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Li Y, Zheng Z, Ramsey A, Chen L. Analysis of peptides and proteins in their binding to GroEL. J Pept Sci 2011; 16:693-700. [PMID: 20814869 DOI: 10.1002/psc.1288] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The GroEL-GroES is an essential molecular chaperon system that assists protein folding in cell. Binding of various substrate proteins to GroEL is one of the key aspects in GroEL-assisted protein folding. Small peptides may mimic segments of the substrate proteins in contact with GroEL and allow detailed structural analysis of the interactions. A model peptide SBP has been shown to bind to a region in GroEL that is important for binding of substrate proteins. Here, we investigated whether the observed GroEL-SBP interaction represented those of GroEL-substrate proteins, and whether SBP was able to mimic various aspects of substrate proteins in GroE-assisted protein folding cycle. We found that SBP competed with substrate proteins, including α-lactalbumin, rhodanese, and malate dehydrogenase, in binding to GroEL. SBP stimulated GroEL ATP hydrolysis rate in a manner similar to that of α-lactalbumin. SBP did not prevent GroES from binding to GroEL, and GroES association reduced the ATPase rates of GroEL/SBP and GroEL/α-lactalbumin to a comparable extent. Binding of both SBP and α-lactalbumin to apo GroEL was dominated by hydrophobic interaction. Interestingly, association of α-lactalbumin to GroEL/GroES was thermodynamically distinct from that to GroEL with reduced affinity and decreased contribution from hydrophobic interaction. However, SBP did not display such differential binding behaviors to apo GroEL and GroEL/GroES, likely due to the lack of a contiguous polypeptide chain that links all of the bound peptide fragments. Nevertheless, studies using peptides provide valuable information on the nature of GroEL-substrate protein interaction, which is central to understand the mechanism of GroEL-assisted protein folding.
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Affiliation(s)
- Yali Li
- Interdisciplinary Biochemistry Program, Indiana University, 212 S. Hawthorne Dr., Bloomington, IN 47405, USA
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52
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Kabir MA, Uddin W, Narayanan A, Reddy PK, Jairajpuri MA, Sherman F, Ahmad Z. Functional Subunits of Eukaryotic Chaperonin CCT/TRiC in Protein Folding. JOURNAL OF AMINO ACIDS 2011; 2011:843206. [PMID: 22312474 PMCID: PMC3268035 DOI: 10.4061/2011/843206] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 04/05/2011] [Indexed: 12/22/2022]
Abstract
Molecular chaperones are a class of proteins responsible for proper folding of a large number of polypeptides in both prokaryotic and eukaryotic cells. Newly synthesized polypeptides are prone to nonspecific interactions, and many of them make toxic aggregates in absence of chaperones. The eukaryotic chaperonin CCT is a large, multisubunit, cylindrical structure having two identical rings stacked back to back. Each ring is composed of eight different but similar subunits and each subunit has three distinct domains. CCT assists folding of actin, tubulin, and numerous other cellular proteins in an ATP-dependent manner. The catalytic cooperativity of ATP binding/hydrolysis in CCT occurs in a sequential manner different from concerted cooperativity as shown for GroEL. Unlike GroEL, CCT does not have GroES-like cofactor, rather it has a built-in lid structure responsible for closing the central cavity. The CCT complex recognizes its substrates through diverse mechanisms involving hydrophobic or electrostatic interactions. Upstream factors like Hsp70 and Hsp90 also work in a concerted manner to transfer the substrate to CCT. Moreover, prefoldin, phosducin-like proteins, and Bag3 protein interact with CCT and modulate its function for the fine-tuning of protein folding process. Any misregulation of protein folding process leads to the formation of misfolded proteins or toxic aggregates which are linked to multiple pathological disorders.
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Affiliation(s)
- M Anaul Kabir
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Kerala 673601, India
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53
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Yébenes H, Mesa P, Muñoz IG, Montoya G, Valpuesta JM. Chaperonins: two rings for folding. Trends Biochem Sci 2011; 36:424-32. [PMID: 21723731 DOI: 10.1016/j.tibs.2011.05.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/13/2011] [Accepted: 05/18/2011] [Indexed: 01/08/2023]
Abstract
Chaperonins are ubiquitous chaperones found in Eubacteria, eukaryotic organelles (group I), Archaea and the eukaryotic cytosol (group II). They all share a common structure and a basic functional mechanism. Although a large amount of information has been gathered for the simpler group I, much less is known about group II chaperonins. Recent crystallographic and electron microscopy structures have provided new insights into the mechanism of these chaperonins and revealed important differences between group I and II chaperonins, mainly in the molecular rearrangements that take place during the functional cycle. These differences are evident for the most complex chaperonin, the eukaryotic cytosolic CCT, which highlights the uniqueness of this important molecular machine.
