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Guerrini G, Mehn D, Fumagalli F, Gioria S, Pedotti M, Simonelli L, Bianchini F, Robbiani DF, Varani L, Calzolai L. Analytical Ultracentrifugation Detects Quaternary Rearrangements and Antibody-Induced Conformational Selection of the SARS-CoV-2 Spike Trimer. Int J Mol Sci 2023; 24:14875. [PMID: 37834322 PMCID: PMC10573103 DOI: 10.3390/ijms241914875] [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: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Analytical ultracentrifugation (AUC) analysis shows that the SARS-CoV-2 trimeric Spike (S) protein adopts different quaternary conformations in solution. The relative abundance of the "open" and "close" conformations is temperature-dependent, and samples with different storage temperature history have different open/close distributions. Neutralizing antibodies (NAbs) targeting the S receptor binding domain (RBD) do not alter the conformer populations; by contrast, a NAb targeting a cryptic conformational epitope skews the Spike trimer toward an open conformation. The results highlight AUC, which is typically applied for molecular mass determination of biomolecules as a powerful tool for detecting functionally relevant quaternary protein conformations.
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Affiliation(s)
- Giuditta Guerrini
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Dora Mehn
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Francesco Fumagalli
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Sabrina Gioria
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
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Lin J, Shorter J, Lucius AL. AAA+ proteins: one motor, multiple ways to work. Biochem Soc Trans 2022; 50:895-906. [PMID: 35356966 PMCID: PMC9115847 DOI: 10.1042/bst20200350] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/15/2022]
Abstract
Numerous ATPases associated with diverse cellular activities (AAA+) proteins form hexameric, ring-shaped complexes that function via ATPase-coupled translocation of substrates across the central channel. Cryo-electron microscopy of AAA+ proteins processing substrate has revealed non-symmetric, staircase-like hexameric structures that indicate a sequential clockwise/2-residue step translocation model for these motors. However, for many of the AAA+ proteins that share similar structural features, their translocation properties have not yet been experimentally determined. In the cases where translocation mechanisms have been determined, a two-residue translocation step-size has not been resolved. In this review, we explore Hsp104, ClpB, ClpA and ClpX as examples to review the experimental methods that have been used to examine, in solution, the translocation mechanisms employed by AAA+ motor proteins. We then ask whether AAA+ motors sharing similar structural features can have different translocation mechanisms. Finally, we discuss whether a single AAA+ motor can adopt multiple translocation mechanisms that are responsive to different challenges imposed by the substrate or the environment. We suggest that AAA+ motors adopt more than one translocation mechanism and are tuned to switch to the most energetically efficient mechanism when constraints are applied.
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Affiliation(s)
- JiaBei Lin
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Aaron L. Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, U.S.A
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3
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Hsp100 Molecular Chaperone ClpB and Its Role in Virulence of Bacterial Pathogens. Int J Mol Sci 2021; 22:ijms22105319. [PMID: 34070174 PMCID: PMC8158500 DOI: 10.3390/ijms22105319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 01/05/2023] Open
Abstract
This review focuses on the molecular chaperone ClpB that belongs to the Hsp100/Clp subfamily of the AAA+ ATPases and its biological function in selected bacterial pathogens, causing a variety of human infectious diseases, including zoonoses. It has been established that ClpB disaggregates and reactivates aggregated cellular proteins. It has been postulated that ClpB’s protein disaggregation activity supports the survival of pathogenic bacteria under host-induced stresses (e.g., high temperature and oxidative stress), which allows them to rapidly adapt to the human host and establish infection. Interestingly, ClpB may also perform other functions in pathogenic bacteria, which are required for their virulence. Since ClpB is not found in human cells, this chaperone emerges as an attractive target for novel antimicrobial therapies in combating bacterial infections.
