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Kim H, Park J, Roh SH. The structural basis of eukaryotic chaperonin TRiC/CCT: Action and folding. Mol Cells 2024; 47:100012. [PMID: 38280673 PMCID: PMC11004407 DOI: 10.1016/j.mocell.2024.100012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/29/2024] Open
Abstract
Accurate folding of proteins in living cells often requires the cooperative support of molecular chaperones. Eukaryotic group II chaperonin Tailless complex polypeptide 1-Ring Complex (TRiC) accomplishes this task by providing a folding chamber for the substrate that is regulated by an Adenosine triphosphate (ATP) hydrolysis-dependent cycle. Once delivered to and recognized by TRiC, the nascent substrate enters the folding chamber and undergoes folding and release in a stepwise manner. During the process, TRiC subunits and cochaperones such as prefoldin and phosducin-like proteins interact with the substrate to assist the overall folding process in a substrate-specific manner. Coevolution between the components is supposed to consult the binding specificity and ultimately expand the substrate repertoire assisted by the chaperone network. This review describes the TRiC chaperonin and the substrate folding process guided by the TRiC network in cooperation with cochaperones, specifically focusing on recent progress in structural analyses.
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Affiliation(s)
- Hyunmin Kim
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsun Park
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Soung-Hun Roh
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea.
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2
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Araki K, Watanabe-Nakayama T, Sasaki D, Sasaki YC, Mio K. Molecular Dynamics Mappings of the CCT/TRiC Complex-Mediated Protein Folding Cycle Using Diffracted X-ray Tracking. Int J Mol Sci 2023; 24:14850. [PMID: 37834298 PMCID: PMC10573753 DOI: 10.3390/ijms241914850] [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: 08/29/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
The CCT/TRiC complex is a type II chaperonin that undergoes ATP-driven conformational changes during its functional cycle. Structural studies have provided valuable insights into the mechanism of this process, but real-time dynamics analyses of mammalian type II chaperonins are still scarce. We used diffracted X-ray tracking (DXT) to investigate the intramolecular dynamics of the CCT complex. We focused on three surface-exposed loop regions of the CCT1 subunit: the loop regions of the equatorial domain (E domain), the E and intermediate domain (I domain) juncture near the ATP-binding region, and the apical domain (A domain). Our results showed that the CCT1 subunit predominantly displayed rotational motion, with larger mean square displacement (MSD) values for twist (χ) angles compared with tilt (θ) angles. Nucleotide binding had a significant impact on the dynamics. In the absence of nucleotides, the region between the E and I domain juncture could act as a pivotal axis, allowing for greater motion of the E domain and A domain. In the presence of nucleotides, the nucleotides could wedge into the ATP-binding region, weakening the role of the region between the E and I domain juncture as the rotational axis and causing the CCT complex to adopt a more compact structure. This led to less expanded MSD curves for the E domain and A domain compared with nucleotide-absent conditions. This change may help to stabilize the functional conformation during substrate binding. This study is the first to use DXT to probe the real-time molecular dynamics of mammalian type II chaperonins at the millisecond level. Our findings provide new insights into the complex dynamics of chaperonins and their role in the functional folding cycle.
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Affiliation(s)
- Kazutaka Araki
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan;
| | - Takahiro Watanabe-Nakayama
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan;
| | - Daisuke Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan (Y.C.S.)
| | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan (Y.C.S.)
| | - Kazuhiro Mio
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan;
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3
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Peck A, Chang HY, Dujardin A, Ramalingam D, Uervirojnangkoorn M, Wang Z, Mancuso A, Poitevin F, Yoon CH. Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules. J Appl Crystallogr 2022; 55:1002-1010. [PMID: 35974743 PMCID: PMC9348890 DOI: 10.1107/s1600576722005994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
X-ray free-electron lasers (XFELs) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges in terms of both experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classifiers using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. Skopi is a resource to aid feasibility studies and advance the development of algorithms for noncrystalline experiments at XFEL facilities.
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Affiliation(s)
- Ariana Peck
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Hsing-Yin Chang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Antoine Dujardin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Deeban Ramalingam
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Monarin Uervirojnangkoorn
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Zhaoyou Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Adrian Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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Subtomogram analysis: The sum of a tomogram's particles reveals molecular structure in situ. J Struct Biol X 2022; 6:100063. [PMID: 36684812 PMCID: PMC9846452 DOI: 10.1016/j.yjsbx.2022.100063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/25/2023] Open
Abstract
Cryo-electron tomography is uniquely suited to provide insights into the molecular architecture of cells and tissue in the native state. While frozen hydrated specimens tolerate sufficient electron doses to distinguish different types of particles in a tomogram, the accumulating beam damage does not allow resolving their detailed molecular structure individually. Statistical methods for subtomogram averaging and classification that coherently enhance the signal of particles corresponding to copies of the same type of macromolecular allow obtaining much higher resolution insights into macromolecules. Here, I review the developments in subtomogram analysis at Wolfgang Baumeister's laboratory that make the dream of structural biology in the native cell become reality.
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Chang WH, Huang SH, Lin HH, Chung SC, Tu IP. Cryo-EM Analyses Permit Visualization of Structural Polymorphism of Biological Macromolecules. FRONTIERS IN BIOINFORMATICS 2021; 1:788308. [PMID: 36303748 PMCID: PMC9580929 DOI: 10.3389/fbinf.2021.788308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
The functions of biological macromolecules are often associated with conformational malleability of the structures. This phenomenon of chemically identical molecules with different structures is coined structural polymorphism. Conventionally, structural polymorphism is observed directly by structural determination at the density map level from X-ray crystal diffraction. Although crystallography approach can report the conformation of a macromolecule with the position of each atom accurately defined in it, the exploration of structural polymorphism and interpreting biological function in terms of crystal structures is largely constrained by the crystal packing. An alternative approach to studying the macromolecule of interest in solution is thus desirable. With the advancement of instrumentation and computational methods for image analysis and reconstruction, cryo-electron microscope (cryo-EM) has been transformed to be able to produce “in solution” structures of macromolecules routinely with resolutions comparable to crystallography but without the need of crystals. Since the sample preparation of single-particle cryo-EM allows for all forms co-existing in solution to be simultaneously frozen, the image data contain rich information as to structural polymorphism. The ensemble of structure information can be subsequently disentangled through three-dimensional (3D) classification analyses. In this review, we highlight important examples of protein structural polymorphism in relation to allostery, subunit cooperativity and function plasticity recently revealed by cryo-EM analyses, and review recent developments in 3D classification algorithms including neural network/deep learning approaches that would enable cryo-EM analyese in this regard. Finally, we brief the frontier of cryo-EM structure determination of RNA molecules where resolving the structural polymorphism is at dawn.
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Affiliation(s)
- Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- *Correspondence: Wei-Hau Chang,
| | | | - Hsin-Hung Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Szu-Chi Chung
- Department of Applied Mathematics, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - I-Ping Tu
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
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Ecoffet A, Woollard G, Kushner A, Poitevin F, Duc KD. Application of transport-based metric for continuous interpolation between cryo-EM density maps. AIMS MATHEMATICS 2021; 7:986-999. [PMID: 35975027 PMCID: PMC9377683 DOI: 10.3934/math.2022059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) has become widely used for the past few years in structural biology, to collect single images of macromolecules "frozen in time". As this technique facilitates the identification of multiple conformational states adopted by the same molecule, a direct product of it is a set of 3D volumes, also called EM maps. To gain more insights on the possible mechanisms that govern transitions between different states, and hence the mode of action of a molecule, we recently introduced a bioinformatic tool that interpolates and generates morphing trajectories joining two given EM maps. This tool is based on recent advances made in optimal transport, that allow efficient evaluation of Wasserstein barycenters of 3D shapes. As the overall performance of the method depends on various key parameters, including the sensitivity of the regularization parameter, we performed various numerical experiments to demonstrate how MorphOT can be applied in different contexts and settings. Finally, we discuss current limitations and further potential connections between other optimal transport theories and the conformational heterogeneity problem inherent with cryo-EM data.
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Affiliation(s)
- Arthur Ecoffet
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC V6T1Z4, Canada
| | - Geoffrey Woollard
- Department of Computer Science, University of British Columbia, 2366 Main Mall #201, Vancouver, BC V6T1Z4, Canada
| | - Artem Kushner
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC V6T1Z4, Canada
| | - Frédéric Poitevin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Khanh Dao Duc
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC V6T1Z4, Canada
- Department of Computer Science, University of British Columbia, 2366 Main Mall #201, Vancouver, BC V6T1Z4, Canada
- Department of Zoology, University of British Columbia, 4200 - 6270 University Blvd., Vancouver, BC V6T1Z4, Canada
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7
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CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin. Nat Commun 2021; 12:4754. [PMID: 34362932 PMCID: PMC8346469 DOI: 10.1038/s41467-021-25099-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/21/2021] [Indexed: 12/05/2022] Open
Abstract
Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here, the authors employ an approach that uses cryo-EM single particle analysis to track the number and distribution of nucleotides bound to each subunit in the homo-oligomeric MmCpn archaeal chaperonin complex and observe that ATP binds in a statistically random manner to MmCpn both within a ring and across the rings, which shows that there is no cooperativity in ATP binding to archaeal group II chaperonins under the conditions used in this study.
