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Rossi MA, Pozhidaeva AK, Clerico EM, Petridis C, Gierasch LM. New insights into the structure and function of the complex between the Escherichia coli Hsp70, DnaK, and its nucleotide-exchange factor, GrpE. J Biol Chem 2024; 300:105574. [PMID: 38110031 PMCID: PMC10825016 DOI: 10.1016/j.jbc.2023.105574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/18/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023] Open
Abstract
The 70 kDa heat shock proteins (Hsp70s) play a pivotal role in many cellular functions using allosteric communication between their nucleotide-binding domain (NBD) and substrate-binding domain, mediated by an interdomain linker, to modulate their affinity for protein clients. Critical to modulation of the Hsp70 allosteric cycle, nucleotide-exchange factors (NEFs) act by a conserved mechanism involving binding to the ADP-bound NBD and opening of the nucleotide-binding cleft to accelerate the release of ADP and binding of ATP. The crystal structure of the complex between the NBD of the Escherichia coli Hsp70, DnaK, and its NEF, GrpE, was reported previously, but the GrpE in the complex carried a point mutation (G122D). Both the functional impact of this mutation and its location on the NEF led us to revisit the DnaK NBD/GrpE complex structurally using AlphaFold modeling and validation by solution methods that report on protein conformation and mutagenesis. This work resulted in a new model for the DnaK NBD in complex with GrpE in which subdomain IIB of the NBD rotates more than in the crystal structure, resulting in an open conformation of the nucleotide-binding cleft, which now resembles more closely what is seen in other Hsp/NEF complexes. Moreover, the new model is consistent with the increased ADP off-rate accompanying GrpE binding. Excitingly, our findings point to an interdomain allosteric signal in DnaK triggered by GrpE binding.
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Affiliation(s)
- Maria-Agustina Rossi
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Alexandra K Pozhidaeva
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Eugenia M Clerico
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Constantine Petridis
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Lila M Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA; Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA.
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2
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Huo Y, Song Z, Wang H, Zhang Z, Xiao N, Fang R, Zhang Y, Zhang L. GrpE is involved in mitochondrial function and is an effective target for RNAi-mediated pest and arbovirus control. INSECT MOLECULAR BIOLOGY 2022; 31:377-390. [PMID: 35141960 PMCID: PMC9306519 DOI: 10.1111/imb.12766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Laodelphax striatellus is a sap-feeding pest and the main insect vector of rice stripe virus (RSV). There is an urgent need to identify molecular targets to control this insect pest and plant arboviruses. In this study, we identified a L. striatellus gene (named LsGrpE) encoding a GroP-E-like protein. We found that the LsGrpE protein localized to mitochondria. Using gene-specific dsRNA to interfere with the expression of LsGrpE led to a significant increase in insect mortality, and most of the surviving insects could not develop into adults. Further analyses revealed that LsGrpE deficiency caused mitochondrial dysfunction and inhibited the insulin pathway, resulting in diabetes-like symptoms such as elevated blood sugar, inactive behaviour, developmental delay, and death. In addition, LsGrpE deficiency significantly reduced the RSV titre in surviving L. striatellus, and indirectly prevented viral vertical transmission by reducing the number of adults. We generated transgenic rice plants expressing LsGrpE-specific dsRNA, and the dsRNA was acquired by L. striatellus during feeding, resulting in increased insect mortality and the prevention of arboviral transmission. This study clarifies the function of LsGrpE and demonstrates that LsGrpE can be used as a molecular target of plant-generated dsRNA to resist this sap-feeding pest, a17nd therefore, its transmitted arboviruses.