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Energetic Dissection of Mab-Specific Reversible Self-Association Reveals Unique Thermodynamic Signatures. Pharm Res 2021; 38:243-255. [PMID: 33604786 DOI: 10.1007/s11095-021-02987-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
PURPOSE Reversible self-association (RSA) remains a challenge in the development of therapeutic monoclonal antibodies (mAbs). We recently analyzed the energetics of RSA for five IgG mAbs (designated as A-E) under matched conditions and using orthogonal methods. Here we examine the thermodynamics of RSA for two of the mAbs that showed the strongest evidence of RSA (mAbs C and E) to identify underlying mechanisms. METHODS Concentration-dependent dynamic light scattering and sedimentation velocity (SV) studies were carried out for each mAb over a range of temperatures. Because self-association was weak, the SV data were globally analyzed via direct boundary fitting to identify best-fit models, accurately determine interaction energetics, and account for the confounding effects of thermodynamic and hydrodynamic nonideality. RESULTS mAb C undergoes isodesmic self-association at all temperatures examined, with the energetics indicative of an enthalpically-driven reaction offset by a significant entropic penalty. By contrast, mAb E undergoes monomer-dimer self-association, with the reaction being entropically-driven and comprised of only a small enthalpic contribution. CONCLUSIONS Classical interpretations implicate van der Waals interactions and H-bond formation for mAb C RSA, and electrostatic interactions for mAb E. However, noting that RSA is likely coupled to additional equilibria, we also discuss the limitations of such interpretations.
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5
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Singh P, Khurana H, Yadav SP, Dhiman K, Singh P, Ashish, Singh R, Sharma D. Biochemical characterization of ClpB protein from Mycobacterium tuberculosis and identification of its small-molecule inhibitors. Int J Biol Macromol 2020; 165:375-387. [PMID: 32987071 DOI: 10.1016/j.ijbiomac.2020.09.131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/25/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022]
Abstract
Tuberculosis, caused by pathogenic M. tuberculosis, remains a global health concern among various infectious diseases. Studies show that ClpB, a major disaggregase, protects the pathogen from various stresses encountered in the host environment. In the present study we have performed a detailed biophysical characterization of M. tuberculosis ClpB followed by a high throughput screening to identify small molecule inhibitors. The sedimentation velocity studies reveal that ClpB oligomerization varies with its concentration and presence of nucleotides. Further, using high throughput malachite green-based screening assay, we identified potential novel inhibitors of ClpB ATPase activity. The enzyme kinetics revealed that the lead molecule inhibits ClpB activity in a competitive manner. These drugs were also able to inhibit ATPase activity associated with E. coli ClpB and yeast Hsp104. The identified drugs inhibited the growth of intracellular bacteria in macrophages. Small angle X-ray scattering based modeling shows that ATP, and not its non-hydrolyzable analogs induce large scale conformational rearrangements in ClpB. Remarkably, the identified small molecules inhibited these ATP inducible conformational changes, suggesting that nucleotide induced shape changes are crucial for ClpB activity. The study broadens our understanding of M. tuberculosis chaperone machinery and provides the basis for designing more potent inhibitors against ClpB chaperone.
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Affiliation(s)
- Prashant Singh
- Council of Scientific and Industrial Research-Institute of Microbial Technology, India
| | - Harleen Khurana
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, India
| | - Shiv Pratap Yadav
- Council of Scientific and Industrial Research-Institute of Microbial Technology, India
| | - Kanika Dhiman
- Council of Scientific and Industrial Research-Institute of Microbial Technology, India
| | - Padam Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, India
| | - Ashish
- Council of Scientific and Industrial Research-Institute of Microbial Technology, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, India
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, India.