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Kommera PR, Ramakrishnaiah V, Sweeney C, Donatelli J, Zwart PH. GPU-accelerated multitiered iterative phasing algorithm for fluctuation X-ray scattering. J Appl Crystallogr 2021; 54:1179-1188. [PMID: 34429723 PMCID: PMC8366419 DOI: 10.1107/s1600576721005744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 06/02/2021] [Indexed: 11/16/2022] Open
Abstract
The multitiered iterative phasing (MTIP) algorithm is used to determine the biological structures of macromolecules from fluctuation scattering data. It is an iterative algorithm that reconstructs the electron density of the sample by matching the computed fluctuation X-ray scattering data to the external observations, and by simultaneously enforcing constraints in real and Fourier space. This paper presents the first ever MTIP algorithm acceleration efforts on contemporary graphics processing units (GPUs). The Compute Unified Device Architecture (CUDA) programming model is used to accelerate the MTIP algorithm on NVIDIA GPUs. The computational performance of the CUDA-based MTIP algorithm implementation outperforms the CPU-based version by an order of magnitude. Furthermore, the Heterogeneous-Compute Interface for Portability (HIP) runtime APIs are used to demonstrate portability by accelerating the MTIP algorithm across NVIDIA and AMD GPUs.
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Affiliation(s)
- Pranay Reddy Kommera
- Applied Computer Science, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Department of Electrical and Computer Engineering, University of Wyoming, Laramie, WY 82071, USA
| | - Vinay Ramakrishnaiah
- Applied Computer Science, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Christine Sweeney
- Applied Computer Science, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jeffrey Donatelli
- Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Applied Mathematics, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Petrus H. Zwart
- Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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9
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Hiller S. Molecular chaperones and their denaturing effect on client proteins. JOURNAL OF BIOMOLECULAR NMR 2021; 75:1-8. [PMID: 33136251 PMCID: PMC7897196 DOI: 10.1007/s10858-020-00353-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/23/2020] [Indexed: 05/05/2023]
Abstract
Advanced NMR methods combined with biophysical techniques have recently provided unprecedented insight into structure and dynamics of molecular chaperones and their interaction with client proteins. These studies showed that several molecular chaperones are able to dissolve aggregation-prone polypeptides in aqueous solution. Furthermore, chaperone-bound clients often feature fluid-like backbone dynamics and chaperones have a denaturing effect on clients. Interestingly, these effects that chaperones have on client proteins resemble the effects of known chaotropic substances. Following this analogy, chaotropicity could be a fruitful concept to describe, quantify and rationalize molecular chaperone function. In addition, the observations raise the possibility that at least some molecular chaperones might share functional similarities with chaotropes. We discuss these concepts and outline future research in this direction.
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Affiliation(s)
- Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstr. 70, 4056, Basel, Switzerland.
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10
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Ecoffet A, Poitevin F, Duc KD. MorphOT: Transport-based interpolation between EM maps with UCSF ChimeraX. Bioinformatics 2020; 36:5528-5529. [PMID: 33325492 DOI: 10.1093/bioinformatics/btaa1019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/06/2020] [Accepted: 11/25/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Cryogenic Electron-Microscopy offers the unique potential to capture conformational heterogeneity, by solving multiple 3 D classes that co-exist within a single cryo-EM image dataset. To investigate the extent and implications of such heterogeneity, we propose to use an optimal-transport based metric to interpolate barycenters between EM maps and produce morphing trajectories. RESULTS While standard linear interpolation mostly fails to produce realistic transitions, our method yields continuous trajectories that displace densities to morph one map into the other, instead of blending them. AVAILABILITY Our method is implemented as a plug-in for ChimeraX called MorphOT, which allows the use of both CPU or GPU resources. The code is publicly available on GitHub (https://github.com/kdd-ubc/MorphOT.git), with documentation containing tutorial and datasets. SUPPLEMENTARY INFORMATION User manual for MorphOT is available at Bioinformatics online.
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Affiliation(s)
- Arthur Ecoffet
- Department of Mathematics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Applied Mathematics, Ecole Polytechnique, Palaiseau, 91120, France
| | - Frédéric Poitevin
- Department of Data Analytics, LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Khanh Dao Duc
- Department of Mathematics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Computer Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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11
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Pretto C, van Hest JCM. Versatile Reversible Cross-Linking Strategy to Stabilize CCMV Virus Like Particles for Efficient siRNA Delivery. Bioconjug Chem 2019; 30:3069-3077. [PMID: 31765129 PMCID: PMC6923791 DOI: 10.1021/acs.bioconjchem.9b00731] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Virus like particles obtained from the Cowpea Chlorotic
Mottle
Virus (CCMV) represent an innovative platform for drug delivery applications.
Their unique reversible self-assembly properties as well as their
suitability for both cargo loading and functionalization make them
a versatile scaffold for numerous purposes. One of the main drawbacks
of this platform is however its limited stability at physiological
conditions. Herein, we report the development of a general reversible
cross-linking strategy involving the homobifunctional cross-linker
DTSSP (3,3′-dithiobis (sulfosuccinimidylpropionate)) which
is suitable for particle stabilization. This methodology is adaptable
to different CCMV variants in the presence or absence of a stabilizing
cargo without varying neither particle shape nor size thus extending
the potential use of these protein cages in nanomedical applications.
Cross-linked particles are stable at neutral pH and 37 °C and
they are capable of protecting loaded cargo against enzymatic digestion.
Furthermore, the reversible nature of the cross-linking ensures particle
disassembly when they are taken up by cells. This was demonstrated
via the highly effective delivery of active siRNA into cells.
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Affiliation(s)
- Chiara Pretto
- Eindhoven University of Technology , Institute for Complex Molecular Systems , PO Box 513, 5600 MB Eindhoven , The Netherlands
| | - Jan C M van Hest
- Eindhoven University of Technology , Institute for Complex Molecular Systems , PO Box 513, 5600 MB Eindhoven , The Netherlands
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12
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Zheng J, Zheng J, Ma Y, Zuo G, Feng Y. The role of Lys2-Cl - -Lys2 salt linkages in oligomeric intermediates of RbsD protein in Escherichia coli. J Basic Microbiol 2019; 60:185-194. [PMID: 31588591 DOI: 10.1002/jobm.201900337] [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: 06/19/2019] [Revised: 09/07/2019] [Accepted: 09/13/2019] [Indexed: 11/06/2022]
Abstract
As a homo-oligomeric protein, the disassembly of Escherichia coli RbsD decamer produces a urea-unfolded oligomeric intermediate structure, as the dissociation speed of the protein is lower than that of the unfolding process. There are five Lys2-Cl- -Lys2 salt linkages to connect these subunits. To explore the role of the salt linkages in these oligomeric intermediates, the Lys2Ala mutated in the N-terminal of E. coli RbsD protein subunit was designed. It was found that the RbsD mutation protein (RbsD:K2A) loses its minor larger oligomers, which exist in RbsD, and displays other several oligomeric states (less than decamers), meanwhile the state of the oligomers depends on the protein concentration. It was also found that compared with RbsD, the crosslinking capability of the subunits of RbsD:K2A is weaker, while the crosslinking rate of dimers is higher, RbsD:K2A needs to substantially adjust its conformation to meet the space requirements when combined with d-ribose. On the basis of these results, we suggest that Lys2-Cl- -Lys2 salt linkages in E. coli RbsD protein play an important role in stabilizing the intermediate products of oligomers and maintaining interaction between the intermediate products of oligomers, which may shed light on the study of these oligomeric proteins.
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Affiliation(s)
- Jing Zheng
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Jie Zheng
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yuanwu Ma
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Guocai Zuo
- School of Software and Information Engineering, Hunan Software Vocational Institute, Xiangtan, China
| | - Yongjun Feng
- School of Life Science, Beijing Institute of Technology, Beijing, China
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13
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An ensemble of cryo-EM structures of TRiC reveal its conformational landscape and subunit specificity. Proc Natl Acad Sci U S A 2019; 116:19513-19522. [PMID: 31492816 PMCID: PMC6765261 DOI: 10.1073/pnas.1903976116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The ATP-fueled TRiC/CCT acts in the folding of 10% cytosolic proteins. TRiC consists of 8 paralogous subunits, each of which plays special roles in TRiC assembly, allosteric cooperativity, and substrate folding. However, due to lack of a thorough picture of TRiC conformational landscape and atomic-resolution details, the underlying structural mechanisms of TRiC subunit specificity in nucleotide usage and substrate binding, and the allosteric transition during ring closure remain unclear. Here, through cryo-electron microscopy (cryo-EM) analysis, we captured a thorough picture of TRiC conformational landscape from open to closed states and its gradually enhanced allosteric coordination, including the N termini, in unprecedented structural detail. Our study also offers insights into the TRiC subunit specificities in nucleotide usage and ring closure. TRiC/CCT assists the folding of ∼10% of cytosolic proteins through an ATP-driven conformational cycle and is essential in maintaining protein homeostasis. Here, we determined an ensemble of cryo-electron microscopy (cryo-EM) structures of yeast TRiC at various nucleotide concentrations, with 4 open-state maps resolved at near-atomic resolutions, and a closed-state map at atomic resolution, revealing an extra layer of an unforeseen N-terminal allosteric network. We found that, during TRiC ring closure, the CCT7 subunit moves first, responding to nucleotide binding; CCT4 is the last to bind ATP, serving as an ATP sensor; and CCT8 remains ADP-bound and is hardly involved in the ATPase-cycle in our experimental conditions; overall, yeast TRiC consumes nucleotide in a 2-ring positively coordinated manner. Our results depict a thorough picture of the TRiC conformational landscape and its allosteric transitions from the open to closed states in more structural detail and offer insights into TRiC subunit specificity in ATP consumption and ring closure, and potentially in substrate processing.