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Affiliation(s)
- Yan Huo
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of SciencesBeijingChina
| | - Zhiyu Song
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of SciencesBeijingChina
| | - Haiting Wang
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Ziyu Zhang
- College of Life Sciences, Hebei UniversityBaodingChina
| | - Na Xiao
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of SciencesBeijingChina
| | - Rongxiang Fang
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of SciencesBeijingChina
| | - Yuman Zhang
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of SciencesBeijingChina
| | - Lili Zhang
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of SciencesBeijingChina
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3
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Hosfelt J, Richards A, Zheng M, Adura C, Nelson B, Yang A, Fay A, Resager W, Ueberheide B, Glickman JF, Lupoli TJ. An allosteric inhibitor of bacterial Hsp70 chaperone potentiates antibiotics and mitigates resistance. Cell Chem Biol 2021; 29:854-869.e9. [PMID: 34818532 DOI: 10.1016/j.chembiol.2021.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/20/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022]
Abstract
DnaK is the bacterial homolog of Hsp70, an ATP-dependent chaperone that helps cofactor proteins to catalyze nascent protein folding and salvage misfolded proteins. In the pathogen Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), DnaK and its cofactors are proposed antimycobacterial targets, yet few small-molecule inhibitors or probes exist for these families of proteins. Here, we describe the repurposing of a drug called telaprevir that is able to allosterically inhibit the ATPase activity of DnaK and to prevent chaperone function by mimicking peptide substrates. In mycobacterial cells, telaprevir disrupts DnaK- and cofactor-mediated cellular proteostasis, resulting in enhanced efficacy of aminoglycoside antibiotics and reduced resistance to the frontline TB drug rifampin. Hence, this work contributes to a small but growing collection of protein chaperone inhibitors, and it demonstrates that these molecules disrupt bacterial mechanisms of survival in the presence of different antibiotic classes.
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Affiliation(s)
- Jordan Hosfelt
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Aweon Richards
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Meng Zheng
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Carolina Adura
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brock Nelson
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Amy Yang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Allison Fay
- Immunology Program, Sloan Kettering Insitute, New York, NY 10065, USA
| | - William Resager
- Departments of Biochemistry and Molecular Pharmacology, Neurology and Director Proteomics Lab, Division of Advanced Research Technologies, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Beatrix Ueberheide
- Departments of Biochemistry and Molecular Pharmacology, Neurology and Director Proteomics Lab, Division of Advanced Research Technologies, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - J Fraser Glickman
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, NY 10003, USA.
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4
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Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET. Proc Natl Acad Sci U S A 2021; 118:2025578118. [PMID: 34389669 DOI: 10.1073/pnas.2025578118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cellular function depends on the correct folding of proteins inside the cell. Heat-shock proteins 70 (Hsp70s), being among the first molecular chaperones binding to nascently translated proteins, aid in protein folding and transport. They undergo large, coordinated intra- and interdomain structural rearrangements mediated by allosteric interactions. Here, we applied a three-color single-molecule Förster resonance energy transfer (FRET) combined with three-color photon distribution analysis to compare the conformational cycle of the Hsp70 chaperones DnaK, Ssc1, and BiP. By capturing three distances simultaneously, we can identify coordinated structural changes during the functional cycle. Besides the known conformations of the Hsp70s with docked domains and open lid and undocked domains with closed lid, we observed additional intermediate conformations and distance broadening, suggesting flexibility of the Hsp70s in adopting the states in a coordinated fashion. Interestingly, the difference of this distance broadening varied between DnaK, Ssc1, and BiP. Study of their conformational cycle in the presence of substrate peptide and nucleotide exchange factors strengthened the observation of additional conformational intermediates, with BiP showing coordinated changes more clearly compared to DnaK and Ssc1. Additionally, DnaK and BiP were found to differ in their selectivity for nucleotide analogs, suggesting variability in the recognition mechanism of their nucleotide-binding domains for the different nucleotides. By using three-color FRET, we overcome the limitations of the usual single-distance approach in single-molecule FRET, allowing us to characterize the conformational space of proteins in higher detail.