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Affiliation(s)
- Hugo Yébenes
- Centro Nacional de Biotecnología (CNB-CSIC), Campus de la Universidad Autónoma de Madrid, Darwin 3, 28049 Madrid, Spain
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54
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Woronowicz K, Sha D, Frese RN, Niederman RA. The accumulation of the light-harvesting 2 complex during remodeling of the Rhodobacter sphaeroides intracytoplasmic membrane results in a slowing of the electron transfer turnover rate of photochemical reaction centers. Biochemistry 2011; 50:4819-29. [PMID: 21366273 DOI: 10.1021/bi101667e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A functional proteomic analysis of the intracytoplasmic membrane (ICM) development process was performed in Rhodobacter sphaeroides during adaptation from high-intensity illumination to indirect diffuse light. This initiated an accelerated synthesis of the peripheral light-harvesting 2 (LH2) complex relative to that of LH1-reaction center (RC) core particles. After 11 days, ICM vesicles (chromatophores) and membrane invagination sites were isolated by rate-zone sedimentation and subjected to clear native gel electrophoresis. Proteomic analysis of gel bands containing the RC-LH1 and -LH2 complexes from digitonin-solubilized chromatophores revealed high levels of comigrating electron transfer enzymes, transport proteins, and membrane assembly factors relative to their equivalent gel bands from cells undergoing adaptation to direct low-level illumination. The GroEL chaperonin accounted for >65% of the spectral counts in the RC-LH1 band from membrane invagination sites, which together with the appearance of a universal stress protein suggested that the viability of these cells was challenged by light limitation. Functional aspects of the photosynthetic unit assembly process were monitored by near-IR fast repetition rate analysis of variable fluorescence arising from LH-bacteriochlorophyll a components. The quantum yield of the primary charge separation during the early stages of adaptation showed a gradual increase (variable/maximal fluorescence = 0.78-0.83 between 0 and 4 h), while the initial value of ~70 for the functional absorption cross section (σ) gradually increased to 130 over 4 days. These dramatic σ increases showed a direct relation to gradual slowing of the RC electron transport turnover rate (τ(QA)) from ~1.6 to 6.4 ms and an ~3-fold slowing of the rate of reoxidation of the ubiquinone pool. These slowed rates are not due to changes in UQ pool size, suggesting that the relation between increasing σ and τ(QA) reflects the imposition of constraints upon free diffusion of ubiquinone redox species between the RC and cytochrome bc(1) complex as the membrane bilayer becomes densely packed with LH2 rings.
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Affiliation(s)
- Kamil Woronowicz
- Department of Molecular Biology and Biochemistry, Rutgers University, Busch Campus, Piscataway, New Jersey 08854-8082, USA
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55
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Vabulas RM, Raychaudhuri S, Hayer-Hartl M, Hartl FU. Protein folding in the cytoplasm and the heat shock response. Cold Spring Harb Perspect Biol 2011; 2:a004390. [PMID: 21123396 DOI: 10.1101/cshperspect.a004390] [Citation(s) in RCA: 284] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins generally must fold into precise three-dimensional conformations to fulfill their biological functions. In the cell, this fundamental process is aided by molecular chaperones, which act in preventing protein misfolding and aggregation. How this machinery assists newly synthesized polypeptide chains in navigating the complex folding energy landscape is now being understood in considerable detail. The mechanisms that ensure the maintenance of a functional proteome under normal and stress conditions are also of great medical relevance, as the aggregation of proteins that escape the cellular quality control underlies a range of debilitating diseases, including many age-of-onset neurodegenerative disorders.
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Affiliation(s)
- R Martin Vabulas
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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56
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Gershenson A, Gierasch LM. Protein folding in the cell: challenges and progress. Curr Opin Struct Biol 2011; 21:32-41. [PMID: 21112769 PMCID: PMC3072030 DOI: 10.1016/j.sbi.2010.11.001] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 11/01/2010] [Accepted: 11/02/2010] [Indexed: 01/02/2023]
Abstract
It is hard to imagine a more extreme contrast than that between the dilute solutions used for in vitro studies of protein folding and the crowded, compartmentalized, sticky, spatially inhomogeneous interior of a cell. This review highlights recent research exploring protein folding in the cell with a focus on issues that are generally not relevant to in vitro studies of protein folding, such as macromolecular crowding, hindered diffusion, cotranslational folding, molecular chaperones, and evolutionary pressures. The technical obstacles that must be overcome to characterize protein folding in the cell are driving methodological advances, and we draw attention to several examples, such as fluorescence imaging of folding in cells and genetic screens for in-cell stability.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA.
