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GroEL—A Versatile Chaperone for Engineering and a Plethora of Applications. Biomolecules 2022; 12:biom12050607. [PMID: 35625535 PMCID: PMC9138447 DOI: 10.3390/biom12050607] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 12/16/2022] Open
Abstract
Chaperones play a vital role in the life of cells by facilitating the correct folding of other proteins and maintaining them in a functional state, being themselves, as a rule, more stable than the rest of cell proteins. Their functional properties naturally tempt investigators to actively adapt them for biotechnology needs. This review will mostly focus on the applications found for the bacterial chaperonin GroE and its counterparts from other organisms, in biotechnology or for research purposes, both in their engineered or intact versions.
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Yurkova MS, Zenin VA, Nagibina GS, Melnik BS, Fedorov AN. Physico-Chemical Characterization of Permutated Variants of Chaperone GroEL Apical Domain. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819130027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kurov KA, Savvin OI, Yurkova MS, Zenin VA, Nagibina GS, Melnik BS, Fedorov AN. Physicochemical Characteristics of a Variant of Chaperon GroEL Apical Domain Designed to Enhance the Expression and Stability of Target Proteins. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819080088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Yurkova MS, Sharapova OA, Zenin VA, Fedorov AN. Versatile format of minichaperone-based protein fusion system. Sci Rep 2019; 9:15063. [PMID: 31636289 PMCID: PMC6803692 DOI: 10.1038/s41598-019-51015-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/17/2019] [Indexed: 11/23/2022] Open
Abstract
Hydrophobic recombinant proteins often tend to aggregate upon expression into inclusion bodies and are difficult to refold. Producing them in soluble forms constitutes a common bottleneck problem. A fusion system for production of insoluble hydrophobic proteins in soluble stable forms with thermophilic minichaperone, GroEL apical domain (GrAD) as a carrier, has recently been developed. To provide the utmost flexibility of the system for interactions between the carrier and various target protein moieties a strategy of making permutated protein variants by gene engineering has been applied: the original N- and C-termini of the minichaperone were linked together by a polypeptide linker and new N- and C-termini were made at desired parts of the protein surface. Two permutated GrAD forms were created and analyzed. Constructs of GrAD and both of its permutated forms fused with the initially insoluble N-terminal fragment of hepatitis C virus' E2 protein were tested. Expressed fusions formed inclusion bodies. After denaturation, all fusions were completely renatured in stable soluble forms. A variety of permutated GrAD variants can be created. The versatile format of the system provides opportunities for choosing an optimal pair between particular target protein moiety and the best-suited original or specific permutated carrier.
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Affiliation(s)
- Maria S Yurkova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russian Federation
- Tropogen Inc, Moscow, Russia
| | - Olga A Sharapova
- Alder BioPharmaceuticals, Inc., 11804 N Creek Pkwy S, Bothell, WA, 98011, USA
| | - Vladimir A Zenin
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russian Federation
| | - Alexey N Fedorov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russian Federation.
- Tropogen Inc, Moscow, Russia.
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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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Sharapova OA, Yurkova MS, Fedorov AN. A minichaperone-based fusion system for producing insoluble proteins in soluble stable forms. Protein Eng Des Sel 2015; 29:57-64. [PMID: 26612097 DOI: 10.1093/protein/gzv060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 10/20/2015] [Indexed: 01/27/2023] Open
Abstract
We have developed a fusion system for reliable production of insoluble hydrophobic proteins in soluble stable forms. A carrier is thermophilic minichaperone, GroEL apical domain (GrAD), a 15 kDa monomer able to bind diverse protein substrates. The Met-less variant of GrAD has been made for further convenient use of Met-specific CNBr chemical cleavage, if desired. The Met-less GrAD retained stability and solubility of the original protein. Target polypeptides can be fused to either C-terminus or N-terminus of GrAD. The system has been tested with two unrelated insoluble proteins fused to the C-terminus of GrAD. One of the proteins was also fused to GrAD N-terminus. The fusions formed inclusion bodies at 25°C and above and were partly soluble only at lower expression temperatures. Most importantly, however, after denaturation in urea, all fusions without exception were completely renatured in soluble stable forms that safely survived freezing-thawing as well as lyophilization. All fusions for both tested target proteins retained solubility at high concentrations for days. Functional analysis revealed that a target protein may retain functionality in the fusion. Convenience features include potential thermostability of GrAD fusions, capacity for chemical and enzymatic cleavage of a target and His6 tag for purification.