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Mitochondrial HSP70 Chaperone System-The Influence of Post-Translational Modifications and Involvement in Human Diseases. Int J Mol Sci 2021; 22:ijms22158077. [PMID: 34360841 PMCID: PMC8347752 DOI: 10.3390/ijms22158077] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 01/25/2023] Open
Abstract
Since their discovery, heat shock proteins (HSPs) have been identified in all domains of life, which demonstrates their importance and conserved functional role in maintaining protein homeostasis. Mitochondria possess several members of the major HSP sub-families that perform essential tasks for keeping the organelle in a fully functional and healthy state. In humans, the mitochondrial HSP70 chaperone system comprises a central molecular chaperone, mtHSP70 or mortalin (HSPA9), which is actively involved in stabilizing and importing nuclear gene products and in refolding mitochondrial precursor proteins, and three co-chaperones (HSP70-escort protein 1-HEP1, tumorous imaginal disc protein 1-TID-1, and Gro-P like protein E-GRPE), which regulate and accelerate its protein folding functions. In this review, we summarize the roles of mitochondrial molecular chaperones with particular focus on the human mtHsp70 and its co-chaperones, whose deregulated expression, mutations, and post-translational modifications are often considered to be the main cause of neurological disorders, genetic diseases, and malignant growth.
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6
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Karunanayake C, Page RC. Cytosolic protein quality control machinery: Interactions of Hsp70 with a network of co-chaperones and substrates. Exp Biol Med (Maywood) 2021; 246:1419-1434. [PMID: 33730888 PMCID: PMC8243209 DOI: 10.1177/1535370221999812] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The chaperone heat shock protein 70 (Hsp70) and its network of co-chaperones serve as a central hub of cellular protein quality control mechanisms. Domain organization in Hsp70 dictates ATPase activity, ATP dependent allosteric regulation, client/substrate binding and release, and interactions with co-chaperones. The protein quality control activities of Hsp70 are classified as foldase, holdase, and disaggregase activities. Co-chaperones directly assisting protein refolding included J domain proteins and nucleotide exchange factors. However, co-chaperones can also be grouped and explored based on which domain of Hsp70 they interact. Here we discuss how the network of cytosolic co-chaperones for Hsp70 contributes to the functions of Hsp70 while closely looking at their structural features. Comparison of domain organization and the structures of co-chaperones enables greater understanding of the interactions, mechanisms of action, and roles played in protein quality control.
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Affiliation(s)
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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7
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Fatima K, Naqvi F, Younas H. A Review: Molecular Chaperone-mediated Folding, Unfolding and Disaggregation of Expressed Recombinant Proteins. Cell Biochem Biophys 2021; 79:153-174. [PMID: 33634426 DOI: 10.1007/s12013-021-00970-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/01/2021] [Indexed: 12/26/2022]
Abstract
The advancements in biotechnology over time have led to an increase in the demand of pure, soluble and functionally active proteins. Recombinant protein production has thus been employed to obtain high expression of purified proteins in bulk. E. coli is considered as the most desirable host for recombinant protein production due to its inexpensive and fast cultivation, simple nutritional requirements and known genetics. Despite all these benefits, recombinant protein production often comes with drawbacks, such as, the most common being the formation of inclusion bodies due to improper protein folding. Consequently, this can lead to the loss of the structure-function relationship of a protein. Apart from various strategies, one major strategy to resolve this issue is the use of molecular chaperones that act as folding modulators for proteins. Molecular chaperones assist newly synthesized, aggregated or misfolded proteins to fold into their native conformations. Chaperones have been widely used to improve the expression of various proteins which are otherwise difficult to produce in E. coli. Here, we discuss the structure, function, and role of major E. coli molecular chaperones in recombinant technology such as trigger factor, GroEL, DnaK and ClpB.
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Affiliation(s)
- Komal Fatima
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan
| | - Fatima Naqvi
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan
| | - Hooria Younas
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan.