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14
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Zhang PF, Su JG. Identification of key sites controlling protein functional motions by using elastic network model combined with internal coordinates. J Chem Phys 2019; 151:045101. [PMID: 31370540 DOI: 10.1063/1.5098542] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The elastic network model (ENM) is an effective method to extract the intrinsic dynamical properties encoded in protein tertiary structures. We have proposed a new ENM-based analysis method to reveal the motion modes directly responsible for a specific protein function, in which an internal coordinate related to the specific function was introduced to construct the internal/Cartesian hybrid coordinate space. In the present work, the function-related internal coordinates combined with a linear perturbation method were applied to identify the key sites controlling specific protein functional motions. The change in the fluctuations of the internal coordinate in response to residue perturbation was calculated in the hybrid coordinate space by using the linear response theory. The residues with the large fluctuation changes were identified to be the key sites that allosterically control the specific protein function. Two proteins, i.e., human DNA polymerase β and the chaperonin from Methanococcus maripaludis, were investigated as case studies, in which several collective and local internal coordinates were applied to identify the functionally key residues of these two studied proteins. The calculation results are consistent with the experimental observations. It is found that different collective internal coordinates lead to similar results, where the predicted functionally key sites are located at similar positions in the protein structure. While for the local internal coordinates, the predicted key sites tend to be situated at the region near to the coordinate-involving residues. Our studies provide a starting point for further exploring other function-related internal coordinates for other interesting proteins.
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Affiliation(s)
- Peng Fei Zhang
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
| | - Ji Guo Su
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
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15
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Balancing the Photoreceptor Proteome: Proteostasis Network Therapeutics for Inherited Retinal Disease. Genes (Basel) 2019; 10:genes10080557. [PMID: 31344897 PMCID: PMC6722924 DOI: 10.3390/genes10080557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 12/17/2022] Open
Abstract
The light sensing outer segments of photoreceptors (PRs) are renewed every ten days due to their high photoactivity, especially of the cones during daytime vision. This demands a tremendous amount of energy, as well as a high turnover of their main biosynthetic compounds, membranes, and proteins. Therefore, a refined proteostasis network (PN), regulating the protein balance, is crucial for PR viability. In many inherited retinal diseases (IRDs) this balance is disrupted leading to protein accumulation in the inner segment and eventually the death of PRs. Various studies have been focusing on therapeutically targeting the different branches of the PR PN to restore the protein balance and ultimately to treat inherited blindness. This review first describes the different branches of the PN in detail. Subsequently, insights are provided on how therapeutic compounds directed against the different PN branches might slow down or even arrest the appalling, progressive blinding conditions. These insights are supported by findings of PN modulators in other research disciplines.
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16
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Gestaut D, Limatola A, Joachimiak L, Frydman J. The ATP-powered gymnastics of TRiC/CCT: an asymmetric protein folding machine with a symmetric origin story. Curr Opin Struct Biol 2019; 55:50-58. [PMID: 30978594 DOI: 10.1016/j.sbi.2019.03.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
Abstract
The eukaryotic chaperonin TRiC/CCT is a large hetero-oligomeric complex that plays an essential role assisting cellular protein folding and suppressing protein aggregation. It consists of two rings, and each composed of eight different subunits; non-native polypeptides bind and fold in an ATP-dependent manner within their central chamber. Here, we review recent advances in our understanding of TRiC structure and mechanism enabled by application of hybrid structural methods including the integration of cryo-electron microscopy with distance constraints from crosslinking mass spectrometry. These new insights are revealing how the different TRiC/CCT subunits create asymmetry in its ATP-driven conformational cycle and its interaction with non-native polypeptides, which ultimately underlie its unique ability to fold proteins that cannot be folded by other chaperones.
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Affiliation(s)
- Daniel Gestaut
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA
| | - Antonio Limatola
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA
| | - Lukasz Joachimiak
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA.
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17
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Conway de Macario E, Yohda M, Macario AJL, Robb FT. Bridging human chaperonopathies and microbial chaperonins. Commun Biol 2019; 2:103. [PMID: 30911678 PMCID: PMC6420498 DOI: 10.1038/s42003-019-0318-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/15/2019] [Indexed: 12/19/2022] Open
Abstract
Chaperonins are molecular chaperones that play critical physiological roles, but they can be pathogenic. Malfunctional chaperonins cause chaperonopathies of great interest within various medical specialties. Although the clinical-genetic aspects of many chaperonopathies are known, the molecular mechanisms causing chaperonin failure and tissue lesions are poorly understood. Progress is necessary to improve treatment, and experimental models that mimic the human situation provide a promising solution. We present two models: one prokaryotic (the archaeon Pyrococcus furiosus) with eukaryotic-like chaperonins and one eukaryotic (Chaetomium thermophilum), both convenient for isolation-study of chaperonins, and report illustrative results pertaining to a pathogenic mutation of CCT5.
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Affiliation(s)
- Everly Conway de Macario
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Columbus Center, Baltimore, MD USA
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Koganei, Tokyo Japan
| | - Alberto J. L. Macario
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Columbus Center, Baltimore, MD USA
- Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Frank T. Robb
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Columbus Center, Baltimore, MD USA
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD USA
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18
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Abstract
The eukaryotic group II chaperonin TRiC/CCT assists the folding of 10% of cytosolic proteins including many key structural and regulatory proteins. TRiC plays an essential role in maintaining protein homeostasis, and dysfunction of TRiC is closely related to human diseases including cancer and neurodegenerative diseases. TRiC consists of eight paralogous subunits, each of which plays a specific role in the assembly, allosteric cooperativity, and substrate recognition and folding of this complex macromolecular machine. TRiC-mediated substrate folding is regulated through its ATP-driven conformational changes. In recent years, progresses have been made on the structure, subunit arrangement, conformational cycle, and substrate folding of TRiC. Additionally, accumulating evidences also demonstrate the linkage between TRiC oligomer or monomer and diseases. In this review, we focus on the TRiC structure itself, TRiC assisted substrate folding, TRiC and disease, and the potential therapeutic application of TRiC in various diseases.
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Affiliation(s)
- Mingliang Jin
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Caixuan Liu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wenyu Han
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yao Cong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China.
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19
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Abstract
Molecular chaperones promote the correct folding of proteins in aggregation-prone cellular environments by stabilizing nascent polypeptide chains and providing appropriate folding conditions. Prefoldins (PFDs) are molecular chaperones found in archaea and eukaryotes, generally characterized by a unique jellyfish-like hexameric structure consisting of a rigid beta-barrel backbone with protruding flexible coiled-coils. Unlike eukaryotic PFDs that mainly interact with cytoskeletal components, archaeal PFDs can stabilize a wide range of substrates; such versatility reflects PFD's role as a key element in archaeal chaperone systems, which often lack general nascent-chain binding chaperone components such as Hsp70. While archaeal PFDs mainly exist as hexameric complexes, their structural diversity ranges from tetramers to filamentous oligomers. PFDs bind and stabilize nonnative proteins using varying numbers of coiled-coils, and subsequently transfer the substrate to a group II chaperonin (CPN) for refolding. The distinct structure and specific function of archaeal PFDs have been exploited for a broad range of applications in biotechnology; furthermore, a filament-forming variant of PFD has been used to fabricate nanoscale architectures of defined shapes, demonstrating archaeal PFDs' potential applicability in nanotechnology.
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Affiliation(s)
- Samuel Lim
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Douglas S Clark
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA.
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20
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Sokolov M, Yadav RP, Brooks C, Artemyev NO. Chaperones and retinal disorders. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:85-117. [PMID: 30635087 DOI: 10.1016/bs.apcsb.2018.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Defects in protein folding and trafficking are a common cause of photoreceptor degeneration, causing blindness. Photoreceptor cells present an unusual challenge to the protein folding and transport machinery due to the high rate of protein synthesis, trafficking and the renewal of the outer segment, a primary cilium that has been modified into a specialized light-sensing compartment. Phototransduction components, such as rhodopsin and cGMP-phosphodiesterase, and multimeric ciliary transport complexes, such as the BBSome, are hotspots for mutations that disrupt proteostasis and lead to the death of photoreceptors. In this chapter, we review recent studies that advance our understanding of the chaperone and transport machinery of phototransduction proteins.
