Wenli Meng
- From the Departments of Biochemistry and Molecular Biology and
| | - Lila M Gierasch
- From the Departments of Biochemistry and Molecular Biology and .,Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 and
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115
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Liu Q, Li H, Yang Y, Tian X, Su J, Zhou L, Liu Q. A disulfide-bonded DnaK dimer is maintained in an ATP-bound state. Cell Stress Chaperones 2017; 22:201-212. [PMID: 27975204 PMCID: PMC5352592 DOI: 10.1007/s12192-016-0752-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/16/2016] [Accepted: 11/28/2016] [Indexed: 01/16/2023] Open
Abstract
DnaK, a major Hsp70 molecular chaperones in Escherichia coli, is a widely used model for studying Hsp70s. We recently solved a crystal structure of DnaK in complex with ATP and showed that DnaK was packed as a dimer in the crystal structure. Our previous biochemical studies supported the formation of a specific DnaK dimer as observed in the crystal structure in solution in the presence of ATP and suggested an important role of this dimer in efficient interaction with Hsp40 co-chaperones. In this study, we dissected the biochemical properties of this DnaK dimer. To restrict DnaK in this dimer form, we mutated two residues on the dimer interface to cysteine, A303C, and H541C. Upon oxidation, this DnaK-A303C-H541C protein formed a specific dimer linked by disulfide bonds formed between A303C and H541C only in the presence of ATP, consistent with the crystal structure. Intriguingly, this disulfide-bond-linked dimer of DnaK-A303C-H541C has reduced ATPase activity and decreased affinity for peptide substrate. More interestingly, unlike wild-type DnaK, the peptide substrate-binding kinetics of this dimer is drastically accelerated even in the absence of ATP, suggesting this dimer is restricted in an ATP-bound conformation regardless of nucleotide bound, which was further supported by our analysis using tryptophan fluorescence and ATP-induced peptide release. Thus, formation of the dimer restricted DnaK in an ATP-bound state and blocked the progression through the chaperone cycle. Productive progression through the chaperone cycle requires the dissociation of this transient dimer. Surprisingly, a significantly compromised interaction with Hsp40 co-chaperone was observed for this disulfide-bond-linked dimer. Thus, dissociation of this DnaK dimer is equally crucial for efficient Hsp40 interaction. An initial interaction between Hsp70 and Hsp40 requires the formation of DnaK dimer; but a stable Hsp70-Hsp40 interaction may follow the dissociation of the dimer.
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Affiliation(s)
- Qingdai Liu
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, 300457, China.
| | - Hongtao Li
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Ying Yang
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, 300457, China
| | - Xueli Tian
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, 300457, China
| | - Jiayue Su
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, 300457, China
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Lei Zhou
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA.
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116
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Ramírez MP, Rivera M, Quiroga-Roger D, Bustamante A, Vega M, Baez M, Puchner EM, Wilson CAM. Single molecule force spectroscopy reveals the effect of BiP chaperone on protein folding. Protein Sci 2017; 26:1404-1412. [PMID: 28176394 DOI: 10.1002/pro.3137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/18/2017] [Accepted: 02/03/2017] [Indexed: 11/10/2022]
Abstract
BiP (Immunoglobulin Binding Protein) is a member of the Hsp70 chaperones that participates in protein folding in the endoplasmic reticulum. The function of BiP relies on cycles of ATP hydrolysis driving the binding and release of its substrate proteins. It still remains unknown how BiP affects the protein folding pathway and there has been no direct demonstration showing which folding state of the substrate protein is bound by BiP, as previous work has used only peptides. Here, we employ optical tweezers for single molecule force spectroscopy experiments to investigate how BiP affects the folding mechanism of a complete protein and how this effect depends on nucleotides. Using the protein MJ0366 as the substrate for BiP, we performed pulling and relaxing cycles at constant velocity to unfold and refold the substrate. In the absence of BiP, MJ0366 unfolded and refolded in every cycle. However, when BiP was added, the frequency of folding events of MJ0366 significantly decreased, and the loss of folding always occurred after a successful unfolding event. This process was dependent on ATP and ADP, since when either ATP was decreased or ADP was added, the duration of periods without folding events increased. Our results show that the affinity of BiP for the substrate protein increased in these conditions, which correlates with previous studies in bulk. Therefore, we conclude that BiP binds to the unfolded state of MJ0366 and prevents its refolding, and that this effect is dependent on both the type and concentration of nucleotides.