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8
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Upadhyay T, Potteth US, Karekar VV, Saraogi I. A Stutter in the Coiled-Coil Domain of Escherichia coli Co-chaperone GrpE Connects Structure with Function. Biochemistry 2021; 60:1356-1367. [PMID: 33881310 DOI: 10.1021/acs.biochem.1c00110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In bacteria, the co-chaperone GrpE acts as a nucleotide exchange factor and plays an important role in controlling the chaperone cycle of DnaK. The functional form of GrpE is an asymmetric dimer, consisting of a non-ideal coiled coil. Partial unfolding of this region during heat stress results in reduced nucleotide exchange and disrupts protein folding by DnaK. In this study, we elucidate the role of non-ideality in the coiled-coil domain of Escherichia coli GrpE in controlling its co-chaperone activity. The presence of a four-residue stutter introduces nonheptad periodicity in the GrpE coiled coil, resulting in global structural changes in GrpE and regulating its interaction with DnaK. Introduction of hydrophobic residues at the stutter core increased the structural stability of the protein. Using an in vitro FRET assay, we show that the enhanced stability of GrpE resulted in an increased affinity for DnaK. However, these mutants were unable to support bacterial growth at 42°C in a grpE-deleted E. coli strain. This work provides valuable insights into the functional role of a stutter in GrpE in regulating the DnaK-chaperone cycle during heat stress. More generally, our findings illustrate how stutters in a coiled-coil domain regulate structure-function trade-off in proteins.
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Affiliation(s)
- Tulsi Upadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India
| | - Upasana S Potteth
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India
| | - Vaibhav V Karekar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India
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9
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Hsp70 molecular chaperones: multifunctional allosteric holding and unfolding machines. Biochem J 2019; 476:1653-1677. [PMID: 31201219 DOI: 10.1042/bcj20170380] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022]
Abstract
The Hsp70 family of chaperones works with its co-chaperones, the nucleotide exchange factors and J-domain proteins, to facilitate a multitude of cellular functions. Central players in protein homeostasis, these jacks-of-many-trades are utilized in a variety of ways because of their ability to bind with selective promiscuity to regions of their client proteins that are exposed when the client is unfolded, either fully or partially, or visits a conformational state that exposes the binding region in a regulated manner. The key to Hsp70 functions is that their substrate binding is transient and allosterically cycles in a nucleotide-dependent fashion between high- and low-affinity states. In the past few years, structural insights into the molecular mechanism of this allosterically regulated binding have emerged and provided deep insight into the deceptively simple Hsp70 molecular machine that is so widely harnessed by nature for diverse cellular functions. In this review, these structural insights are discussed to give a picture of the current understanding of how Hsp70 chaperones work.
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10
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Regulation of Human Hsc70 ATPase and Chaperone Activities by Apg2: Role of the Acidic Subdomain. J Mol Biol 2018; 431:444-461. [PMID: 30521813 DOI: 10.1016/j.jmb.2018.11.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/30/2018] [Accepted: 11/26/2018] [Indexed: 12/28/2022]
Abstract
Protein aggregate reactivation in metazoans is accomplished by the combined activity of Hsp70, Hsp40 and Hsp110 chaperones. Hsp110s support the refolding of aggregated polypeptides acting as specialized nucleotide exchange factors of Hsp70. We have studied how Apg2, one of the three human Hsp110s, regulates the activity of Hsc70 (HspA8), the constitutive Hsp70 in our cells. Apg2 shows a biphasic behavior: at low concentration, it stimulates the ATPase cycle of Hsc70, binding of the chaperone to protein aggregates and the refolding activity of the system, while it inhibits these three processes at high concentration. When the acidic subdomain of Apg2, a characteristic sequence present in the substrate binding domain of all Hsp110s, is deleted, the detrimental effects occur at lower concentration and are more pronounced, which concurs with an increase in the affinity of the Apg2 mutant for Hsc70. Our data support a mechanism in which Apg2 arrests the chaperone cycle through an interaction with Hsc70(ATP) that might lead to premature ATP dissociation before hydrolysis. In this line, the acidic subdomain might serve as a conformational switch to support dissociation of the Hsc70:Apg2 complex.