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Affiliation(s)
- Maxim Sokolov
- Department of Ophthalmology, West Virginia University, Morgantown, WV, United States
| | - Ravi P Yadav
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Celine Brooks
- Department of Ophthalmology, West Virginia University, Morgantown, WV, United States
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, United States.
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21
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Mas G, Guan JY, Crublet E, Debled EC, Moriscot C, Gans P, Schoehn G, Macek P, Schanda P, Boisbouvier J. Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. SCIENCE ADVANCES 2018; 4:eaau4196. [PMID: 30255156 PMCID: PMC6154984 DOI: 10.1126/sciadv.aau4196] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/01/2018] [Indexed: 05/03/2023]
Abstract
Chaperonins are ubiquitous protein assemblies present in bacteria, eukaryota, and archaea, facilitating the folding of proteins, preventing protein aggregation, and thus participating in maintaining protein homeostasis in the cell. During their functional cycle, they bind unfolded client proteins inside their double ring structure and promote protein folding by closing the ring chamber in an adenosine 5'-triphosphate (ATP)-dependent manner. Although the static structures of fully open and closed forms of chaperonins were solved by x-ray crystallography or electron microscopy, elucidating the mechanisms of such ATP-driven molecular events requires studying the proteins at the structural level under working conditions. We introduce an approach that combines site-specific nuclear magnetic resonance observation of very large proteins, enabled by advanced isotope labeling methods, with an in situ ATP regeneration system. Using this method, we provide functional insight into the 1-MDa large hsp60 chaperonin while processing client proteins and reveal how nucleotide binding, hydrolysis, and release control switching between closed and open states. While the open conformation stabilizes the unfolded state of client proteins, the internalization of the client protein inside the chaperonin cavity speeds up its functional cycle. This approach opens new perspectives to study structures and mechanisms of various ATP-driven biological machineries in the heat of action.
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Affiliation(s)
| | | | | | | | | | | | | | - Pavel Macek
- Corresponding author. (P.M.); (P.S.); (J.B.)
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22
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Bhatt JM, Enriquez AS, Wang J, Rojo HM, Molugu SK, Hildenbrand ZL, Bernal RA. Single-Ring Intermediates Are Essential for Some Chaperonins. Front Mol Biosci 2018; 5:42. [PMID: 29755985 PMCID: PMC5934643 DOI: 10.3389/fmolb.2018.00042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/13/2018] [Indexed: 11/20/2022] Open
Abstract
Chaperonins are macromolecular complexes found throughout all kingdoms of life that assist unfolded proteins reach a biologically active state. Historically, chaperonins have been classified into two groups based on sequence, subunit structure, and the requirement for a co-chaperonin. Here, we present a brief review of chaperonins that can form double- and single-ring conformational intermediates in their protein-folding catalytic pathway. To date, the bacteriophage encoded chaperonins ϕ-EL and OBP, human mitochondrial chaperonin and most recently, the bacterial groEL/ES systems, have been reported to form single-ring intermediates as part of their normal protein-folding activity. These double-ring chaperonins separate into single-ring intermediates that have the ability to independently fold a protein. We discuss the structural and functional features along with the biological relevance of single-ring intermediates in cellular protein folding. Of special interest are the ϕ-EL and OBP chaperonins which demonstrate features of both group I and II chaperonins in addition to their ability to function via single-ring intermediates.
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Affiliation(s)
- Jay M Bhatt
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Adrian S Enriquez
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Jinliang Wang
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Humberto M Rojo
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Sudheer K Molugu
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | | | - Ricardo A Bernal
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
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23
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Time-Resolved Measurement of the ATP-Dependent Motion of the Group II Chaperonin by Diffracted Electron Tracking. Int J Mol Sci 2018; 19:ijms19040950. [PMID: 29565826 PMCID: PMC5979372 DOI: 10.3390/ijms19040950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/18/2018] [Accepted: 03/19/2018] [Indexed: 11/24/2022] Open
Abstract
Previously, we demonstrated the ATP-dependent dynamics of a group II chaperonin at the single-molecule level by diffracted X-ray tracking (DXT). The disadvantage of DXT is that it requires a strong X-ray source and also perfect gold nano-crystals. To resolve this problem, we developed diffracted electron tracking (DET). Electron beams have scattering cross-sections that are approximately 1000 times larger than those of X-rays. Thus, DET enables us to perform super-accurate measurements of the time-resolved 3D motion of proteins labeled with commercially available gold nanorods using a scanning electron microscope. In this study, we compared DXT and DET using the group II chaperonin from Methanococcus maripaludis (MmCpn) as a model protein. In DET, the samples are prepared in an environmental cell (EC). To reduce the electron beam-induced protein damage, we immobilized MmCpn on the bottom of the EC to expose gold nanorods close to the carbon thin film. The sample setup worked well, and the motions of gold nanorods were clearly traced. Compared with the results of DXT, the mobility in DET was significantly higher, which is probably due to the difference in the method for immobilization. In DET, MmCpn was immobilized on a film of triacetyl cellulose. Whereas proteins are directly attached on the surface of solid support in DXT. Therefore, MmCpn could move relatively freely in DET. DET will be a state-of-the-art technology for analyzing protein dynamics.
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24
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Ding J, Li J, Yang D, Yang F, Nie H, Huo Z, Yan X. Molecular characteristics of a novel HSP60 gene and its differential expression in Manila clams (Ruditapes philippinarum) under thermal and hypotonic stress. Cell Stress Chaperones 2018; 23:179-187. [PMID: 29273967 PMCID: PMC5823800 DOI: 10.1007/s12192-017-0796-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/07/2017] [Accepted: 04/05/2017] [Indexed: 11/26/2022] Open
Abstract
The Manila clam Ruditapes philippinarum inhabits the intertidal zone and must therefore tolerate broad fluctuations in water temperature and salinity. Heat shock protein 60 (HSP60) is an evolutionarily conserved, multi-functional protein that plays a significant role in protecting organisms from harmful stress conditions. We cloned the R. philippinarum HSP60 (RpHSP60) gene and analyzed its transcriptional responses to thermal and low-salinity stresses. The complete sequence of RpHSP60 cDNA was 1777 nucleotides, containing a 1728-bp open reading frame encoding a polypeptide of 576-amino acids, with a calculated molecular mass of 61.25 kDa and predicted isoelectric point of 5.08. Comparisons of amino acid sequences and three-dimensional structures of HSP60 revealed that RpHSP60 was highly conserved in the signature HSP60-family domains. RpHSP60 mRNA was detected in all the tested tissues of R. philippinarum, with the highest expression levels in hemocytes. We measured RpHSP60 mRNA levels in the gills under thermal and low-salinity stresses using quantitative real-time reverse transcription-polymerase chain reaction. Following the thermal challenge, RpHSP60 mRNA was significantly upregulated at 6 h, and then progressively downregulated under high-temperature stress (30 °C), while only slight fluctuations were observed under low-temperature stress (-1 °C). Under low-salinity (17 ppt) stress, RpHSP60 mRNA levels were significantly increased at 3, 72, and 96 h (P < 0.05). These results suggest that HSP60 of R. philippinarum may play important roles in responding to high-temperature and low-salinity stresses.
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Affiliation(s)
- Jianfeng Ding
- Dalian Ocean University, 52 Heishijiao street, Dalian, 116023, China
- Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China
| | - Jia Li
- Dalian Ocean University, 52 Heishijiao street, Dalian, 116023, China
- Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China
| | - Dongmin Yang
- Dalian Ocean University, 52 Heishijiao street, Dalian, 116023, China
- Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China
| | - Feng Yang
- Dalian Ocean University, 52 Heishijiao street, Dalian, 116023, China
- Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China
| | - Hongtao Nie
- Dalian Ocean University, 52 Heishijiao street, Dalian, 116023, China
- Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China
| | - Zhongming Huo
- Dalian Ocean University, 52 Heishijiao street, Dalian, 116023, China
- Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China
| | - Xiwu Yan
- Dalian Ocean University, 52 Heishijiao street, Dalian, 116023, China.
- Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China.
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25
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Shoemark DK, Sessions RB, Brancaccio A, Bigotti MG. Intraring allostery controls the function and assembly of a hetero-oligomeric class II chaperonin. FASEB J 2018; 32:2223-2234. [PMID: 29233859 PMCID: PMC5983026 DOI: 10.1096/fj.201701061r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Class II chaperonins are essential multisubunit complexes that aid the folding of nonnative proteins in the cytosol of archaea and eukarya. They use energy derived from ATP to drive a series of structural rearrangements that enable polypeptides to fold within their central cavity. These events are regulated by an elaborate allosteric mechanism in need of elucidation. We employed mutagenesis and experimental analysis in concert with in silico molecular dynamics simulations and interface-binding energy calculations to investigate the class II chaperonin from Thermoplasma acidophilum. Here we describe the effects on the asymmetric allosteric mechanism and on hetero-oligomeric complex formation in a panel of mutants in the ATP-binding pocket of the α and β subunits. Our observations reveal a potential model for a nonconcerted folding mechanism optimized for protecting and refolding a range of nonnative substrates under different environmental conditions, starting to unravel the role of subunit heterogeneity in this folding machine and establishing important links with the behavior of the most complex eukaryotic chaperonins.—Shoemark, D. K., Sessions, R. B., Brancaccio, A., Bigotti, M. G. Intraring allostery controls the function and assembly of a hetero-oligomeric class II chaperonin.