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57
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Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin. Nat Struct Mol Biol 2010; 18:14-9. [PMID: 21151115 DOI: 10.1038/nsmb.1971] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 11/03/2010] [Indexed: 12/11/2022]
Abstract
Protein folding is assisted by molecular chaperones. CCT (chaperonin containing TCP-1, or TRiC) is a 1-MDa oligomer that is built by two rings comprising eight different 60-kDa subunits. This chaperonin regulates the folding of important proteins including actin, α-tubulin and β-tubulin. We used an electron density map at 5.5 Å resolution to reconstruct CCT, which showed a substrate in the inner cavities of both rings. Here we present the crystal structure of the open conformation of this nanomachine in complex with tubulin, providing information about the mechanism by which it aids tubulin folding. The structure showed that the substrate interacts with loops in the apical and equatorial domains of CCT. The organization of the ATP-binding pockets suggests that the substrate is stretched inside the cavity. Our data provide the basis for understanding the function of this chaperonin.
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58
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Rao VB, Black LW. Structure and assembly of bacteriophage T4 head. Virol J 2010; 7:356. [PMID: 21129201 PMCID: PMC3012670 DOI: 10.1186/1743-422x-7-356] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 12/03/2010] [Indexed: 12/20/2022] Open
Abstract
The bacteriophage T4 capsid is an elongated icosahedron, 120 nm long and 86 nm wide, and is built with three essential proteins; gp23*, which forms the hexagonal capsid lattice, gp24*, which forms pentamers at eleven of the twelve vertices, and gp20, which forms the unique dodecameric portal vertex through which DNA enters during packaging and exits during infection. The past twenty years of research has greatly elevated the understanding of phage T4 head assembly and DNA packaging. The atomic structure of gp24 has been determined. A structural model built for gp23 using its similarity to gp24 showed that the phage T4 major capsid protein has the same fold as that found in phage HK97 and several other icosahedral bacteriophages. Folding of gp23 requires the assistance of two chaperones, the E. coli chaperone GroEL and the phage coded gp23-specific chaperone, gp31. The capsid also contains two non-essential outer capsid proteins, Hoc and Soc, which decorate the capsid surface. The structure of Soc shows two capsid binding sites which, through binding to adjacent gp23 subunits, reinforce the capsid structure. Hoc and Soc have been extensively used in bipartite peptide display libraries and to display pathogen antigens including those from HIV, Neisseria meningitides, Bacillus anthracis, and FMDV. The structure of Ip1*, one of the components of the core, has been determined, which provided insights on how IPs protect T4 genome against the E. coli nucleases that degrade hydroxymethylated and glycosylated T4 DNA. Extensive mutagenesis combined with the atomic structures of the DNA packaging/terminase proteins gp16 and gp17 elucidated the ATPase and nuclease functional motifs involved in DNA translocation and headful DNA cutting. Cryo-EM structure of the T4 packaging machine showed a pentameric motor assembled with gp17 subunits on the portal vertex. Single molecule optical tweezers and fluorescence studies showed that the T4 motor packages DNA at a rate of up to 2000 bp/sec, the fastest reported to date of any packaging motor. FRET-FCS studies indicate that the DNA gets compressed during the translocation process. The current evidence suggests a mechanism in which electrostatic forces generated by ATP hydrolysis drive the DNA translocation by alternating the motor between tensed and relaxed states.
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Affiliation(s)
- Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC, USA.
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59
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The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion. Virology 2010; 409:319-27. [PMID: 21071053 DOI: 10.1016/j.virol.2010.10.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 08/22/2010] [Accepted: 10/16/2010] [Indexed: 01/16/2023]
Abstract
Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven't been well understood. It was previously reported that two unidentified proteins were present in bacteriophage Sf6 virion (Casjens et al, 2004, J.Mol.Biol. 339, 379-394, Fig. 2A). Using tandem mass spectrometry, we have identified the two proteins as outer membrane proteins (OMPs) OmpA and OmpC from its host Shigella flexneri. The transmission electron cryo-microscopy structure of Sf6 shows significant density at specific sites at the phage capsid inner surface. This density fit well with the characteristic beta-barrel domains of OMPs, thus may be due to the two host proteins. Locations of this density suggest a role in Sf6 morphogenesis reminiscent of phage-encoded cementing proteins. These data indicate a new, OMP-related phage:host linkage, adding to previous knowledge that some lambdoid bacteriophage genomes contain OmpC-like genes that express phage-encoded porins in the lysogenic state.