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11
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Adell M, Calisto BM, Fita I, Martinelli L. The nucleotide-bound/substrate-bound conformation of the Mycoplasma genitalium DnaK chaperone. Protein Sci 2018; 27:1000-1007. [PMID: 29520883 PMCID: PMC5916121 DOI: 10.1002/pro.3401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/04/2018] [Accepted: 03/05/2018] [Indexed: 11/07/2022]
Abstract
Hsp70 chaperones keep protein homeostasis facilitating the response of organisms to changes in external and internal conditions. Hsp70s have two domains-nucleotide binding domain (NBD) and substrate binding domain (SBD)-connected by a conserved hydrophobic linker. Functioning of Hsp70s depend on tightly regulated cycles of ATP hydrolysis allosterically coupled, often together with cochaperones, to the binding/release of peptide substrates. Here we describe the crystal structure of the Mycoplasma genitalium DnaK (MgDnaK) protein, an Hsp70 homolog, in the noncompact, nucleotide-bound/substrate-bound conformation. The MgDnaK structure resembles the one from the thermophilic eubacteria DnaK trapped in the same state. However, in MgDnaK the NBD and SBD domains remain close to each other despite the lack of direct interaction between them and with the linker contacting the two subdomains of SBD. These observations suggest that the structures might represent an intermediate of the protein where the conserved linker binds to the SBD to favor the noncompact state of the protein by stabilizing the SBDβ-SBDα subdomains interaction, promoting the capacity of the protein to sample different conformations, which is critical for proper functioning of the molecular chaperone allosteric mechanism. Comparison of the solved structures indicates that the NBD remains essentially invariant in presence or absence of nucleotide.
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Affiliation(s)
- Maria Adell
- Instituto de Biología Molecular de Barcelona (IBMB‐CSIC), Parc Científic de BarcelonaBarcelonaSpain
| | - Bárbara M. Calisto
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, Grenoble, France and ALBA SynchrotronCarrer de la Llum 2‐26, 08290 Cerdanyola del VallèsBarcelonaSpain
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB‐CSIC), Parc Científic de BarcelonaBarcelonaSpain
| | - Luca Martinelli
- Instituto de Biología Molecular de Barcelona (IBMB‐CSIC), Parc Científic de BarcelonaBarcelonaSpain
- Present address:
Division of Biochemistry and Cancer Genomics CenterThe Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Medical Biochemistry, Academic Medical CenterAmsterdamThe Netherlands.
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12
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Activation of the DnaK-ClpB Complex is Regulated by the Properties of the Bound Substrate. Sci Rep 2018; 8:5796. [PMID: 29643454 PMCID: PMC5895705 DOI: 10.1038/s41598-018-24140-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 03/28/2018] [Indexed: 12/20/2022] Open
Abstract
The chaperone ClpB in bacteria is responsible for the reactivation of aggregated proteins in collaboration with the DnaK system. Association of these chaperones at the aggregate surface stimulates ATP hydrolysis, which mediates substrate remodeling. However, a question that remains unanswered is whether the bichaperone complex can be selectively activated by substrates that require remodeling. We find that large aggregates or bulky, native-like substrates activates the complex, whereas a smaller, permanently unfolded protein or extended, short peptides fail to stimulate it. Our data also indicate that ClpB interacts differently with DnaK in the presence of aggregates or small peptides, displaying a higher affinity for aggregate-bound DnaK, and that DnaK-ClpB collaboration requires the coupled ATPase-dependent remodeling activities of both chaperones. Complex stimulation is mediated by residues at the β subdomain of DnaK substrate binding domain, which become accessible to the disaggregase when the lid is allosterically detached from the β subdomain. Complex activation also requires an active NBD2 and the integrity of the M domain-ring of ClpB. Disruption of the M-domain ring allows the unproductive stimulation of the DnaK-ClpB complex in solution. The ability of the DnaK-ClpB complex to discrimínate different substrate proteins might allow its activation when client proteins require remodeling.