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Affiliation(s)
- María Paz Ramírez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile.,Laboratory of Cellular and Molecular Biophysics, School of Physics & Astronomy, University of Minnesota, Twin Cities, Minnesota
| | - Maira Rivera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Diego Quiroga-Roger
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Andrés Bustamante
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Marcela Vega
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Elias M Puchner
- Laboratory of Cellular and Molecular Biophysics, School of Physics & Astronomy, University of Minnesota, Twin Cities, Minnesota
| | - Christian A M Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
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117
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Weyer FA, Gumiero A, Gesé GV, Lapouge K, Sinning I. Structural insights into a unique Hsp70-Hsp40 interaction in the eukaryotic ribosome-associated complex. Nat Struct Mol Biol 2017; 24:144-151. [PMID: 28067917 DOI: 10.1038/nsmb.3349] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/01/2016] [Indexed: 01/19/2023]
Abstract
Cotranslational chaperones assist de novo folding of nascent polypeptides, prevent them from aggregating and modulate translation. The ribosome-associated complex (RAC) is unique in that the Hsp40 protein Zuo1 and the atypical Hsp70 chaperone Ssz1 form a stable heterodimer, which acts as a cochaperone for the Hsp70 chaperone Ssb. Here we present the structure of the Chaetomium thermophilum RAC core comprising Ssz1 and the Zuo1 N terminus. We show how the conserved allostery of Hsp70 proteins is abolished and this Hsp70-Hsp40 pair is molded into a functional unit. Zuo1 stabilizes Ssz1 in trans through interactions that in canonical Hsp70s occur in cis. Ssz1 is catalytically inert and cannot adopt the closed conformation, but the substrate binding domain β is completed by Zuo1. Our study offers insights into the coupling of a special Hsp70-Hsp40 pair, which evolved to link protein folding and translation.
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Affiliation(s)
| | - Andrea Gumiero
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | | | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
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118
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Ma YM, Peng YM, Zhu QH, Gao AH, Chao B, He QJ, Li J, Hu YH, Zhou YB. Novel CHOP activator LGH00168 induces necroptosis in A549 human lung cancer cells via ROS-mediated ER stress and NF-κB inhibition. Acta Pharmacol Sin 2016; 37:1381-1390. [PMID: 27264312 DOI: 10.1038/aps.2016.61] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 03/06/2016] [Indexed: 12/14/2022] Open
Abstract
AIM C/EBP homologous protein (CHOP) is a transcription factor that is activated at multiple levels during ER stress and plays an important role in ER stress-induced apoptosis. In this study we identified a novel CHOP activator, and further investigated its potential to be a therapeutic agent for human lung cancer. METHODS HEK293-CHOP-luc reporter cells were used in high-throughput screening (HTS) to identify CHOP activators. The cytotoxicity against cancer cells in vitro was measured with MTT assay. The anticancer effects were further examined in A549 human non-small cell lung cancer xenograft mice. The mechanisms underlying CHOP activation were analyzed using luciferase assays, and the anticancer mechanisms were elucidated in A549 cells. RESULTS From chemical libraries of 50 000 compounds, LGH00168 was identified as a CHOP activator, which showed cytotoxic activities against a panel of 9 cancer cell lines with an average IC50 value of 3.26 μmol/L. Moreover, administration of LGH00168 significantly suppressed tumor growth in A549 xenograft bearing mice. LGH00168 activated CHOP promoter via AARE1 and AP1 elements, increased DR5 expression, decreased Bcl-2 expression, and inhibited the NF-κB pathway. Treatment of A549 cells with LGH00168 (10 μmol/L) did not induce apoptosis, but lead to RIP1-dependent necroptosis, accompanied by cell swelling, plasma membrane rupture, lysosomal membrane permeabilization, MMP collapse and caspase 8 inhibition. Furthermore, LGH00168 (10 and 20 μmol/L) dose-dependently induced mito-ROS production in A549 cells, which was reversed by the ROS scavenger N-acetyl-L-cysteine (NAC, 10 mmol/L). Moreover, NAC significantly diminished LGH00168-induced CHOP activation, NF-κB inhibition and necroptosis in A549 cells. CONCLUSION LGH00168 is a CHOP activator that inhibits A549 cell growth in vitro and lung tumor growth in vivo.
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119
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A Conserved Cysteine within the ATPase Domain of the Endoplasmic Reticulum Chaperone BiP is Necessary for a Complete Complement of BiP Activities. J Mol Biol 2016; 428:4168-4184. [PMID: 27543005 DOI: 10.1016/j.jmb.2016.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/04/2016] [Accepted: 08/06/2016] [Indexed: 01/25/2023]
Abstract
Among the amino acids, cysteine stands apart based on its highly reactive sulfur group. In general, cysteine is underrepresented in proteins. Yet, when present, the features of cysteine often afford unique function. We have shown previously that a cysteine within the ATPase domain of yeast BiP (Kar2) serves as a sensor of the endoplasmic reticulum (ER) redox environment [1, 2]. Under conditions of increased oxidant (oxidative stress), this cysteine becomes oxidized, changing Kar2 from an ATP-dependent foldase to an ATP-independent holdase. We were struck by the high degree of conservation for this cysteine between BiP orthologs, and we sought to determine how cysteine substitution impacts Kar2 function. We observed that no single amino acid replacement is capable of recreating the range of functions that can be achieved by wild-type Kar2 with its cysteine in either unmodified or oxidized states. However, we were able to generate mutants that could selectively replicate the distinct activities exhibited by either unmodified or oxidized Kar2. We found that the ATPase activity displayed by unmodified Kar2 is fully maintained when Cys63 is replaced with Ala or Val. Conversely, we demonstrate that several amino acid substitutions (including His, Phe, Pro, Trp, and Tyr) support an enhanced viability during oxidative stress associated with oxidized Kar2, although these alleles are compromised as an ATPase. We reveal that the range of activity demonstrated by wild-type Kar2 can be replicated by co-expression of Kar2 mutants that mimic either the unmodified or oxidized Kar2 state, allowing for growth during standard and oxidative stress conditions.