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Affiliation(s)
| | | | - Andrea Brancaccio
- School of Biochemistry, University of Bristol, Bristol, United Kingdom.,Istituto di Chimica del Riconoscimento Molecolare-Consiglio Nazionale delle Ricerche (CNR), Università Cattolica del Sacro Cuore, Rome, Italy
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26
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An YJ, Rowland SE, Na JH, Spigolon D, Hong SK, Yoon YJ, Lee JH, Robb FT, Cha SS. Structural and mechanistic characterization of an archaeal-like chaperonin from a thermophilic bacterium. Nat Commun 2017; 8:827. [PMID: 29018216 PMCID: PMC5635000 DOI: 10.1038/s41467-017-00980-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/08/2017] [Indexed: 11/13/2022] Open
Abstract
The chaperonins (CPNs) are megadalton sized hollow complexes with two cavities that open and close to encapsulate non-native proteins. CPNs are assigned to two sequence-related groups that have distinct allosteric mechanisms. In Group I CPNs a detachable co-chaperone, GroES, closes the chambers whereas in Group II a built-in lid closes the chambers. Group I CPNs have a bacterial ancestry, whereas Group II CPNs are archaeal in origin. Here we describe open and closed crystal structures representing a new phylogenetic branch of CPNs. These Group III CPNs are divergent in sequence and structure from extant CPNs, but are closed by a built-in lid like Group II CPNs. A nucleotide-sensing loop, present in both Group I and Group II CPNs, is notably absent. We identified inter-ring pivot joints that articulate during ring closure. These Group III CPNs likely represent a relic from the ancestral CPN that formed distinct bacterial and archaeal branches. Chaperonins (CPNs) are ATP-dependent protein-folding machines. Here the authors present the open and closed crystal structures of a Group III CPN from the thermophilic bacterium Carboxydothermus hydrogenoformans, discuss its mechanism and structurally compare it with Group I and II CPNs.
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Affiliation(s)
- Young Jun An
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Sara E Rowland
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA.,Institute of Marine and Environmental Technology, Baltimore, MD, 21201, USA
| | - Jung-Hyun Na
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Dario Spigolon
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA.,Institute of Marine and Environmental Technology, Baltimore, MD, 21201, USA
| | - Seung Kon Hong
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Frank T Robb
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA. .,Institute of Marine and Environmental Technology, Baltimore, MD, 21201, USA.
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea.
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27
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Lopez T, Dalton K, Tomlinson A, Pande V, Frydman J. An information theoretic framework reveals a tunable allosteric network in group II chaperonins. Nat Struct Mol Biol 2017; 24:726-733. [PMID: 28741612 PMCID: PMC5986071 DOI: 10.1038/nsmb.3440] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 06/22/2017] [Indexed: 12/19/2022]
Abstract
ATP-dependent allosteric regulation of the ring-shaped group II chaperonins remains ill defined, in part because their complex oligomeric topology has limited the success of structural techniques in suggesting allosteric determinants. Further, their high sequence conservation has hindered the prediction of allosteric networks using mathematical covariation approaches. Here, we develop an information theoretic strategy that is robust to residue conservation and apply it to group II chaperonins. We identify a contiguous network of covarying residues that connects all nucleotide-binding pockets within each chaperonin ring. An interfacial residue between the networks of neighboring subunits controls positive cooperativity by communicating nucleotide occupancy within each ring. Strikingly, chaperonin allostery is tunable through single mutations at this position. Naturally occurring variants at this position that double the extent of positive cooperativity are less prevalent in nature. We propose that being less cooperative than attainable allows chaperonins to support robust folding over a wider range of metabolic conditions.
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Affiliation(s)
- Tom Lopez
- Department of Biology, Stanford University, Stanford, California, USA
| | - Kevin Dalton
- Biophysics Program, Stanford University, Stanford, California, USA
| | - Anthony Tomlinson
- Department of Biology, Stanford University, Stanford, California, USA
| | - Vijay Pande
- Biophysics Program, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, California, USA
- Biophysics Program, Stanford University, Stanford, California, USA
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28
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Roh SH, Hryc CF, Jeong HH, Fei X, Jakana J, Lorimer GH, Chiu W. Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM. Proc Natl Acad Sci U S A 2017; 114:8259-8264. [PMID: 28710336 PMCID: PMC5547627 DOI: 10.1073/pnas.1704725114] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many particles with presumed identical conformations. We used a 3.5-Å cryo-EM reconstruction with imposed D7 symmetry to further analyze structural heterogeneity among chemically identical subunits in each GroEL oligomer. Focused classification of the 14 subunits in each oligomer revealed three dominant classes of subunit conformations. Each class resembled a distinct GroEL crystal structure in the Protein Data Bank. The conformational differences stem from the orientations of the apical domain. We mapped each conformation class to its subunit locations within each GroEL oligomer in our dataset. The spatial distributions of each conformation class differed among oligomers, and most oligomers contained 10-12 subunits of the three dominant conformation classes. Adjacent subunits were found to more likely assume the same conformation class, suggesting correlation among subunits in the oligomer. This study demonstrates the utility of cryo-EM in revealing structure dynamics within a single protein oligomer.
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Affiliation(s)
- Soung-Hun Roh
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Corey F Hryc
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030
| | - Hyun-Hwan Jeong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Xue Fei
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - George H Lorimer
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030;
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030
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29
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Ashraf R, Muhammad MA, Rashid N, Akhtar M. Cloning and characterization of thermostable GroEL/GroES homologues from Geobacillus thermopakistaniensis and their applications in protein folding. J Biotechnol 2017; 254:9-16. [PMID: 28583821 DOI: 10.1016/j.jbiotec.2017.05.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 05/25/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023]
Abstract
The chaperonin genes encoding GroELGt (ESU72018) and GroESGt (ESU72017), homologues of bacterial GroEL and GroES, from Geobacillus thermopakistaniensis were cloned and expressed in Escherichia coli. The purified gene products possessed the ATPase activity similar to other bacterial and eukaryal counterparts. Recombinant GroELGt and GroESGt were able to refold the denatured insoluble aggregates of α-amylase from Bacillus licheniformis into soluble and active form. Furthermore, GroELGt and GroESGt successfully enhanced the thermostability of porcine heart malate dehydrogenase. Expression of GroELGt gene in E. coli cells enhanced the thermotolerance of the host. Furthermore, soluble production of recombinant alcohol dehydrogenase from Bacillus subtilis strain R5 in E. coli, initially produced as insoluble aggregates, was achieved by co-expressing the gene with GroELGt. Our results implied that GroELGt could assist folding of nascent protein in E. coli with the help of host co-chaperonin without requiring additional ATP. This system can be used for soluble production of recombinant proteins which otherwise are produced in insoluble form in E. coli. To the best of our knowledge this is the first report on functional characterization and applications of chaperonins from genus Geobacillus.
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Affiliation(s)
- Raza Ashraf
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Majida Atta Muhammad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan.
| | - Muhammad Akhtar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan; School of Biological Sciences, University of Southampton, Southampton SO16 7PX, UK
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30
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Abstract
The human chaperonin TRiC consists of eight non-identical subunits, and its protein-folding activity is critical for cellular health. Misfolded proteins are associated with many human diseases, such as amyloid diseases, cancer, and neuropathies, making TRiC a potential therapeutic target. A detailed structural understanding of its ATP-dependent folding mechanism and substrate recognition is therefore of great importance. Of particular health-related interest is the mutation Histidine 147 to Arginine (H147R) in human TRiC subunit 5 (CCT5), which has been associated with hereditary sensory neuropathy. In this paper, we describe the crystal structures of CCT5 and the CCT5-H147R mutant, which provide important structural information for this vital protein-folding machine in humans. This first X-ray crystallographic study of a single human CCT subunit in the context of a hexadecameric complex can be expanded in the future to the other 7 subunits that form the TRiC complex.
