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Žoldák G, Knappe TA, Geitner AJ, Scholz C, Dobbek H, Schmid FX, Jakob RP. Bacterial Chaperone Domain Insertions Convert Human FKBP12 into an Excellent Protein-Folding Catalyst-A Structural and Functional Analysis. Molecules 2024; 29:1440. [PMID: 38611720 PMCID: PMC11013033 DOI: 10.3390/molecules29071440] [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: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Many folding enzymes use separate domains for the binding of substrate proteins and for the catalysis of slow folding reactions such as prolyl isomerization. FKBP12 is a small prolyl isomerase without a chaperone domain. Its folding activity is low, but it could be increased by inserting the chaperone domain from the homolog SlyD of E. coli near the prolyl isomerase active site. We inserted two other chaperone domains into human FKBP12: the chaperone domain of SlpA from E. coli, and the chaperone domain of SlyD from Thermococcus sp. Both stabilized FKBP12 and greatly increased its folding activity. The insertion of these chaperone domains had no influence on the FKBP12 and the chaperone domain structure, as revealed by two crystal structures of the chimeric proteins. The relative domain orientations differ in the two crystal structures, presumably representing snapshots of a more open and a more closed conformation. Together with crystal structures from SlyD-like proteins, they suggest a path for how substrate proteins might be transferred from the chaperone domain to the prolyl isomerase domain.
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Affiliation(s)
- Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, Pavol Jozef Šafárik University in Košice, 040 11 Kosice, Slovakia
| | - Thomas A. Knappe
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Anne-Juliane Geitner
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | | | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany;
| | - Franz X. Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Roman P. Jakob
- Departement Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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2
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Dreydoppel M, Balbach J, Weininger U. Monitoring protein unfolding transitions by NMR-spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2022; 76:3-15. [PMID: 34984658 PMCID: PMC9018662 DOI: 10.1007/s10858-021-00389-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/28/2021] [Indexed: 06/01/2023]
Abstract
NMR-spectroscopy has certain unique advantages for recording unfolding transitions of proteins compared e.g. to optical methods. It enables per-residue monitoring and separate detection of the folded and unfolded state as well as possible equilibrium intermediates. This allows a detailed view on the state and cooperativity of folding of the protein of interest and the correct interpretation of subsequent experiments. Here we summarize in detail practical and theoretical aspects of such experiments. Certain pitfalls can be avoided, and meaningful simplification can be made during the analysis. Especially a good understanding of the NMR exchange regime and relaxation properties of the system of interest is beneficial. We show by a global analysis of signals of the folded and unfolded state of GB1 how accurate values of unfolding can be extracted and what limits different NMR detection and unfolding methods. E.g. commonly used exchangeable amides can lead to a systematic under determination of the thermodynamic protein stability. We give several perspectives of how to deal with more complex proteins and how the knowledge about protein stability at residue resolution helps to understand protein properties under crowding conditions, during phase separation and under high pressure.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Jochen Balbach
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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3
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Geitner AJ, Weininger U, Paulsen H, Balbach J, Kovermann M. Structure-Based Insights into the Dynamics and Function of Two-Domain SlpA from Escherichia coli. Biochemistry 2017; 56:6533-6543. [PMID: 29155566 DOI: 10.1021/acs.biochem.7b00786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SlpA (SlyD-like protein A) comprises two domains, a FK506 binding domain (FKBP fold) of moderate prolyl cis/trans-isomerase activity and an inserted in flap (IF) domain that hosts its chaperone activity. Here we present the nuclear magnetic resonance (NMR) solution structure of apo Escherichia coli SlpA determined by NMR that mirrors the structural properties seen for various SlyD homologues. Crucial structural differences in side-chain orientation arise for F37, which points directly into the hydrophobic core of the active site. It forms a prominent aromatic stacking with F15, one of the key residues for PPIase activity, thus giving a possible explanation for the inherently low PPIase activity of SlpA. The IF domain reveals the highest stability within the FKBP-IF protein family, most likely arising from an aromatic cluster formed by four phenylalanine residues. Both the thermodynamic stability and the PPIase and chaperone activity let us speculate that SlpA is a backup system for homologous bacterial systems under unfavorable conditions.