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120
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Hughes SJ, Antoshchenko T, Chen Y, Lu H, Pizarro JC, Park HW. Probing the ATP Site of GRP78 with Nucleotide Triphosphate Analogs. PLoS One 2016; 11:e0154862. [PMID: 27144892 PMCID: PMC4856263 DOI: 10.1371/journal.pone.0154862] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/20/2016] [Indexed: 01/07/2023] Open
Abstract
GRP78, a member of the ER stress protein family, can relocate to the surface of cancer cells, playing key roles in promoting cell proliferation and metastasis. GRP78 consists of two major functional domains: the ATPase and protein/peptide-binding domains. The protein/peptide-binding domain of cell-surface GRP78 has served as a novel functional receptor for delivering cytotoxic agents (e.g., a apoptosis-inducing peptide or taxol) across the cell membrane. Here, we report our study on the ATPase domain of GRP78 (GRP78ATPase), whose potential as a transmembrane delivery system of cytotoxic agents (e.g., ATP-based nucleotide triphosphate analogs) remains unexploited. As the binding of ligands (ATP analogs) to a receptor (GRP78ATPase) is a pre-requisite for internalization, we determined the binding affinities and modes of GRP78ATPase for ADP, ATP and several ATP analogs using surface plasmon resonance and x-ray crystallography. The tested ATP analogs contain one of the following modifications: the nitrogen at the adenine ring 7-position to a carbon atom (7-deazaATP), the oxygen at the β-γ bridge position to a carbon atom (AMPPCP), or the removal of the 2'-OH group (2'-deoxyATP). We found that 7-deazaATP displays an affinity and a binding mode that resemble those of ATP regardless of magnesium ion (Mg++) concentration, suggesting that GRP78 is tolerant to modifications at the 7-position. By comparison, AMPPCP's binding affinity was lower than ATP and Mg++-dependent, as the removal of Mg++ nearly abolished binding to GRP78ATPase. The AMPPCP-Mg++ structure showed evidence for the critical role of Mg++ in AMPPCP binding affinity, suggesting that while GRP78 is sensitive to modifications at the β-γ bridge position, these can be tolerated in the presence of Mg++. Furthermore, 2'-deoxyATP's binding affinity was significantly lower than those for all other nucleotides tested, even in the presence of Mg++. The 2'-deoxyATP structure showed the conformation of the bound nucleotide flipped out of the active site, explaining the low affinity binding to GRP78 and suggesting that the 2'-OH group is essential for the high affinity binding to GRP78. Together, our results demonstrate that GRP78ATPase possesses nucleotide specificity more relaxed than previously anticipated and can tolerate certain modifications to the nucleobase 7-position and, to a lesser extent, the β-γ bridging atom, thereby providing a possible atomic mechanism underlying the transmembrane transport of the ATP analogs.
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Affiliation(s)
- Scott J. Hughes
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Tetyana Antoshchenko
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, LA 70112, United States of America
| | - Yun Chen
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, LA 70112, United States of America
| | - Hua Lu
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, LA 70112, United States of America
| | - Juan C. Pizarro
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, United States of America
| | - Hee-Won Park
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, LA 70112, United States of America
- * E-mail:
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121
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Preissler S, Rato C, Chen R, Antrobus R, Ding S, Fearnley IM, Ron D. AMPylation matches BiP activity to client protein load in the endoplasmic reticulum. eLife 2015; 4:e12621. [PMID: 26673894 PMCID: PMC4739761 DOI: 10.7554/elife.12621] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/14/2015] [Indexed: 01/11/2023] Open
Abstract
The endoplasmic reticulum (ER)-localized Hsp70 chaperone BiP affects protein folding homeostasis and the response to ER stress. Reversible inactivating covalent modification of BiP is believed to contribute to the balance between chaperones and unfolded ER proteins, but the nature of this modification has so far been hinted at indirectly. We report that deletion of FICD, a gene encoding an ER-localized AMPylating enzyme, abolished detectable modification of endogenous BiP enhancing ER buffering of unfolded protein stress in mammalian cells, whilst deregulated FICD activity had the opposite effect. In vitro, FICD AMPylated BiP to completion on a single residue, Thr(518). AMPylation increased, in a strictly FICD-dependent manner, as the flux of proteins entering the ER was attenuated in vivo. In vitro, Thr(518) AMPylation enhanced peptide dissociation from BiP 6-fold and abolished stimulation of ATP hydrolysis by J-domain cofactor. These findings expose the molecular basis for covalent inactivation of BiP.
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Affiliation(s)
- Steffen Preissler
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Cláudia Rato
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Ruming Chen
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Shujing Ding
- MRC Mitochondrial Biology Unit, Cambridge, United Kingdom
| | - Ian M Fearnley
- MRC Mitochondrial Biology Unit, Cambridge, United Kingdom
| | - David Ron
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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