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Kędzierska-Mieszkowska S, Arent Z. AAA+ Molecular Chaperone ClpB in Leptospira interrogans: Its Role and Significance in Leptospiral Virulence and Pathogenesis of Leptospirosis. Int J Mol Sci 2020; 21:E6645. [PMID: 32932775 PMCID: PMC7555560 DOI: 10.3390/ijms21186645] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial ClpB is an ATP-dependent disaggregase that belongs to the Hsp100/Clp subfamily of the AAA+ ATPases and cooperates with the DnaK chaperone system in the reactivation of aggregated proteins, as well as promotes bacterial survival under adverse environmental conditions, including thermal and oxidative stresses. In addition, extensive evidence indicates that ClpB supports the virulence of numerous bacteria, including pathogenic spirochaete Leptospira interrogans responsible for leptospirosis in animals and humans. However, the specific function of ClpB in leptospiral virulence still remains to be fully elucidated. Interestingly, ClpB was predicted as one of the L. interrogans hub proteins interacting with human proteins, and pathogen-host protein interactions are fundamental for successful invasion of the host immune system by bacteria. The aim of this review is to discuss the most important aspects of ClpB's function in L. interrogans, including contribution of ClpB to leptospiral virulence and pathogenesis of leptospirosis, a zoonotic disease with a significant impact on public health worldwide.
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Affiliation(s)
| | - Zbigniew Arent
- University Centre of Veterinary Medicine, University of Agriculture in Krakow, 30-059 Krakow, Poland;
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7
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Batista FA, Dores-Silva PR, Borges JC. Molecular Chaperones Involved in Protein Recovery from Aggregates are Present in Protozoa Causative of Malaria and Leishmaniasis. CURR PROTEOMICS 2018. [DOI: 10.2174/1570164615666180626123823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular chaperones have several critical functions in protein metabolism. Among them,
some are involved in processes that culminate in the extraction of entangled polypeptides from protein
aggregates, releasing unfolded structures prone to be refolded or directed to degradation. This action
avoids the effect of toxic aggregates on cells and tissues. Molecular chaperones belonging to the
Hsp100 family are widely distributed from unicellular and sessile organisms up to fungi and plants,
exerting key functions related to the reduction of the effects caused by different forms of stress. The
Hsp100 proteins belong to the AAA+ (ATPases Associated with diverse cellular Activities) family and
form multichaperone systems with Hsp70 and small Hsp chaperones families. However, Hsp100 are
absent in metazoan, where protein disaggregation action is performed by a system involving the Hsp70
family, including Hsp110 and J-protein co-chaperones. Here, the structural and functional aspects of
these protein disaggregation systems will be reviewed and discussed in the perspective of the Hsp100
system absent in the metazoan kingdom. This feature focuses on Hsp100 as a hot spot for drug discovery
against human infectious diseases such as leishmaniasis and malaria, as Hsp100 is critical for microorganisms.
The current data available for Hsp100 in Leishmania spp. and Plasmodium spp. are also
reviewed.
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Affiliation(s)
- Fernanda A.H. Batista
- Instituto de Quimica de Sao Carlos, Universidade de Sao Paulo, Sao Carlos, SP, Brazil
| | - Paulo R. Dores-Silva
- Instituto de Quimica de Sao Carlos, Universidade de Sao Paulo, Sao Carlos, SP, Brazil
| | - Júlio C. Borges
- Instituto de Quimica de Sao Carlos, Universidade de Sao Paulo, Sao Carlos, SP, Brazil
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8
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Durie CL, Duran EC, Lucius AL. Escherichia coli DnaK Allosterically Modulates ClpB between High- and Low-Peptide Affinity States. Biochemistry 2018; 57:3665-3675. [PMID: 29812913 DOI: 10.1021/acs.biochem.8b00045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
ClpB and DnaKJE provide protection to Escherichia coli cells during extreme environmental stress. Together, this co-chaperone system can resolve protein aggregates, restoring misfolded proteins to their native form and function in solubilizing damaged proteins for removal by the cell's proteolytic systems. DnaK is the component of the KJE system that directly interacts with ClpB. There are many hypotheses for how DnaK affects ClpB-catalyzed disaggregation, each with some experimental support. Here, we build on our recent work characterizing the molecular mechanism of ClpB-catalyzed polypeptide translocation by developing a stopped-flow FRET assay that allows us to detect ClpB's movement on model polypeptide substrates in the absence or presence of DnaK. We find that DnaK induces ClpB to dissociate from the polypeptide substrate. We propose that DnaK acts as a peptide release factor, binding ClpB and causing the ClpB conformation to change to a low-peptide affinity state. Such a role for DnaK would allow ClpB to rebind to another portion of an aggregate and continue nonprocessive translocation to disrupt the aggregate.