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13
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Penkler D, Sensoy Ö, Atilgan C, Tastan Bishop Ö. Perturbation-Response Scanning Reveals Key Residues for Allosteric Control in Hsp70. J Chem Inf Model 2017; 57:1359-1374. [PMID: 28505454 DOI: 10.1021/acs.jcim.6b00775] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hsp70 molecular chaperones play an important role in maintaining cellular homeostasis, and are implicated in a wide array of cellular processes, including protein recovery from aggregates, cross-membrane protein translocation, and protein biogenesis. Hsp70 consists of two domains, a nucleotide binding domain (NBD) and a substrate binding domain (SBD), each of which communicates via an allosteric mechanism such that the protein interconverts between two functional states, an ATP-bound open conformation and an ADP-bound closed conformation. The exact mechanism for interstate conversion is not as yet fully understood. However, the ligand-bound states of the NBD and SBD as well as interactions with cochaperones such as DnaJ and nucleotide exchange factor are thought to play crucial regulatory roles. In this study, we apply the perturbation-response scanning (PRS) method in combination with molecular dynamics simulations as a computational tool for the identification of allosteric hot residues in the large multidomain Hsp70 protein. We find evidence in support of the hypothesis that substrate binding triggers ATP hydrolysis and that the ADP-substrate complex favors interstate conversion to the closed state. Furthermore, our data are in agreement with the proposal that there is an allosterically active intermediate state between the open and closed states and vice versa, as we find evidence that ATP binding to the closed structure and peptide binding to the open structure allosterically "activate" the respective complexes. We conclude our analysis by showing how our PRS data fit the current opinion on the Hsp70 conformational cycle and present several allosteric hot residues that may provide a platform for further studies to gain additional insight into Hsp70 allostery.
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Affiliation(s)
- David Penkler
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University , Grahamstown 6140, South Africa
| | - Özge Sensoy
- School of Engineering and Natural Sciences, Istanbul Medipol University , Beykoz 34810, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University , Tuzla 34956, Istanbul, Turkey
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University , Grahamstown 6140, South Africa
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14
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Shlar I, Droby S, Rodov V. Modes of antibacterial action of curcumin under dark and light conditions: A toxicoproteomics approach. J Proteomics 2017; 160:8-20. [PMID: 28315482 DOI: 10.1016/j.jprot.2017.03.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/01/2017] [Accepted: 03/12/2017] [Indexed: 12/20/2022]
Abstract
Curcumin is a potent natural food-grade antimicrobial compound. Exposure to light further enhances its antimicrobial capacity. Proteomic methods were used in this study for investigating the mechanistic aspects of the antibacterial curcumin effects in the dark and upon illumination. Escherichia coli cells exposed to water-dispersible curcumin-methyl-β-cyclodextrin inclusion complex under dark and light conditions were compared with the non-treated cells kept under the same illumination regimes. Curcumin treatment in the dark evoked adaptive responses aimed at mitigation of oxidative stress, DNA protection, proteostasis, modulation of redox state via changing NADH level, and gasotransmitter (H2S and NH3) biosynthesis. Although part of these phenomena were also present in E. coli treated under light, the light-induced curcumin toxicity was prevailed by maladaptive responses. The ROS burst induced upon curcumin treatment under light overrode the cellular adaptive mechanisms disrupting the iron metabolism, deregulating the iron-sulfur cluster biosynthesis and eventually leading to cell death. The toxicoproteomic findings were validated by transcriptomic analysis and by assessment of intracellular ROS, NADH, NADPH and iron levels. SIGNIFICANCE The results of this study elucidate putative mechanistic basis of antibacterial effects of curcumin, suggesting ways towards more efficient contamination control. In particular, the antimicrobial efficacy of curcumin can be potentiated by targeting bacterial systems that remediate its dark toxicity by free radical detoxification and modulation of cell redox status. To the best of the authors' knowledge, this is the first proteomic study differentiating between the dark and light-induced antimicrobial activity of curcumin.
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Affiliation(s)
- Ilya Shlar
- Institute of Postharvest and Food Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7528809, Israel; Institute of Biochemistry, Food Science and Nutrition, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Samir Droby
- Institute of Postharvest and Food Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7528809, Israel
| | - Victor Rodov
- Institute of Postharvest and Food Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7528809, Israel.