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60
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Mitsuoka K. Obtaining high-resolution images of biological macromolecules by using a cryo-electron microscope with a liquid-helium cooled stage. Micron 2010; 42:100-6. [PMID: 20869255 DOI: 10.1016/j.micron.2010.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 08/20/2010] [Accepted: 08/21/2010] [Indexed: 10/19/2022]
Abstract
To obtain high-resolution images of biological macromolecules, a cryo-electron microscope (cryo-EM) is useful to preserve the hydrated state of the molecules. In addition, the cryo-conditions reduce some of the electron radiation damage, although averaging is necessary to obtain the molecular resolution from biological macromolecules. For the averaging, the three reconstruction methods of electron crystallography, helical reconstruction, and single particle analysis facilitate the determination of the atomic models. Here we describe suitable techniques for high-resolution imaging in these three different methods, based on our experiences using cryo-EM with a liquid-helium cooled stage. Irradiation damage by the electron beam is the most serious problem in the structural analysis of a biological specimen, and we clearly show that further reduction of the specimen temperature, from liquid nitrogen to liquid helium temperature, improves the cryo-protection factor by at least two-fold for both glucose-embedded and frozen-hydrated specimens. We review the image processing, and then discuss the future prospects of cryo-EM.
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Affiliation(s)
- Kaoru Mitsuoka
- National Institute of Advanced Industrial Science and Technology, Biomedicinal Information Research Center, 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan.
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61
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Pereira JH, Ralston CY, Douglas NR, Meyer D, Knee KM, Goulet DR, King JA, Frydman J, Adams PD. Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J Biol Chem 2010; 285:27958-66. [PMID: 20573955 PMCID: PMC2934662 DOI: 10.1074/jbc.m110.125344] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 06/02/2010] [Indexed: 11/06/2022] Open
Abstract
Chaperonins are large protein complexes consisting of two stacked multisubunit rings, which open and close in an ATP-dependent manner to create a protected environment for protein folding. Here, we describe the first crystal structure of a group II chaperonin in an open conformation. We have obtained structures of the archaeal chaperonin from Methanococcus maripaludis in both a peptide acceptor (open) state and a protein folding (closed) state. In contrast with group I chaperonins, in which the equatorial domains share a similar conformation between the open and closed states and the largest motions occurs at the intermediate and apical domains, the three domains of the archaeal chaperonin subunit reorient as a single rigid body. The large rotation observed from the open state to the closed state results in a 65% decrease of the folding chamber volume and creates a highly hydrophilic surface inside the cage. These results suggest a completely distinct closing mechanism in the group II chaperonins as compared with the group I chaperonins.
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Affiliation(s)
- Jose H. Pereira
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Corie Y. Ralston
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Nicholai R. Douglas
- the Department of Biological Sciences and BioX Program, Stanford University, Stanford, California 94305
| | - Daniel Meyer
- the Department of Biological Sciences and BioX Program, Stanford University, Stanford, California 94305
| | - Kelly M. Knee
- the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and
| | - Daniel R. Goulet
- the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and
| | - Jonathan A. King
- the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and
| | - Judith Frydman
- the Department of Biological Sciences and BioX Program, Stanford University, Stanford, California 94305
| | - Paul D. Adams
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- the Department of Bioengineering, University of California, Berkeley, California 94720
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62
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Single-molecule spectroscopy of protein folding in a chaperonin cage. Proc Natl Acad Sci U S A 2010; 107:11793-8. [PMID: 20547872 DOI: 10.1073/pnas.1002356107] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular chaperones are known to be essential for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms. We use single-molecule Förster resonance energy transfer to follow the folding of a protein inside the GroEL/GroES chaperonin cavity over a time range from milliseconds to hours. Our results show that confinement in the chaperonin decelerates the folding of the C-terminal domain in the substrate protein rhodanese, but leaves the folding rate of the N-terminal domain unaffected. Microfluidic mixing experiments indicate that strong interactions of the substrate with the cavity walls impede the folding process, but the folding hierarchy is preserved. Our results imply that no universal chaperonin mechanism exists. Rather, a competition between intra- and intermolecular interactions determines the folding rates and mechanisms of a substrate inside the GroEL/GroES cage.
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63
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Zernike phase plate cryoelectron microscopy facilitates single particle analysis of unstained asymmetric protein complexes. Structure 2010; 18:17-27. [PMID: 20152149 DOI: 10.1016/j.str.2009.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 11/25/2009] [Accepted: 12/02/2009] [Indexed: 10/20/2022]
Abstract
Single particle reconstruction from cryoelectron microscopy images, though emerging as a powerful means in structural biology, is faced with challenges as applied to asymmetric proteins smaller than megadaltons due to low contrast. Zernike phase plate can improve the contrast by restoring the microscope contrast transfer function. Here, by exploiting simulated Zernike and conventional defocused cryoelectron microscope images with noise characteristics comparable to those of experimental data, we quantified the efficiencies of the steps in single particle analysis of ice-embedded RNA polymerase II (500 kDa), transferrin receptor complex (290 kDa), and T7 RNA polymerase lysozyme (100 kDa). Our results show Zernike phase plate imaging is more effective as to particle identification and also sorting of orientations, conformations, and compositions. Moreover, our analysis on image alignment indicates that Zernike phase plate can, in principle, reduce the number of particles required to attain near atomic resolution by 10-100 fold for proteins between 100 kDa and 500 kDa.