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Affiliation(s)
- Clarissa L Durie
- Department of Chemistry , University of Alabama at Birmingham , Birmingham , Alabama 35294-1240 , United States
| | - Elizabeth C Duran
- Department of Chemistry , University of Alabama at Birmingham , Birmingham , Alabama 35294-1240 , United States
| | - Aaron L Lucius
- Department of Chemistry , University of Alabama at Birmingham , Birmingham , Alabama 35294-1240 , United States
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9
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Hopkins MM, Lambert CL, Bee JS, Parupudi A, Bain DL. Determination of Interaction Parameters for Reversibly Self-Associating Antibodies: A Comparative Analysis. J Pharm Sci 2018; 107:1820-1830. [PMID: 29571738 DOI: 10.1016/j.xphs.2018.03.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 12/22/2022]
Abstract
Monoclonal antibodies (mAbs) represent a major class of biotherapeutics and are the fastest growing category of biologic drugs on the market. However, mAb development and formulation are often impeded by reversible self-association (RSA), defined as the dynamic exchange of monomers with native-state oligomers. Here, we present a comparative analysis of the self-association properties for 5 IgG mAbs, under matched conditions and using orthogonal methods. Concentration-dependent dynamic light scattering and sedimentation velocity studies revealed that the majority of mAbs examined exhibited weak to moderate RSA. However, because these studies were carried out at mAb concentrations in the mg/mL range, we also observed significant nonideality. Noting that nonideality frequently masks RSA and vice versa, we conducted direct boundary fitting of the sedimentation velocity data to determine stoichiometric binding models, interaction affinities, and nonideality terms for each mAb. These analyses revealed equilibrium constants from micromolar to millimolar and stoichiometric models from monomer-dimer to isodesmic. Moreover, even for those mAbs described by identical models, we observed distinct kinetics of self-association. The accuracy of the models and their corresponding equilibrium constants were addressed using sedimentation equilibrium and simulations. Overall, these results serve as the starting point for the comparative dissection of RSA mechanisms in therapeutic mAbs.
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Affiliation(s)
- Mandi M Hopkins
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Cherie L Lambert
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Jared S Bee
- Analytical Sciences Department, MedImmune, LLC, Gaithersburg, Maryland 20878
| | - Arun Parupudi
- Analytical Sciences Department, MedImmune, LLC, Gaithersburg, Maryland 20878
| | - David L Bain
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045.
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10
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Duran EC, Weaver CL, Lucius AL. Comparative Analysis of the Structure and Function of AAA+ Motors ClpA, ClpB, and Hsp104: Common Threads and Disparate Functions. Front Mol Biosci 2017; 4:54. [PMID: 28824920 PMCID: PMC5540906 DOI: 10.3389/fmolb.2017.00054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/13/2017] [Indexed: 11/25/2022] Open
Abstract
Cellular proteostasis involves not only the expression of proteins in response to environmental needs, but also the timely repair or removal of damaged or unneeded proteins. AAA+ motor proteins are critically involved in these pathways. Here, we review the structure and function of AAA+ proteins ClpA, ClpB, and Hsp104. ClpB and Hsp104 rescue damaged proteins from toxic aggregates and do not partner with any protease. ClpA functions as the regulatory component of the ATP dependent protease complex ClpAP, and also remodels inactive RepA dimers into active monomers in the absence of the protease. Because ClpA functions both with and without a proteolytic component, it is an ideal system for developing strategies that address one of the major challenges in the study of protein remodeling machines: how do we observe a reaction in which the substrate protein does not undergo covalent modification? Here, we review experimental designs developed for the examination of polypeptide translocation catalyzed by the AAA+ motors in the absence of proteolytic degradation. We propose that transient state kinetic methods are essential for the examination of elementary kinetic mechanisms of these motor proteins. Furthermore, rigorous kinetic analysis must also account for the thermodynamic properties of these complicated systems that reside in a dynamic equilibrium of oligomeric states, including the biologically active hexamer.