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31
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Enriquez AS, Rojo HM, Bhatt JM, Molugu SK, Hildenbrand ZL, Bernal RA. The human mitochondrial Hsp60 in the APO conformation forms a stable tetradecameric complex. Cell Cycle 2017; 16:1309-1319. [PMID: 28594255 PMCID: PMC5531633 DOI: 10.1080/15384101.2017.1321180] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The human mitochondrial chaperonin is a macromolecular machine that catalyzes the proper folding of mitochondrial proteins and is of vital importance to all cells. This chaperonin is composed of 2 distinct proteins, Hsp60 and Hsp10, that assemble into large oligomeric complexes that mediate the folding of non-native polypeptides in an ATP dependent manner. Here, we report the bacterial expression and purification of fully assembled human Hsp60 and Hsp10 recombinant proteins and that Hsp60 forms a stable tetradecameric double-ring conformation in the absence of co-chaperonin and nucleotide. Evidence of the stable double-ring conformation is illustrated by the 15 Å resolution electron microscopy reconstruction presented here. Furthermore, our biochemical analyses reveal that the presence of a non-native substrate initiates ATP-hydrolysis within the Hsp60/10 chaperonin to commence protein folding. Collectively, these data provide insight into the architecture of the intermediates used by the human mitochondrial chaperonin along its protein folding pathway and lay a foundation for subsequent high resolution structural investigations into the conformational changes of the mitochondrial chaperonin.
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Affiliation(s)
- Adrian S Enriquez
- a Department of Chemistry , The University of Texas at El Paso , El Paso , TX , USA
| | - Humberto M Rojo
- a Department of Chemistry , The University of Texas at El Paso , El Paso , TX , USA
| | - Jay M Bhatt
- a Department of Chemistry , The University of Texas at El Paso , El Paso , TX , USA
| | - Sudheer K Molugu
- b Department of Pharmacology , School of Medicine, Case Western Reserve University , Cleveland , OH , USA
| | | | - Ricardo A Bernal
- a Department of Chemistry , The University of Texas at El Paso , El Paso , TX , USA
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32
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Biswas A, Ranjan D, Zubair M, Zeil S, Nasr KA, He J. An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:578-586. [PMID: 27008671 PMCID: PMC5071113 DOI: 10.1109/tcbb.2016.2543721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A key idea in de novo modeling of a medium-resolution density image obtained from cryo-electron microscopy is to compute the optimal mapping between the secondary structure traces observed in the density image and those predicted on the protein sequence. When secondary structures are not determined precisely, either from the image or from the amino acid sequence of the protein, the computational problem becomes more complex. We present an efficient method that addresses the secondary structure placement problem in presence of multiple secondary structure predictions and computes the optimal mapping. We tested the method using 12 simulated images from α-proteins and two Cryo-EM images of α-β proteins. We observed that the rank of the true topologies is consistently improved by using multiple secondary structure predictions instead of a single prediction. The results show that the algorithm is robust and works well even when errors/misses in the predicted secondary structures are present in the image or the sequence. The results also show that the algorithm is efficient and is able to handle proteins with as many as 33 helices.
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Affiliation(s)
- Abhishek Biswas
- Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529
| | - Desh Ranjan
- Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529
| | - Mohammad Zubair
- Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529
| | - Stephanie Zeil
- Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529
| | - Kamal Al Nasr
- Dept. of Computer Science, Tennessee State University, Nashville, TN 37209
| | - Jing He
- Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529
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33
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Conway de Macario E, Robb FT, Macario AJL. Prokaryotic Chaperonins as Experimental Models for Elucidating Structure-Function Abnormalities of Human Pathogenic Mutant Counterparts. Front Mol Biosci 2017; 3:84. [PMID: 28119916 PMCID: PMC5220055 DOI: 10.3389/fmolb.2016.00084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/12/2016] [Indexed: 01/29/2023] Open
Abstract
All archaea have a chaperonin of Group II (thermosome) in their cytoplasm and some have also a chaperonin of Group I (GroEL; Cpn60; Hsp60). Conversely, all bacteria have GroEL, some in various copies, but only a few have, in addition, a chaperonin (tentatively designated Group III chaperonin) very similar to that occurring in all archaea, i.e., the thermosome subunit, and in the cytosol of eukaryotic cells, named CCT. Thus, nature offers a range of prokaryotic organisms that are potentially useful as experimental models to study the human CCT and its abnormalities. This is important because many diseases, the chaperonopathies, have been identified in which abnormal chaperones, including mutant CCT, are determinant etiologic-pathogenic factors and, therefore, research is needed to elucidate their pathologic features at the molecular level. Such research should lead to the clarification of the molecular mechanisms underlying the pathologic lesions observed in the tissues and organs of patients with chaperonopathies. Information on these key issues is necessary to make progress in diagnosis and treatment. Some of the archaeal organisms as well as some of the bacterial models suitable for studying molecular aspects pertinent to human mutant chaperones are discussed here, focusing on CCT. Results obtained with the archaeon Pyrococcus furiosus model to investigate the impact of a pathogenic CCT5 mutation on molecular properties and chaperoning functions are reviewed. The pathogenic mutation examined weakens the ability of the chaperonin subunit to form stable hexadecamers and as a consequence, the chaperoning functions of the complex are impaired. The future prospect is to find means for stabilizing the hexadecamer, which should lead to a recovering of chaperone function and the improving of lesions and clinical condition.
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Affiliation(s)
- Everly Conway de Macario
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Columbus Center; Institute of Marine and Environmental TechnologyBaltimore, MD, USA; Euro-Mediterranean Institute of Science and TechnologyPalermo, Italy
| | - Frank T Robb
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Columbus Center; Institute of Marine and Environmental TechnologyBaltimore, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College ParkRockville, MD, USA
| | - Alberto J L Macario
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Columbus Center; Institute of Marine and Environmental TechnologyBaltimore, MD, USA; Euro-Mediterranean Institute of Science and TechnologyPalermo, Italy
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34
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Zang Y, Jin M, Wang H, Cui Z, Kong L, Liu C, Cong Y. Staggered ATP binding mechanism of eukaryotic chaperonin TRiC (CCT) revealed through high-resolution cryo-EM. Nat Struct Mol Biol 2016; 23:1083-1091. [PMID: 27775711 DOI: 10.1038/nsmb.3309] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/20/2016] [Indexed: 01/04/2023]
Abstract
The eukaryotic chaperonin TRiC (or CCT) assists in the folding of 10% of cytosolic proteins. Here we present two cryo-EM structures of Saccharomyces cerevisiae TRiC in a newly identified nucleotide partially preloaded (NPP) state and in the ATP-bound state, at 4.7-Å and 4.6-Å resolution, respectively. Through inner-subunit eGFP tagging, we identified the subunit locations in open-state TRiC and found that the CCT2 subunit pair forms an unexpected Z shape. ATP binding induces a dramatic conformational change on the CCT2 side, thereby suggesting that CCT2 plays an essential role in TRiC allosteric cooperativity. Our structural and biochemical data reveal a staggered ATP binding mechanism of TRiC with preloaded nucleotide on the CCT6 side of NPP-TRiC and demonstrate that TRiC has evolved into a complex that is structurally divided into two sides. This work offers insight into how the TRiC nucleotide cycle coordinates with its mechanical cycle in preparing folding intermediates for further productive folding.
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Affiliation(s)
- Yunxiang Zang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mingliang Jin
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Huping Wang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhicheng Cui
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liangliang Kong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Caixuan Liu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yao Cong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
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35
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Nussbaumer MG, Duskey JT, Rother M, Renggli K, Chami M, Bruns N. Chaperonin-Dendrimer Conjugates for siRNA Delivery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2016; 3:1600046. [PMID: 27840795 PMCID: PMC5096033 DOI: 10.1002/advs.201600046] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/13/2016] [Indexed: 05/19/2023]
Abstract
The group II chaperonin thermosome (THS) is a hollow protein nanoparticle that can encapsulate macromolecular guests. Two large pores grant access to the interior of the protein cage. Poly(amidoamine) (PAMAM) is conjugated into THS to act as an anchor for small interfering RNA (siRNA), allowing to load the THS with therapeutic payload. THS-PAMAM protects siRNA from degradation by RNase A and traffics KIF11 and GAPDH siRNA into U87 cancer cells. By modification of the protein cage with the cell-penetrating peptide TAT, RNA interference is also induced in PC-3 cells. THS-PAMAM protein-polymer conjugates are therefore promising siRNA transfection reagents and greatly expand the scope of protein cages in drug delivery applications.
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Affiliation(s)
- Martin G. Nussbaumer
- Department of ChemistryUniversity of BaselKlingelbergstrasse 804056BaselSwitzerland
| | - Jason T. Duskey
- Department of ChemistryUniversity of BaselKlingelbergstrasse 804056BaselSwitzerland
| | - Martin Rother
- Department of ChemistryUniversity of BaselKlingelbergstrasse 804056BaselSwitzerland
| | - Kasper Renggli
- Department of ChemistryUniversity of BaselKlingelbergstrasse 804056BaselSwitzerland
| | - Mohamed Chami
- C‐CINACenter for Cellular Imaging and NanoAnalytics BiozentrumUniversity of BaselMattenstrasse 264058BaselSwitzerland
| | - Nico Bruns
- Department of ChemistryUniversity of BaselKlingelbergstrasse 804056BaselSwitzerland
- Adolphe Merkle InstituteUniversity of FribourgChemin des Verdiers 41700FribourgSwitzerland
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36
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Kuzu G, Keskin O, Nussinov R, Gursoy A. PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Acta Crystallogr D Struct Biol 2016; 72:1137-1148. [PMID: 27710935 PMCID: PMC5053140 DOI: 10.1107/s2059798316013541] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/23/2016] [Indexed: 12/29/2022] Open
Abstract
The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.