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64
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Tompa P, Kovacs D. Intrinsically disordered chaperones in plants and animalsThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process. Biochem Cell Biol 2010; 88:167-74. [DOI: 10.1139/o09-163] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are widespread in eukaryotes and fulfill important functions associated with signaling and regulation. Recent evidence points to a special and thus largely disrespected functional capacity of IDPs—that they can assist the folding of other proteins and prevent their aggregation, i.e., that they can act as chaperones. In this paper, we survey current information available on this phenomenon, with particular focus on (i) the structure and function of IDPs in general, (ii) disordered chaperones in plants, (iii) disordered chaperones in other organisms spanning from insects to mammals, (iv) the possible mechanisms of action of disordered chaperones, and (v) the possibility of two-faced (Janus) chaperone activity of disordered chaperones, which can assist the folding of both RNA and protein substrates. The evidence is most conclusive in the case of plant stress proteins, such as late embryogenesis abundant (LEA) proteins or dehydrins. We will show that the cellular function of LEA proteins in mitigating the damage caused by stress is clear; nevertheless, experiments carried out in vivo must be extended and the molecular mechanism of the action of IDP chaperones also requires clarification. Using these details, we chart out how far the field has progressed only to emphasize the long road ahead before chaperone function can be firmly established as part of the physiological mechanistic arsenal of the emerging group of IDPs.
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Affiliation(s)
- Peter Tompa
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina ut 29, H-1113 Budapest, Hungary
| | - Denes Kovacs
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina ut 29, H-1113 Budapest, Hungary
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65
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Eronina TB, Chebotareva NA, Bazhina SG, Kleymenov SY, Naletova IN, Muronetz VI, Kurganov BI. Effect of GroEL on Thermal Aggregation of Glycogen Phosphorylase b
from Rabbit Skeletal Muscle. Macromol Biosci 2010; 10:768-74. [DOI: 10.1002/mabi.200900396] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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66
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Markossian KA, Golub NV, Chebotareva NA, Asryants RA, Naletova IN, Muronetz VI, Muranov KO, Kurganov BI. Comparative analysis of the effects of alpha-crystallin and GroEL on the kinetics of thermal aggregation of rabbit muscle glyceraldehyde-3-phosphate dehydrogenase. Protein J 2010; 29:11-25. [PMID: 19936900 DOI: 10.1007/s10930-009-9217-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Effects of alpha-crystallin and GroEL on the kinetics of thermal aggregation of rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH) have been studied using dynamic light scattering and analytical ultracentrifugation. The analysis of the initial parts of the dependences of the hydrodynamic radius of protein aggregates on time shows that in the presence of alpha-crystallin or GroEL the kinetic regime of GAPDH aggregation is changed from the regime of diffusion-limited cluster-cluster aggregation to the regime of reaction-limited cluster-cluster aggregation, wherein the sticking probability for the colliding particles becomes lower the unity. In contrast to alpha-crystallin, GroEL does not interfere with formation of the start aggregates which include denatured GAPDH molecules. On the basis of the analytical ultracentrifugation data the conclusion has been made that the products of dissociation of GAPDH and alpha-crystallin or GroEL play an important role in the interactions of GAPDH and chaperones at elevated temperatures.
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Affiliation(s)
- Kira A Markossian
- Bach Institute of Biochemistry, Russian Academy of Sciences, 119071, Moscow, Russia.
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67
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Calmat S, Hendriks J, van Heerikhuizen H, Schmidt CF, van der Vies SM, Peterman EJG. Dissociation kinetics of the GroEL-gp31 chaperonin complex studied with Förster resonance energy transfer. Biochemistry 2010; 48:11692-8. [PMID: 19899806 DOI: 10.1021/bi9013962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Propagation of bacteriophage T4 in its host Escherichia coli involves the folding of the major capsid protein gp23, which is facilitated by a hybrid chaperone complex consisting of the bacterial chaperonin GroEL and the phage-encoded co-chaperonin, gp31. It has been well established that the GroEL-gp31 complex is capable of folding gp23 whereas the homologous GroEL-GroES complex cannot perform this function. To assess whether this is a consequence of differences in the interactions of the proteins within the chaperonin complex, we have investigated the dissociation kinetics of GroEL-gp31 and GroEL-GroES complexes using Forster resonance energy transfer. Here we report that the dissociation of gp31 from GroEL is slightly faster than that of GroES from GroEL and is further accelerated by the binding of gp23. In contrast to what had been observed previously, we found that gp23 is able to interact with the GroEL-GroES complex, which might explain how bacteriophage T4 redirects the folding machinery of Escherichia coli during morphogenesis.