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Affiliation(s)
- Elizabeth C Duran
- Department of Chemistry, University of Alabama at BirminghamBirmingham, AL, United States
| | - Clarissa L Weaver
- Department of Chemistry, University of Alabama at BirminghamBirmingham, AL, United States
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at BirminghamBirmingham, AL, United States
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11
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Krajewska J, Modrak-Wójcik A, Arent ZJ, Więckowski D, Zolkiewski M, Bzowska A, Kędzierska-Mieszkowska S. Characterization of the molecular chaperone ClpB from the pathogenic spirochaete Leptospira interrogans. PLoS One 2017; 12:e0181118. [PMID: 28700685 PMCID: PMC5507356 DOI: 10.1371/journal.pone.0181118] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/26/2017] [Indexed: 11/18/2022] Open
Abstract
Leptospira interrogans is a spirochaete responsible for leptospirosis in mammals. The molecular mechanisms of the Leptospira virulence remain mostly unknown. Recently, it has been demonstrated that an AAA+ chaperone ClpB (a member of the Hsp100 family) from L. interrogans (ClpBLi) is not only essential for survival of Leptospira under the thermal and oxidative stresses, but also during infection of a host. The aim of this study was to provide further insight into the role of ClpB in the pathogenic spirochaetes and explore its biochemical properties. We found that a non-hydrolysable ATP analogue, ATPγS, but not AMP-PNP induces the formation of ClpBLi hexamers and stabilizes the associated form of the chaperone. ADP also induces structural changes in ClpBLi and promotes its self-assembly, but does not produce full association into the hexamers. We also demonstrated that ClpBLi exhibits a weak ATPase activity that is stimulated by κ-casein and poly-lysine, and may mediate protein disaggregation independently from the DnaK chaperone system. Unexpectedly, the presence of E. coli DnaK/DnaJ/GrpE did not significantly affect the disaggregation activity of ClpBLi and ClpBLi did not substitute for the ClpBEc function in the clpB-null E. coli strain. This result underscores the species-specificity of the ClpB cooperation with the co-chaperones and is most likely due to a loss of interactions between the ClpBLi middle domain and the E. coli DnaK. We also found that ClpBLi interacts more efficiently with the aggregated G6PDH in the presence of ATPγS rather than ATP. Our results indicate that ClpB's importance during infection might be due to its role as a molecular chaperone involved in reactivation of protein aggregates.
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Affiliation(s)
- Joanna Krajewska
- Department of General and Medical Biochemistry, University of Gdańsk, Faculty of Biology, Gdańsk, Poland
| | - Anna Modrak-Wójcik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Zbigniew J. Arent
- University Centre of Veterinary Medicine UJ-UR, University of Agriculture in Krakow, Krakow, Poland
| | - Daniel Więckowski
- Department of General and Medical Biochemistry, University of Gdańsk, Faculty of Biology, Gdańsk, Poland
| | - Michal Zolkiewski
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
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12
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Weaver CL, Duran EC, Mack KL, Lin J, Jackrel ME, Sweeny EA, Shorter J, Lucius AL. Avidity for Polypeptide Binding by Nucleotide-Bound Hsp104 Structures. Biochemistry 2017; 56:2071-2075. [PMID: 28379007 DOI: 10.1021/acs.biochem.7b00225] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent Hsp104 structural studies have reported both planar and helical models of the hexameric structure. The conformation of Hsp104 monomers within the hexamer is affected by nucleotide ligation. After nucleotide-driven hexamer formation, Hsp104-catalyzed disruption of protein aggregates requires binding to the peptide substrate. Here, we examine the oligomeric state of Hsp104 and its peptide binding competency in the absence of nucleotide and in the presence of ADP, ATPγS, AMPPNP, or AMPPCP. Surprisingly, we found that only ATPγS facilitates avid peptide binding by Hsp104. We propose that the modulation between high- and low-peptide affinity states observed with these ATP analogues is an important component of the disaggregation mechanism of Hsp104.