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15
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Zuiderweg ERP, Hightower LE, Gestwicki JE. The remarkable multivalency of the Hsp70 chaperones. Cell Stress Chaperones 2017; 22:173-189. [PMID: 28220454 PMCID: PMC5352603 DOI: 10.1007/s12192-017-0776-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 02/07/2017] [Indexed: 01/01/2023] Open
Abstract
Hsp70 proteins are key to maintaining intracellular protein homeostasis. To carry out this task, they employ a large number of cochaperones and adapter proteins. Here, we review what is known about the interaction between the chaperones and partners, with a strong slant toward structural biology. Hsp70s in general, and Hsc70 (HSPA8) in particular, display an amazing array of interfaces with their protein cofactors. We also review the known interactions between Hsp70s with lipids and with active compounds that may become leads toward Hsp70 modulation for treatment of a variety of diseases.
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Affiliation(s)
- Erik R P Zuiderweg
- Department of Biological Chemistry, The University of Michigan Medical School, 1500 Medical Center Drive, Ann Arbor, MI, 48109, USA.
| | - Lawrence E Hightower
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Jason E Gestwicki
- Institute for Neurodegenerative Disease, University of California at San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA
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16
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Marada A, Karri S, Singh S, Allu PK, Boggula Y, Krishnamoorthy T, Guruprasad L, V Sepuri NB. A Single Point Mutation in Mitochondrial Hsp70 Cochaperone Mge1 Gains Thermal Stability and Resistance. Biochemistry 2016; 55:7065-7072. [DOI: 10.1021/acs.biochem.6b00232] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Adinarayana Marada
- Department
of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, T.S., India
| | - Srinivasu Karri
- Department
of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, T.S., India
| | - Swati Singh
- School
of Chemistry, University of Hyderabad, Hyderabad 500046, T.S., India
| | - Praveen Kumar Allu
- Department
of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, T.S., India
| | - Yerranna Boggula
- Department
of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, T.S., India
| | - Thanuja Krishnamoorthy
- Department
of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, T.S., India
| | - Lalitha Guruprasad
- School
of Chemistry, University of Hyderabad, Hyderabad 500046, T.S., India
| | - Naresh Babu V Sepuri
- Department
of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, T.S., India
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17
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Rauch JN, Zuiderweg ERP, Gestwicki JE. Non-canonical Interactions between Heat Shock Cognate Protein 70 (Hsc70) and Bcl2-associated Anthanogene (BAG) Co-Chaperones Are Important for Client Release. J Biol Chem 2016; 291:19848-57. [PMID: 27474739 PMCID: PMC5025674 DOI: 10.1074/jbc.m116.742502] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/26/2016] [Indexed: 01/17/2023] Open
Abstract
Heat shock cognate protein 70 (Hsc70) regulates protein homeostasis through its reversible interactions with client proteins. Hsc70 has two major domains: a nucleotide-binding domain (NBD), that hydrolyzes ATP, and a substrate-binding domain (SBD), where clients are bound. Members of the BAG family of co-chaperones, including Bag1 and Bag3, are known to accelerate release of both ADP and client from Hsc70. The release of nucleotide is known to be mediated by interactions between the conserved BAG domain and the Hsc70 NBD. However, less is known about the regions required for client release, and it is often assumed that this activity also requires the BAG domain. It is important to better understand this step because it determines how long clients remain in the inactive, bound state. Here, we report the surprising observation that truncated versions of either human Bag1 or Bag3, comprised only the BAG domain, promoted rapid release of nucleotide, but not client, in vitro Rather, we found that a non-canonical interaction between Bag1/3 and the Hsc70 SBD is sufficient for accelerating this step. Moreover, client release did not seem to require the BAG domain or Hsc70 NBD. These results suggest that Bag1 and Bag3 control the stability of the Hsc70-client complex using at least two distinct protein-protein contacts, providing a previously under-appreciated layer of molecular regulation in the human Hsc70 system.