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Affiliation(s)
- Stéphane Calmat
- Department of Physics and Astronomy and Laser Centre, VU University, Amsterdam, The Netherlands
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68
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Albert A, Yunta C, Arranz R, Peña A, Salido E, Valpuesta JM, Martín-Benito J. Structure of GroEL in complex with an early folding intermediate of alanine glyoxylate aminotransferase. J Biol Chem 2010; 285:6371-6. [PMID: 20056599 DOI: 10.1074/jbc.m109.062471] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Primary hyperoxaluria type 1 is a rare autosomal recessive disease caused by mutations in the alanine glyoxylate aminotransferase gene (AGXT). We have previously shown that P11L and I340M polymorphisms together with I244T mutation (AGXT-LTM) represent a conformational disease that could be amenable to pharmacological intervention. Thus, the study of the folding mechanism of AGXT is crucial to understand the molecular basis of the disease. Here, we provide biochemical and structural data showing that AGXT-LTM is able to form non-native folding intermediates. The three-dimensional structure of a complex between the bacterial chaperonin GroEL and a folding intermediate of AGXT-LTM mutant has been solved by cryoelectron microscopy. The electron density map shows the protein substrate in a non-native extended conformation that crosses the GroEL central cavity. Addition of ATP to the complex induces conformational changes on the chaperonin and the internalization of the protein substrate into the folding cavity. The structure provides a three-dimensional picture of an in vivo early ATP-dependent step of the folding reaction cycle of the chaperonin and supports a GroEL functional model in which the chaperonin promotes folding of the AGXT-LTM mutant protein through forced unfolding mechanism.
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Affiliation(s)
- Armando Albert
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid E-28006, Spain.
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69
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Abstract
Electron microscopy (EM) has developed into an important method for determining the three-dimensional (3D) structures of biological complexes, in particular of isolated macromolecular complexes in vitrified solution (cryo-EM of "single particles"). One of the consequences of studying complexes in solution rather than in a crystal lattice is that they are less constrained to adopt a single conformation. It is a common problem in single-particle analysis that samples of purified macromolecules can be structurally heterogeneous, with molecules adopting different conformations, corresponding to different functional states. In the case of multisubunit assemblies, there may also be heterogeneity of assembly or ligand binding. Heterogeneity limits the accuracy and resolution of 3D structures, since different conformations will contribute to a single 3D map and variable parts of the structure will be smeared out. Therefore, a new group of image processing methods has been developed to deal with the problems of detecting and sorting structural heterogeneity. The basic problem is to discriminate the source of image variations, and then to separate the images into homogeneous subsets for separate reconstruction. Variations in image features can arise from different particle orientations, variations in conformation and/or ligand binding, and noise fluctuations in the low signal-to-noise ratio images typical of cryo-EM. Here, we present a review of approaches developed to deal with these problems, along with examples of the application of a method based on multivariate statistical analysis to both model and real data. The methods have been used to discriminate small differences in size, conformation and ligand binding, and to obtain high quality, reliable reconstructions of multiple structures from mixed data sets.
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70
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Jewett AI, Shea JE. Reconciling theories of chaperonin accelerated folding with experimental evidence. Cell Mol Life Sci 2010; 67:255-76. [PMID: 19851829 PMCID: PMC11115962 DOI: 10.1007/s00018-009-0164-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/14/2009] [Accepted: 09/25/2009] [Indexed: 10/20/2022]
Abstract
For the last 20 years, a large volume of experimental and theoretical work has been undertaken to understand how chaperones like GroEL can assist protein folding in the cell. The most accepted explanation appears to be the simplest: GroEL, like most other chaperones, helps proteins fold by preventing aggregation. However, evidence suggests that, under some conditions, GroEL can play a more active role by accelerating protein folding. A large number of models have been proposed to explain how this could occur. Focused experiments have been designed and carried out using different protein substrates with conclusions that support many different mechanisms. In the current article, we attempt to see the forest through the trees. We review all suggested mechanisms for chaperonin-mediated folding and weigh the plausibility of each in light of what we now know about the most stringent, essential, GroEL-dependent protein substrates.