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Affiliation(s)
- Clarissa L Weaver
- Department of Chemistry, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Elizabeth C Duran
- Department of Chemistry, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Korrie L Mack
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - JiaBei Lin
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Meredith E Jackrel
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Elizabeth A Sweeny
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
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13
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Kentache T, Jouenne T, Dé E, Hardouin J. Proteomic characterization of Nα- and Nε-acetylation in Acinetobacter baumannii. J Proteomics 2016; 144:148-58. [PMID: 27222042 DOI: 10.1016/j.jprot.2016.05.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/12/2016] [Accepted: 05/18/2016] [Indexed: 12/25/2022]
Abstract
Nα- and Nε-acetylation represent a pivotal post-translational modification used by both eukaryotes and prokaryotes to modulate diverse biological processes. Acinetobacter baumannii has been described as an important nosocomial pathogen for the past 30 years, frequently involved in ventilator-associated pneumonia, bloodstream and urinary tract infections. Many aspects of the biology of A. baumannii remain elusive, in particular the extent and function of N-acetylation. We investigated here N-acetylation in A. baumannii strain ATCC 17978 by proteomic analysis, and we showed the usefulness of using different analytical approaches. Overall, we identified 525 N-acetylated proteins in which, 145 were Nα-acetylated and 411 were Nε-acetylated. Among them, 41 proteins carried both types of N-acetylation. We found that N-acetylation may play a role in biofilm formation, bacterial virulence (e.g. in several iron acquisition pathways), as well as a number of phenotypes, such as, stress adaptation and drug resistance. BIOLOGICAL SIGNIFICANCE This study is the first to perform the N-acetylome of A. baumannii using different analytical approaches. Each analytical tool permitted to characterize distinctive modified peptides. The combination of all these methods allowed us to identify 145 and 411 Nα- and Nε-acetylated proteins. Besides the fact that acetylation was involved in central metabolism as previously described in other bacteria, some N-acetylated proteins showed interesting role in bacterial virulence (iron acquisition), biofilm formation, stress adaptation and drug resistance of A. baumannii.
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Affiliation(s)
- Takfarinas Kentache
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Emmanuelle Dé
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France.
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Lin J, Lucius AL. Examination of ClpB Quaternary Structure and Linkage to Nucleotide Binding. Biochemistry 2016; 55:1758-71. [PMID: 26891079 DOI: 10.1021/acs.biochem.6b00122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Escherichia coli caseinolytic peptidase B (ClpB) is a molecular chaperone with the unique ability to catalyze protein disaggregation in collaboration with the KJE system of chaperones. Like many AAA+ molecular motors, ClpB assembles into hexameric rings, and this reaction is thermodynamically linked to nucleotide binding. Here we show that ClpB exists in a dynamic equilibrium of monomers, dimers, tetramers, and hexamers in the presence of both limiting and excess ATPγS. We find that ClpB monomer is only able to bind one nucleotide, whereas all 12 sites in the hexameric ring are bound by nucleotide at saturating concentrations. Interestingly, dimers and tetramers exhibit stoichiometries of ∼3 and 7, respectively, which is one fewer than the maximum number of binding sites in the formed oligomer. This observation suggests an open conformation for the intermediates based on the need for an adjacent monomer to fully form the binding pocket. We also report the protein-protein interaction constants for dimers, tetramers, and hexamers and their dependencies on nucleotide. These interaction constants make it possible to predict the concentration of hexamers present and able to bind to cochaperones and polypeptide substrates. Such information is essential for the interpretation of many in vitro studies. Finally, the strategies presented here are broadly applicable to a large number of AAA+ molecular motors that assemble upon nucleotide binding and interact with partner proteins.
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Affiliation(s)
- JiaBei Lin
- Department of Chemistry, The University of Alabama at Birmingham , 1530 Third Avenue S, Birmingham, Alabama 35294-1240, United States
| | - Aaron L Lucius
- Department of Chemistry, The University of Alabama at Birmingham , 1530 Third Avenue S, Birmingham, Alabama 35294-1240, United States
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