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Affiliation(s)
- Jennifer N Rauch
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Erik R P Zuiderweg
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Jason E Gestwicki
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158
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18
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Sorzano COS, Martín-Ramos A, Prieto F, Melero R, Martín-Benito J, Jonic S, Navas-Calvente J, Vargas J, Otón J, Abrishami V, de la Rosa-Trevín JM, Gómez-Blanco J, Vilas JL, Marabini R, Carazo JM. Local analysis of strains and rotations for macromolecular electron microscopy maps. J Struct Biol 2016; 195:123-8. [PMID: 27102900 DOI: 10.1016/j.jsb.2016.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 01/23/2023]
Abstract
Macromolecular complexes perform their physiological functions by local rearrangements of their constituents and biochemically interacting with their reaction partners. These rearrangements may involve local rotations and the induction of local strains causing different mechanical efforts and stretches at the different areas of the protein. The analysis of these local deformations may reveal important insight into the way proteins perform their tasks. In this paper we introduce a method to perform this kind of local analysis using Electron Microscopy volumes in a fully objective and automatic manner. For doing so, we exploit the continuous nature of the result of an elastic image registration using B-splines as its basis functions. We show that the results obtained by the new automatic method are consistent with previous observations on these macromolecules.
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Affiliation(s)
- C O S Sorzano
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain.
| | - A Martín-Ramos
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - F Prieto
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - R Melero
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Martín-Benito
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - S Jonic
- IMPMC, Sorbonne Universités - CNRS UMR 7590, UPMC University Paris 6, MNHN, IRDUMR206, 75005 Paris, France
| | - J Navas-Calvente
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Vargas
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Otón
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - V Abrishami
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | | | - J Gómez-Blanco
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J L Vilas
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Univ. Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
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19
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Durech M, Trcka F, Man P, Blackburn EA, Hernychova L, Dvorakova P, Coufalova D, Kavan D, Vojtesek B, Muller P. Novel Entropically Driven Conformation-specific Interactions with Tomm34 Protein Modulate Hsp70 Protein Folding and ATPase Activities. Mol Cell Proteomics 2016; 15:1710-27. [PMID: 26944342 DOI: 10.1074/mcp.m116.058131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 12/18/2022] Open
Abstract
Co-chaperones containing tetratricopeptide repeat (TPR) domains enable cooperation between Hsp70 and Hsp90 to maintain cellular proteostasis. Although the details of the molecular interactions between some TPR domains and heat shock proteins are known, we describe a novel mechanism by which Tomm34 interacts with and coordinates Hsp70 activities. In contrast to the previously defined Hsp70/Hsp90-organizing protein (Hop), Tomm34 interaction is dependent on the Hsp70 chaperone cycle. Tomm34 binds Hsp70 in a complex process; anchorage of the Hsp70 C terminus by the TPR1 domain is accompanied by additional contacts formed exclusively in the ATP-bound state of Hsp70 resulting in a high affinity entropically driven interaction. Tomm34 induces structural changes in determinants within the Hsp70-lid subdomain and modulates Hsp70/Hsp40-mediated refolding and Hsp40-stimulated Hsp70 ATPase activity. Because Tomm34 recruits Hsp90 through its TPR2 domain, we propose a model in which Tomm34 enables Hsp70/Hsp90 scaffolding and influences the Hsp70 chaperone cycle, providing an additional role for co-chaperones that contain multiple TPR domains in regulating protein homeostasis.
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Affiliation(s)
- Michal Durech
- From the ‡Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Filip Trcka
- From the ‡Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Petr Man
- ¶Institute of Microbiology, The Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; ‖Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague, Czech Republic
| | - Elizabeth A Blackburn
- **Centre for Translational and Chemical Biology, Institute of Structural and Molecular Biology, University of Edinburgh, Max Born Crescent, The King's Buildings, Edinburgh EH9 3JR, United Kingdom
| | - Lenka Hernychova
- From the ‡Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Petra Dvorakova
- From the ‡Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Dominika Coufalova
- From the ‡Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Daniel Kavan
- ¶Institute of Microbiology, The Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; ‖Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague, Czech Republic
| | - Borivoj Vojtesek
- From the ‡Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656 53 Brno, Czech Republic;
| | - Petr Muller
- From the ‡Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656 53 Brno, Czech Republic;
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