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Affiliation(s)
- Guray Kuzu
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, 34450 Istanbul, Turkey
- Chemical and Biological Engineering, College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Attila Gursoy
- Computer Engineering, Koc University, 34450 Istanbul, Turkey
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37
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Chen M, Baldwin PR, Ludtke SJ, Baker ML. De Novo modeling in cryo-EM density maps with Pathwalking. J Struct Biol 2016; 196:289-298. [PMID: 27436409 DOI: 10.1016/j.jsb.2016.06.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 11/26/2022]
Abstract
As electron cryo-microscopy (cryo-EM) can now frequently achieve near atomic resolution, accurate interpretation of these density maps in terms of atomistic detail has become paramount in deciphering macromolecular structure and function. However, there are few software tools for modeling protein structure from cryo-EM density maps in this resolution range. Here, we present an extension of our original Pathwalking protocol, which can automatically trace a protein backbone directly from a near-atomic resolution (3-6Å) density map. The original Pathwalking approach utilized a Traveling Salesman Problem solver for backbone tracing, but manual adjustment was still required during modeling. In the new version, human intervention is minimized and we provide a more robust approach for backbone modeling. This includes iterative secondary structure identification, termini detection and the ability to model multiple subunits without prior segmentation. Overall, the new Pathwalking procedure provides a more complete and robust tool for annotating protein structure function in near-atomic resolution density maps.
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Affiliation(s)
- Muyuan Chen
- Program in Structural and Computational Biology and Molecular Biophysics, United States; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Philip R Baldwin
- Department of Psychology, United States; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Matthew L Baker
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States.
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38
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Abstract
CryoEM single-particle reconstruction has been growing rapidly over the last 3 years largely due to the development of direct electron detectors, which have provided data with dramatic improvements in image quality. It is now possible in many cases to produce near-atomic resolution structures, and yet 2/3 of published structures remain at substantially lower resolutions. One important cause for this is compositional and conformational heterogeneity, which is both a resolution-limiting factor and presenting a unique opportunity to better relate structure to function. This manuscript discusses the canonical methods for high-resolution refinement in EMAN2.12, and then considers the wide range of available methods within this package for resolving structural variability, targeting both improved resolution and additional knowledge about particle dynamics.
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Affiliation(s)
- S J Ludtke
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, United States.
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39
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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40
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Peng S, Chu Z, Lu J, Li D, Wang Y, Yang S, Zhang Y. Co-expression of chaperones from P. furiosus enhanced the soluble expression of the recombinant hyperthermophilic α-amylase in E. coli. Cell Stress Chaperones 2016; 21:477-84. [PMID: 26862080 PMCID: PMC4837189 DOI: 10.1007/s12192-016-0675-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 01/14/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022] Open
Abstract
The extracellular α-amylase from the hyperthermophilic archaeum Pyrococcus furiosus (PFA) is extremely thermostable and of an industrial importance and interest. PFA aggregates and accumulates as insoluble inclusion bodies when expressed as a heterologous protein at a high level in Escherichia coli. In the present study, we investigated the roles of chaperones from P. furiosus in the soluble expression of recombinant PFA in E. coli. The results indicate that co-expression of PFA with the molecular chaperone prefoldin alone significantly increased the soluble expression of PFA. Although, co-expression of other main chaperone components from P. furiosus, such as the small heat shock protein (sHSP) or chaperonin (HSP60), was also able to improve the soluble expression of PFA to a certain extent. Co-expression of chaperonin or sHSP in addition to prefoldin did not further increase the soluble expression of PFA. This finding emphasizes the biotechnological potentials of the molecular chaperone prefoldin from P. furiosus, which may facilitate the production of recombinant PFA.
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Affiliation(s)
- Shuaiying Peng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhongmei Chu
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jianfeng Lu
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences, Shanghai, China
| | - Dongxiao Li
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yonghong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
| | - Shengli Yang
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhang
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences, Shanghai, China.
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41
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Clare DK, Saibil HR. ATP-driven molecular chaperone machines. Biopolymers 2016; 99:846-59. [PMID: 23877967 PMCID: PMC3814418 DOI: 10.1002/bip.22361] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/08/2013] [Indexed: 01/17/2023]
Abstract
This review is focused on the mechanisms by which ATP binding and hydrolysis drive chaperone machines assisting protein folding and unfolding. A survey of the key, general chaperone systems Hsp70 and Hsp90, and the unfoldase Hsp100 is followed by a focus on the Hsp60 chaperonin machine which is understood in most detail. Cryo-electron microscopy analysis of the E. coli Hsp60 GroEL reveals intermediate conformations in the ATPase cycle and in substrate folding. These structures suggest a mechanism by which GroEL can forcefully unfold and then encapsulate substrates for subsequent folding in isolation from all other binding surfaces.
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Affiliation(s)
- Daniel K Clare
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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42
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Hoersch D, Kortemme T. A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine. Structure 2016; 24:576-584. [PMID: 27021162 DOI: 10.1016/j.str.2016.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 02/11/2016] [Accepted: 02/22/2016] [Indexed: 01/28/2023]
Abstract
Controllable protein-based machines and materials are of considerable interest for diverse biotechnological applications. We previously re-engineered an ATP-driven protein machine, a group II chaperonin, to function as a light-gated nanocage. Here we develop and test a model for the molecular mechanism of the re-engineered chaperonin, which undergoes a large-scale closed to open conformational change triggered by reversible photo-isomerization of a site-specifically attached azobenzene crosslinker. In silico experiments using all-atom simulations suggest that rigid body motions of protein subdomains couple the length changes of the crosslinker to rearrangements of the nucleotide-binding pocket, leading to cage opening. We tested this model by designing a mutant for which the orientation of the two protein subdomains forming the nucleotide-binding pocket is directly controlled by the crosslinker, and confirmed successful reversible photoswitching in vitro. The model probes the conformational cycle of group II chaperonins and offers a design principle for engineering other light-driven protein-based molecular machines.
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Affiliation(s)
- Daniel Hoersch
- Department of Physics, Freie Universität Berlin, Berlin 14195, Germany; Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
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43
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Paul DM, Beuron F, Sessions RB, Brancaccio A, Bigotti MG. Internal (His)₆-tagging delivers a fully functional hetero-oligomeric class II chaperonin in high yield. Sci Rep 2016; 6:20696. [PMID: 26856373 PMCID: PMC4746591 DOI: 10.1038/srep20696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/11/2016] [Indexed: 11/09/2022] Open
Abstract
Group II chaperonins are ATP-ases indispensable for the folding of many proteins that play a crucial role in Archaea and Eukarya. They display a conserved two-ringed assembly enclosing an internal chamber where newly translated or misfolded polypeptides can fold to their native structure. They are mainly hexadecamers, with each eight-membered ring composed of one or two (in Archaea) or eight (in Eukarya) different subunits. A major recurring problem within group II chaperonin research, especially with the hetero-oligomeric forms, is to establish an efficient recombinant system for the expression of large amounts of wild-type as well as mutated variants. Herein we show how we can produce, in E. coli cells, unprecedented amounts of correctly assembled and active αβ-thermosome, the class II chaperonin from Thermoplasma acidophilum, by introducing a (His)6-tag within a loop in the α subunit of the complex. The specific location was identified via a rational approach and proved not to disturb the structure of the chaperonin, as demonstrated by size-exclusion chromatography, native gel electrophoresis and electron microscopy. Likewise, the tagged protein showed an ATP-ase activity and an ability to refold substrates identical to the wild type. This tagging strategy might be employed for the overexpression of other recombinant chaperonins.
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Affiliation(s)
- Danielle M. Paul
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol BS8 1TD, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | | | - Andrea Brancaccio
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- Istituto di Chimica del Riconoscimento Molecolare, CNR c/o Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
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Chaston JJ, Smits C, Aragão D, Wong ASW, Ahsan B, Sandin S, Molugu SK, Molugu SK, Bernal RA, Stock D, Stewart AG. Structural and Functional Insights into the Evolution and Stress Adaptation of Type II Chaperonins. Structure 2016; 24:364-74. [PMID: 26853941 DOI: 10.1016/j.str.2015.12.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 12/14/2015] [Accepted: 12/16/2015] [Indexed: 12/12/2022]
Abstract
Chaperonins are essential biological complexes assisting protein folding in all kingdoms of life. Whereas homooligomeric bacterial GroEL binds hydrophobic substrates non-specifically, the heterooligomeric eukaryotic CCT binds specifically to distinct classes of substrates. Sulfolobales, which survive in a wide range of temperatures, have evolved three different chaperonin subunits (α, β, γ) that form three distinct complexes tailored for different substrate classes at cold, normal, and elevated temperatures. The larger octadecameric β complexes cater for substrates under heat stress, whereas smaller hexadecameric αβ complexes prevail under normal conditions. The cold-shock complex contains all three subunits, consistent with greater substrate specificity. Structural analysis using crystallography and electron microscopy reveals the geometry of these complexes and shows a novel arrangement of the α and β subunits in the hexadecamer enabling incorporation of the γ subunit.