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Affiliation(s)
| | - Maria S Yurkova
- Tropogen Inc., Privolnaya, 2, bld.1, G15, Moscow 109145, Russia
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Burmann BM, Hiller S. Chaperones and chaperone-substrate complexes: Dynamic playgrounds for NMR spectroscopists. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 86-87:41-64. [PMID: 25919198 DOI: 10.1016/j.pnmrs.2015.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/19/2015] [Accepted: 02/19/2015] [Indexed: 05/20/2023]
Abstract
The majority of proteins depend on a well-defined three-dimensional structure to obtain their functionality. In the cellular environment, the process of protein folding is guided by molecular chaperones to avoid misfolding, aggregation, and the generation of toxic species. To this end, living cells contain complex networks of molecular chaperones, which interact with substrate polypeptides by a multitude of different functionalities: transport them towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver them towards a proteolysis machinery. Despite the availability of high-resolution crystal structures of many important chaperones in their substrate-free apo forms, structural information about how substrates are bound by chaperones and how they are protected from misfolding and aggregation is very sparse. This lack of information arises from the highly dynamic nature of chaperone-substrate complexes, which so far has largely hindered their crystallization. This highly dynamic nature makes chaperone-substrate complexes good targets for NMR spectroscopy. Here, we review the results achieved by NMR spectroscopy to understand chaperone function in general and details of chaperone-substrate interactions in particular. We assess the information content and applicability of different NMR techniques for the characterization of chaperones and chaperone-substrate complexes. Finally, we highlight three recent studies, which have provided structural descriptions of chaperone-substrate complexes at atomic resolution.
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Affiliation(s)
- Björn M Burmann
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
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Joachimiak LA, Walzthoeni T, Liu CW, Aebersold R, Frydman J. The structural basis of substrate recognition by the eukaryotic chaperonin TRiC/CCT. Cell 2015; 159:1042-1055. [PMID: 25416944 DOI: 10.1016/j.cell.2014.10.042] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 08/17/2014] [Accepted: 10/20/2014] [Indexed: 12/20/2022]
Abstract
The eukaryotic chaperonin TRiC (also called CCT) is the obligate chaperone for many essential proteins. TRiC is hetero-oligomeric, comprising two stacked rings of eight different subunits each. Subunit diversification from simpler archaeal chaperonins appears linked to proteome expansion. Here, we integrate structural, biophysical, and modeling approaches to identify the hitherto unknown substrate-binding site in TRiC and uncover the basis of substrate recognition. NMR and modeling provided a structural model of a chaperonin-substrate complex. Mutagenesis and crosslinking-mass spectrometry validated the identified substrate-binding interface and demonstrate that TRiC contacts full-length substrates combinatorially in a subunit-specific manner. The binding site of each subunit has a distinct, evolutionarily conserved pattern of polar and hydrophobic residues specifying recognition of discrete substrate motifs. The combinatorial recognition of polypeptides broadens the specificity of TRiC and may direct the topology of bound polypeptides along a productive folding trajectory, contributing to TRiC's unique ability to fold obligate substrates.
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Affiliation(s)
- Lukasz A Joachimiak
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA.
| | - Thomas Walzthoeni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland; Ph.D. Program in Molecular Life Sciences, University of Zurich/ETH Zurich, 8057 Zurich, Switzerland
| | - Corey W Liu
- Stanford Magnetic Resonance Laboratory, Stanford University, Stanford, CA 94305, USA
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA.