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Affiliation(s)
- Andrew I. Jewett
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Department of Physics, University of California, Santa Barbara, CA 93106 USA
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Department of Physics, University of California, Santa Barbara, CA 93106 USA
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71
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Kovács E, Sun Z, Liu H, Scott DJ, Karsisiotis AI, Clarke AR, Burston SG, Lund PA. Characterisation of a GroEL single-ring mutant that supports growth of Escherichia coli and has GroES-dependent ATPase activity. J Mol Biol 2009; 396:1271-83. [PMID: 20006619 DOI: 10.1016/j.jmb.2009.11.074] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 11/26/2009] [Accepted: 11/30/2009] [Indexed: 11/30/2022]
Abstract
Binding and folding of substrate proteins by the molecular chaperone GroEL alternates between its two seven-membered rings in an ATP-regulated manner. The association of ATP and GroES to a polypeptide-bound ring of GroEL encapsulates the folding proteins in the central cavity of that ring (cis ring) and allows it to fold in a protected environment where the risk of aggregation is reduced. ATP hydrolysis in the cis ring changes the potentials within the system such that ATP binding to the opposite (trans) ring triggers the release of all ligands from the cis ring of GroEL through a complex network of allosteric communication between the rings. Inter-ring allosteric communication thus appears indispensable for the function of GroEL, and an engineered single-ring version (SR1) cannot substitute for GroEL in vivo. We describe here the isolation and characterisation of an active single-ring form of the GroEL protein (SR-A92T), which has an exceptionally low ATPase activity that is strongly stimulated by the addition of GroES. Dissection of the kinetic pathway of the ATP-induced structural changes in this active single ring can be explained by the fact that the mutation effectively blocks progression through the full allosteric pathway of the GroEL reaction cycle, thus trapping an early allosteric intermediate. Addition of GroES is able to overcome this block by binding this intermediate and pulling the allosteric pathway to completion via mass action, explaining how bacterial cells expressing this protein as their only chaperonin are viable.
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Affiliation(s)
- Eszter Kovács
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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72
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Promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone. Cell 2009; 138:923-34. [PMID: 19737520 DOI: 10.1016/j.cell.2009.07.044] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 03/28/2009] [Accepted: 07/31/2009] [Indexed: 11/22/2022]
Abstract
Trigger factor (TF) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but TF is also abundant free in the cytosol where its activity is less well characterized. In vitro studies show that TF promotes protein refolding. We find here that ribosome-free TF stably associates with and rescues from misfolding a large repertoire of full-length proteins. We identify over 170 members of this cytosolic Escherichia coli TF substrate proteome, including ribosomal protein S7. We analyzed the biochemical properties of a TF:S7 complex from Thermotoga maritima and determined its crystal structure. Thereby, we obtained an atomic-level picture of a promiscuous chaperone in complex with a physiological substrate protein. The structure of the complex reveals the molecular basis of substrate recognition by TF, indicates how TF could accelerate protein folding, and suggests a role for TF in the biogenesis of protein complexes.
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73
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Chaperonin-mediated protein folding: using a central cavity to kinetically assist polypeptide chain folding. Q Rev Biophys 2009; 42:83-116. [PMID: 19638247 DOI: 10.1017/s0033583509004764] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The chaperonin ring assembly GroEL provides kinetic assistance to protein folding in the cell by binding non-native protein in the hydrophobic central cavity of an open ring and subsequently, upon binding ATP and the co-chaperonin GroES to the same ring, releasing polypeptide into a now hydrophilic encapsulated cavity where productive folding occurs in isolation. The fate of polypeptide during binding, encapsulation, and folding in the chamber has been the subject of recent experimental studies and is reviewed and considered here. We conclude that GroEL, in general, behaves passively with respect to its substrate proteins during these steps. While binding appears to be able to rescue non-native polypeptides from kinetic traps, such rescue is most likely exerted at the level of maximizing hydrophobic contact, effecting alteration of the topology of weakly structured states. Encapsulation does not appear to involve 'forced unfolding', and if anything, polypeptide topology is compacted during this step. Finally, chamber-mediated folding appears to resemble folding in solution, except that major kinetic complications of multimolecular association are prevented.
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74
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Abstract
Most proteins must fold into precise three-dimensional conformations to fulfill their biological functions. Here we review recent concepts emerging from studies of protein folding in vitro and in vivo, with a focus on how proteins navigate the complex folding energy landscape inside cells with the aid of molecular chaperones. Understanding these reactions is also of considerable medical relevance, as the aggregation of misfolding proteins that escape the cellular quality-control machinery underlies a range of debilitating diseases, including many age-onset neurodegenerative disorders.