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Affiliation(s)
- Jessica J Chaston
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Callum Smits
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia
| | - David Aragão
- Australian Synchrotron, Clayton, VIC 3168, Australia
| | - Andrew S W Wong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551; NTU Institute of Structural Biology, Nanyang Technological University, Singapore 637551
| | - Bilal Ahsan
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Sara Sandin
- School of Biological Sciences, Nanyang Technological University, Singapore 637551; NTU Institute of Structural Biology, Nanyang Technological University, Singapore 637551
| | - Sudheer K Molugu
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Sanjay K Molugu
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Ricardo A Bernal
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Daniela Stock
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia.
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia.
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45
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Rother M, Nussbaumer MG, Renggli K, Bruns N. Protein cages and synthetic polymers: a fruitful symbiosis for drug delivery applications, bionanotechnology and materials science. Chem Soc Rev 2016; 45:6213-6249. [DOI: 10.1039/c6cs00177g] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein cages have become essential tools in bionanotechnology due to their well-defined, monodisperse, capsule-like structure. Combining them with synthetic polymers greatly expands their application, giving rise to novel nanomaterials fore.g.drug-delivery, sensing, electronic devices and for uses as nanoreactors.
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Affiliation(s)
- Martin Rother
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | - Martin G. Nussbaumer
- Wyss Institute for Biologically Inspired Engineering
- Harvard University
- Cambridge
- USA
| | - Kasper Renggli
- Department of Biosystems Science and Engineering
- ETH Zürich
- 4058 Basel
- Switzerland
| | - Nico Bruns
- Adolphe Merkle Institute
- University of Fribourg
- CH-1700 Fribourg
- Switzerland
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46
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Skjærven L, Cuellar J, Martinez A, Valpuesta JM. Dynamics, flexibility, and allostery in molecular chaperonins. FEBS Lett 2015; 589:2522-32. [PMID: 26140986 DOI: 10.1016/j.febslet.2015.06.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 06/18/2015] [Accepted: 06/23/2015] [Indexed: 12/26/2022]
Abstract
The chaperonins are a family of molecular chaperones present in all three kingdoms of life. They are classified into Group I and Group II. Group I consists of the bacterial variants (GroEL) and the eukaryotic ones from mitochondria and chloroplasts (Hsp60), while Group II consists of the archaeal (thermosomes) and eukaryotic cytosolic variants (CCT or TRiC). Both groups assemble into a dual ring structure, with each ring providing a protective folding chamber for nascent and denatured proteins. Their functional cycle is powered by ATP binding and hydrolysis, which drives a series of structural rearrangements that enable encapsulation and subsequent release of the substrate protein. Chaperonins have elaborate allosteric mechanisms to regulate their functional cycle. Long-range negative cooperativity between the two rings ensures alternation of the folding chambers. Positive intra-ring cooperativity, which facilitates concerted conformational transitions within the protein subunits of one ring, has only been demonstrated for Group I chaperonins. In this review, we describe our present understanding of the underlying mechanisms and the structure-function relationships in these complex protein systems with a particular focus on the structural dynamics, allostery, and associated conformational rearrangements.
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Affiliation(s)
- Lars Skjærven
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Jorge Cuellar
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - José María Valpuesta
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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47
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The Mechanism and Function of Group II Chaperonins. J Mol Biol 2015; 427:2919-30. [PMID: 25936650 DOI: 10.1016/j.jmb.2015.04.013] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 12/19/2022]
Abstract
Protein folding in the cell requires the assistance of enzymes collectively called chaperones. Among these, the chaperonins are 1-MDa ring-shaped oligomeric complexes that bind unfolded polypeptides and promote their folding within an isolated chamber in an ATP-dependent manner. Group II chaperonins, found in archaea and eukaryotes, contain a built-in lid that opens and closes over the central chamber. In eukaryotes, the chaperonin TRiC/CCT is hetero-oligomeric, consisting of two stacked rings of eight paralogous subunits each. TRiC facilitates folding of approximately 10% of the eukaryotic proteome, including many cytoskeletal components and cell cycle regulators. Folding of many cellular substrates of TRiC cannot be assisted by any other chaperone. A complete structural and mechanistic understanding of this highly conserved and essential chaperonin remains elusive. However, recent work is beginning to shed light on key aspects of chaperonin function and how their unique properties underlie their contribution to maintaining cellular proteostasis.
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Dalton KM, Frydman J, Pande VS. The dynamic conformational cycle of the group I chaperonin C-termini revealed via molecular dynamics simulation. PLoS One 2015; 10:e0117724. [PMID: 25822285 PMCID: PMC4379175 DOI: 10.1371/journal.pone.0117724] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/31/2014] [Indexed: 11/24/2022] Open
Abstract
Chaperonins are large ring shaped oligomers that facilitate protein folding by encapsulation within a central cavity. All chaperonins possess flexible C-termini which protrude from the equatorial domain of each subunit into the central cavity. Biochemical evidence suggests that the termini play an important role in the allosteric regulation of the ATPase cycle, in substrate folding and in complex assembly and stability. Despite the tremendous wealth of structural data available for numerous orthologous chaperonins, little structural information is available regarding the residues within the C-terminus. Herein, molecular dynamics simulations are presented which localize the termini throughout the nucleotide cycle of the group I chaperonin, GroE, from Escherichia coli. The simulation results predict that the termini undergo a heretofore unappreciated conformational cycle which is coupled to the nucleotide state of the enzyme. As such, these results have profound implications for the mechanism by which GroE utilizes nucleotide and folds client proteins.
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Affiliation(s)
- Kevin M. Dalton
- Biophysics Program, Stanford University, Stanford, California, United States of America
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Vijay S. Pande
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- * E-mail:
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49
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Structures of the Gβ-CCT and PhLP1-Gβ-CCT complexes reveal a mechanism for G-protein β-subunit folding and Gβγ dimer assembly. Proc Natl Acad Sci U S A 2015; 112:2413-8. [PMID: 25675501 DOI: 10.1073/pnas.1419595112] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
G-protein signaling depends on the ability of the individual subunits of the G-protein heterotrimer to assemble into a functional complex. Formation of the G-protein βγ (Gβγ) dimer is particularly challenging because it is an obligate dimer in which the individual subunits are unstable on their own. Recent studies have revealed an intricate chaperone system that brings Gβ and Gγ together. This system includes cytosolic chaperonin containing TCP-1 (CCT; also called TRiC) and its cochaperone phosducin-like protein 1 (PhLP1). Two key intermediates in the Gβγ assembly process, the Gβ-CCT and the PhLP1-Gβ-CCT complexes, were isolated and analyzed by a hybrid structural approach using cryo-electron microscopy, chemical cross-linking coupled with mass spectrometry, and unnatural amino acid cross-linking. The structures show that Gβ interacts with CCT in a near-native state through interactions of the Gγ-binding region of Gβ with the CCTγ subunit. PhLP1 binding stabilizes the Gβ fold, disrupting interactions with CCT and releasing a PhLP1-Gβ dimer for assembly with Gγ. This view provides unique insight into the interplay between CCT and a cochaperone to orchestrate the folding of a protein substrate.
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50
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Baker MR, Fan G, Serysheva II. Single-Particle Cryo-EM of the Ryanodine Receptor Channel in an Aqueous Environment. Eur J Transl Myol 2015; 25:4803. [PMID: 26913144 PMCID: PMC4748972 DOI: 10.4081/ejtm.2015.4803] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/22/2014] [Accepted: 12/31/2014] [Indexed: 12/31/2022] Open
Abstract
Ryanodine receptors (RyRs) are tetrameric ligand-gated Ca2+ release channels that are responsible for the increase of cytosolic Ca2+ concentration leading to muscle contraction. Our current understanding of RyR channel gating and regulation is greatly limited due to the lack of a high-resolution structure of the channel protein. The enormous size and unwieldy shape of Ca2+ release channels make X-ray or NMR methods difficult to apply for high-resolution structural analysis of the full-length functional channel. Single-particle electron cryo-microscopy (cryo-EM) is one of the only effective techniques for the study of such a large integral membrane protein and its molecular interactions. Despite recent developments in cryo-EM technologies and break-through single-particle cryo-EM studies of ion channels, cryospecimen preparation, particularly the presence of detergent in the buffer, remains the main impediment to obtaining atomic-resolution structures of ion channels and a multitude of other integral membrane protein complexes. In this review we will discuss properties of several detergents that have been successfully utilized in cryo-EM studies of ion channels and the emergence of the detergent alternative amphipol to stabilize ion channels for structure-function characterization. Future structural studies of challenging specimen like ion channels are likely to be facilitated by cryo-EM amenable detergents or alternative surfactants.
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Affiliation(s)
- Mariah R Baker
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
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