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Varghese S, Yang F, Pacheco V, Wrede K, Medvedev A, Ogata H, Knipp M, Heise H. Expression, purification, and solid-state NMR characterization of the membrane binding heme protein nitrophorin 7 in two electronic spin states. Biochemistry 2013; 52:7031-40. [PMID: 24033104 DOI: 10.1021/bi401020t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nitrophorins (NPs) comprise a group of NO transporting ferriheme b proteins found in the saliva of the blood sucking insect Rhodnius prolixus . In contrast to other nitrophorins (NP1-4), the recently identified membrane binding isoform NP7 tends to form oligomers and precipitates at higher concentrations in solution. Hence, solid-state NMR (ssNMR) was employed as an alternative method to gain structural insights on the precipitated protein. We report the expression and purification of (13)C,(15)N isotopically labeled protein together with the first ssNMR characterization of NP7. Because the size of NP7 (21 kDa) still provides a challenge for ssNMR, the samples were reverse labeled with Lys and Val to reduce the number of crosspeaks in two-dimensional spectra. The two electronic spin states with S = 1/2 and S = 0 at the ferriheme iron were generated by the complexation with imidazole and NO, respectively. ssNMR spectra of both forms are well resolved, which allows for sequential resonance assignments of 22 residues. Importantly, the ssNMR spectra demonstrate that aggregation does not affect the protein fold. Comparison of the spectra of the two electronic spin states allows the determination of paramagnetically shifted cross peaks due to pseudocontact shifts, which assists the assignment of residues close to the heme center.
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Affiliation(s)
- Sabu Varghese
- ICS-6 Institute of Complex Systems-Structural Biochemistry, Forschungszentrum Jülich , D-2425 Jülich, Germany
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Ippel JH, Koutsopoulos S, Nabuurs SM, van Berkel WJH, van der Oost J, van Mierlo CPM. NMR characterization of a 264-residue hyperthermostable endo-beta-1,3-glucanase. Biochem Biophys Res Commun 2010; 391:370-5. [PMID: 19913513 DOI: 10.1016/j.bbrc.2009.11.065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 11/07/2009] [Indexed: 11/29/2022]
Abstract
Insight into the hyperthermostable endo-beta-1,3-glucanase pfLamA from Pyrococcus furiosus is obtained by using NMR spectroscopy. pfLamA functions optimally at 104 degrees C and recently the X-ray structure of pfLamA has been obtained at 20 degrees C, a temperature at which the enzyme is inactive. In this study, near-complete (>99%) NMR assignments are presented of chemical shifts of pfLamA in presence and absence of calcium at 62 degrees C, a temperature at which the enzyme is biologically active. The protein contains calcium and the effects of calcium on the protein are assessed. Calcium binding results in relatively small chemical shift changes in a region distant from the active site of pfLamA and thus causes only minor conformational modifications. Removal of calcium does not significantly alter the denaturation temperature of pfLamA, implying that calcium does not stabilize the enzyme against global unfolding. The data obtained form the basis for elucidation of the molecular origins involved in conformational stability and biological activity of hyperthermophilic endo-beta-1,3-glucanases at extreme temperatures.
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Affiliation(s)
- Johannes H Ippel
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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Romanuka J, van den Bulke H, Kaptein R, Boelens R, Folkers GE. Novel strategies to overcome expression problems encountered with toxic proteins: application to the production of Lac repressor proteins for NMR studies. Protein Expr Purif 2009; 67:104-12. [PMID: 19460439 DOI: 10.1016/j.pep.2009.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 05/01/2009] [Accepted: 05/12/2009] [Indexed: 11/19/2022]
Abstract
NMR studies of structural aspects of allosteric regulation by the Lac repressor requires overexpression and isotope labeling of the protein. The size of the repressor makes it a challenging target, putting constraints on both expression conditions and sample preparation methods to overcome problems associated with studies of larger proteins by NMR. We optimized protocols for the production of deuterated functionally active thermostable dimeric Lac repressor and its core domain mutants. The Lac repressor core domain has never been obtained as a recombinant protein, possibly due to the observed toxicity to the host cells. We overcame the core domain induced toxicity by co-expression of this domain with the full length Lac repressor, combined with a stringent control of culture conditions. Significant overexpression was only obtained if during all stages of pre-culturing the bacteria were kept in their exponential growth phase at low density. The sensitivity of NMR measurements is dramatically affected by buffer conditions; we therefore used a thermofluor buffer optimization screen to determine the optimal buffer conditions. The combined thermofluor and NMR screening method yielded thermostable fully functional Lac repressor domain samples suitable for high-resolution NMR studies. The optimized procedures to adapt Escherichia coli to growth in D2O, to overcome toxicity, and to optimize protein sample conditions provides a broad range of universally applicable techniques for production of larger proteins for NMR spectroscopy.