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75
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Horwich AL, Apetri AC, Fenton WA. The GroEL/GroES cis cavity as a passive anti-aggregation device. FEBS Lett 2009; 583:2654-62. [PMID: 19577567 PMCID: PMC2759771 DOI: 10.1016/j.febslet.2009.06.049] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 06/27/2009] [Accepted: 06/30/2009] [Indexed: 10/20/2022]
Abstract
The GroEL/GroES chaperonin folding chamber is an encapsulated space of approximately 65 A diameter with a hydrophilic wall, inside of which many cellular proteins reach the native state. The question of whether the cavity wall actively directs folding reactions or is playing a passive role has been open. We review past and recent observations and conclude that the chamber functions as a passive "Anfinsen cage" that prevents folding monomers from multimolecular aggregation.
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Affiliation(s)
- Arthur L Horwich
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA.
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76
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GroEL-assisted protein folding: does it occur within the chaperonin inner cavity? Int J Mol Sci 2009; 10:2066-2083. [PMID: 19564940 PMCID: PMC2695268 DOI: 10.3390/ijms10052066] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 05/08/2009] [Accepted: 05/11/2009] [Indexed: 11/22/2022] Open
Abstract
The folding of protein molecules in the GroEL inner cavity under the co-chaperonin GroES lid is widely accepted as a crucial event of GroEL-assisted protein folding. This review is focused on the data showing that GroEL-assisted protein folding may proceed out of the complex with the chaperonin. The models of GroEL-assisted protein folding assuming ligand-controlled dissociation of nonnative proteins from the GroEL surface and their folding in the bulk solution are also discussed.
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77
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Cheng Y. Toward an atomic model of the 26S proteasome. Curr Opin Struct Biol 2009; 19:203-8. [PMID: 19286367 DOI: 10.1016/j.sbi.2009.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 02/10/2009] [Indexed: 01/19/2023]
Abstract
Since the discovery of the 26S proteasome, much progress has been made in determining the structure of this large dynamic protein complex. Until now, a vast amount of structural information of the proteasome has been obtained from all kinds of structure determination techniques, and the function of the protease core is well understood at atomic detail. Yet our understanding of the entire 26S proteasome structure, particularly its 19S regulatory complex, is still limited at a low-resolution blob-ology level. In this review, we highlight the recent progress made in understanding the mechanism of 20S gate opening by the proteasomal activators. We also emphasized the recent methodological advances, particularly in achieving the near atomic resolution by single particle electron cryomicroscopy, and the possible approaches that will enable more detailed structural analysis of the entire 26S proteasome.
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Affiliation(s)
- Yifan Cheng
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California-San Francisco, 600 16th Street, San Francisco, CA 94158, USA.
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78
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Banach M, Stąpor K, Roterman I. Chaperonin structure: the large multi-subunit protein complex. Int J Mol Sci 2009; 10:844-861. [PMID: 19399224 PMCID: PMC2672005 DOI: 10.3390/ijms10030844] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 02/23/2009] [Accepted: 02/26/2009] [Indexed: 11/16/2022] Open
Abstract
The multi sub-unit protein structure representing the chaperonins group is analyzed with respect to its hydrophobicity distribution. The proteins of this group assist protein folding supported by ATP. The specific axial symmetry GroEL structure (two rings of seven units stacked back to back - 524 aa each) and the GroES (single ring of seven units - 97 aa each) polypeptide chains are analyzed using the hydrophobicity distribution expressed as excess/deficiency all over the molecule to search for structure-to-function relationships. The empirically observed distribution of hydrophobic residues is confronted with the theoretical one representing the idealized hydrophobic core with hydrophilic residues exposure on the surface. The observed discrepancy between these two distributions seems to be aim-oriented, determining the structure-to-function relation. The hydrophobic force field structure generated by the chaperonin capsule is presented. Its possible influence on substrate folding is suggested.
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Affiliation(s)
- Mateusz Banach
- Department of Bioinformatics and Telemedicine – Jagiellonian University, Collegium Medicum, Lazarza 16, 31-531 Krakow, Poland; E-Mail:
- Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Reymonta 4, 30-059 Krakow, Poland; E-Mail:
| | - Katarzyna Stąpor
- Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Reymonta 4, 30-059 Krakow, Poland; E-Mail:
- Silesian Technical University, Institute of Computer Science, Akademicka 16 44-100 Gliwice, Poland; E-Mail:
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine – Jagiellonian University, Collegium Medicum, Lazarza 16, 31-531 Krakow, Poland; E-Mail:
- Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Reymonta 4, 30-059 Krakow, Poland; E-Mail:
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +48-12-619-96-94; Fax: +48-12-619-96-93
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79
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Engel A. Chapter 9 Scanning Transmission Electron Microscopy. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1076-5670(09)59009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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