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Affiliation(s)
- Julija Romanuka
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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12
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Abstract
Solution NMR spectroscopy represents a powerful tool for examining the structure and function of biological macromolecules. The advent of multidimensional (2D-4D) NMR, together with the widespread use of uniform isotopic labeling of proteins and RNA with the NMR-active isotopes, 15N and 13C, opened the door to detailed analyses of macromolecular structure, dynamics, and interactions of smaller macromolecules (< approximately 25 kDa). Over the past 10 years, advances in NMR and isotope labeling methods have expanded the range of NMR-tractable targets by at least an order of magnitude. Here we briefly describe the methodological advances that allow NMR spectroscopy of large macromolecules and their complexes and provide a perspective on the wide range of applications of NMR to biochemical problems.
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Affiliation(s)
- Mark P Foster
- Department of Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.
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13
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Shimamura T, Koike-Takeshita A, Yokoyama K, Masui R, Murai N, Yoshida M, Taguchi H, Iwata S. Crystal Structure of the Native Chaperonin Complex from Thermus thermophilus Revealed Unexpected Asymmetry at the cis-Cavity. Structure 2004; 12:1471-80. [PMID: 15296740 DOI: 10.1016/j.str.2004.05.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2004] [Revised: 05/05/2004] [Accepted: 05/18/2004] [Indexed: 11/23/2022]
Abstract
The chaperonins GroEL and GroES are essential mediators of protein folding. GroEL binds nonnative protein, ATP, and GroES, generating a ternary complex in which protein folding occurs within the cavity capped by GroES (cis-cavity). We determined the crystal structure of the native GroEL-GroES-ADP homolog from Thermus thermophilus, with substrate proteins in the cis-cavity, at 2.8 A resolution. Twenty-four in vivo substrate proteins within the cis-cavity were identified from the crystals. The structure around the cis-cavity, which encapsulates substrate proteins, shows significant differences from that observed for the substrate-free Escherichia coli GroEL-GroES complex. The apical domain around the cis-cavity of the Thermus GroEL-GroES complex exhibits a large deviation from the 7-fold symmetry. As a result, the GroEL-GroES interface differs considerably from the previously reported E. coli GroEL-GroES complex, including a previously unknown contact between GroEL and GroES.
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Affiliation(s)
- Tatsuro Shimamura
- Department of Biological Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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Heller M, John M, Coles M, Bosch G, Baumeister W, Kessler H. NMR studies on the substrate-binding domains of the thermosome: structural plasticity in the protrusion region. J Mol Biol 2004; 336:717-29. [PMID: 15095983 DOI: 10.1016/j.jmb.2003.12.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2003] [Revised: 12/01/2003] [Accepted: 12/10/2003] [Indexed: 10/26/2022]
Abstract
Group II chaperonins close their cavity with the help of conserved, helical extensions, the so-called protrusions, which emanate from the apical or substrate-binding domains. A comparison of previously solved crystal structures of the apical domains of the thermosome from Thermoplasma acidophilum showed structural plasticity in the protrusion parts induced by extensive packing interactions. In order to assess the influence of the crystal contacts we investigated both the alpha and beta-apical domains (alpha-ADT and beta-ADT) in solution by NMR spectroscopy. Secondary structure assignments and 15N backbone relaxation measurements showed mostly rigid structural elements in the globular parts of the domains, but revealed intrinsic structural disorder and partial helix fraying in the protrusion regions. On the other hand, a beta-turn-motif conserved in archaeal group II chaperonins might facilitate substrate recognition. Our results help us to specify the idea of the open, substrate-accepting state of the thermosome and may provide an additional jigsaw piece in understanding the mode of substrate binding of group II chaperonins.
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Affiliation(s)
- Markus Heller
- Institut für Organische Chemie und Biochemie II, Technische Universität München, Garching, Germany
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