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Affiliation(s)
| | - Ulrich Weininger
- Institut für Physik, Biophysik, Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle (Saale), Germany
| | - Hauke Paulsen
- Institut für Physik, Universität Lübeck , Ratzeburger Allee 160, D-23562 Lübeck, Germany
| | - Jochen Balbach
- Institut für Physik, Biophysik, Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle (Saale), Germany.,Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle (Saale), Germany
| | - Michael Kovermann
- Institut für Physik, Biophysik, Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle (Saale), Germany.,Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle (Saale), Germany.,Universität Konstanz , Fachbereich Chemie, Universitätsstraße 10, D-78457 Konstanz, Germany
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4
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Quistgaard EM, Weininger U, Ural-Blimke Y, Modig K, Nordlund P, Akke M, Löw C. Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD. BMC Biol 2016; 14:82. [PMID: 27664121 PMCID: PMC5034536 DOI: 10.1186/s12915-016-0300-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/18/2016] [Indexed: 11/25/2022] Open
Abstract
Background Peptidyl-prolyl isomerases (PPIases) catalyze cis/trans isomerization of peptidyl-prolyl bonds, which is often rate-limiting for protein folding. SlyD is a two-domain enzyme containing both a PPIase FK506-binding protein (FKBP) domain and an insert-in-flap (IF) chaperone domain. To date, the interactions of these domains with unfolded proteins have remained rather obscure, with structural information on binding to the FKBP domain being limited to complexes involving various inhibitor compounds or a chemically modified tetrapeptide. Results We have characterized the binding of 15-residue-long unmodified peptides to SlyD from Thermus thermophilus (TtSlyD) in terms of binding thermodynamics and enzyme kinetics through the use of isothermal titration calorimetry, nuclear magnetic resonance spectroscopy, and site-directed mutagenesis. We show that the affinities and enzymatic activity of TtSlyD towards these peptides are much higher than for the chemically modified tetrapeptides that are typically used for activity measurements on FKBPs. In addition, we present a series of crystal structures of TtSlyD with the inhibitor FK506 bound to the FKBP domain, and with 15-residue-long peptides bound to either one or both domains, which reveals that substrates bind in a highly adaptable fashion to the IF domain through β-strand augmentation, and can bind to the FKBP domain as both types VIa1 and VIb-like cis-proline β-turns. Our results furthermore provide important clues to the catalytic mechanism and support the notion of inter-domain cross talk. Conclusions We found that 15-residue-long unmodified peptides can serve as better substrate mimics for the IF and FKBP domains than chemically modified tetrapeptides. We furthermore show how such peptides are recognized by each of these domains in TtSlyD, and propose a novel general model for the catalytic mechanism of FKBPs that involves C-terminal rotation around the peptidyl-prolyl bond mediated by stabilization of the twisted transition state in the hydrophobic binding site. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0300-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Esben M Quistgaard
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177, Stockholm, Sweden.,Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22603, Hamburg, Germany
| | - Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Yonca Ural-Blimke
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22603, Hamburg, Germany
| | - Kristofer Modig
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Pär Nordlund
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177, Stockholm, Sweden.,School of Biological Sciences, Nanyang Technological University, 639798, Singapore, Singapore
| | - Mikael Akke
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Christian Löw
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177, Stockholm, Sweden. .,Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22603, Hamburg, Germany.
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5
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Ginn C, Choi JW, Brocchini S. Disulfide-bridging PEGylation during refolding for the more efficient production of modified proteins. Biotechnol J 2016; 11:1088-99. [DOI: 10.1002/biot.201600035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 03/07/2016] [Accepted: 05/17/2016] [Indexed: 01/18/2023]
Affiliation(s)
| | - Ji-won Choi
- PolyTherics Ltd; Babraham Research Campus, Babraham; Cambridge UK
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6
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Schmidpeter PAM, Schmid FX. Prolyl isomerization and its catalysis in protein folding and protein function. J Mol Biol 2015; 427:1609-31. [PMID: 25676311 DOI: 10.1016/j.jmb.2015.01.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/30/2015] [Indexed: 12/20/2022]
Abstract
Prolyl isomerizations are intrinsically slow processes. They determine the rates of many protein folding reactions and control regulatory events in folded proteins. Prolyl isomerases are able to catalyze these isomerizations, and thus, they have the potential to assist protein folding and to modulate protein function. Here, we provide examples for how prolyl isomerizations limit protein folding and are accelerated by prolyl isomerases and how native-state prolyl isomerizations regulate protein functions. The roles of prolines in protein folding and protein function are closely interrelated because both of them depend on the coupling between cis/trans isomerization and conformational changes that can involve extended regions of a protein.
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Affiliation(s)
- Philipp A M Schmidpeter
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Franz X Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany.
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7
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Godin-Roulling A, Schmidpeter PAM, Schmid FX, Feller G. Functional adaptations of the bacterial chaperone trigger factor to extreme environmental temperatures. Environ Microbiol 2015; 17:2407-20. [PMID: 25389111 DOI: 10.1111/1462-2920.12707] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 08/27/2014] [Accepted: 09/03/2014] [Indexed: 01/26/2023]
Abstract
Trigger factor (TF) is the first molecular chaperone interacting cotranslationally with virtually all nascent polypeptides synthesized by the ribosome in bacteria. Thermal adaptation of chaperone function was investigated in TFs from the Antarctic psychrophile Pseudoalteromonas haloplanktis, the mesophile Escherichia coli and the hyperthermophile Thermotoga maritima. This series covers nearly all temperatures encountered by bacteria. Although structurally homologous, these TFs display strikingly distinct properties that are related to the bacterial environmental temperature. The hyperthermophilic TF strongly binds model proteins during their folding and protects them from heat-induced misfolding and aggregation. It decreases the folding rate and counteracts the fast folding rate imposed by high temperature. It also functions as a carrier of partially folded proteins for delivery to downstream chaperones ensuring final maturation. By contrast, the psychrophilic TF displays weak chaperone activities, showing that these functions are less important in cold conditions because protein folding, misfolding and aggregation are slowed down at low temperature. It efficiently catalyses prolyl isomerization at low temperature as a result of its increased cellular concentration rather than from an improved activity. Some chaperone properties of the mesophilic TF possibly reflect its function as a cold shock protein in E. coli.
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Affiliation(s)
- Amandine Godin-Roulling
- Laboratory of Biochemistry, Centre for Protein Engineering, University of Liège, Liège, B-4000, Belgium
| | - Philipp A M Schmidpeter
- Laboratorium für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, Bayreuth, D-95447, Germany
| | - Franz X Schmid
- Laboratorium für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, Bayreuth, D-95447, Germany
| | - Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, University of Liège, Liège, B-4000, Belgium
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8
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Jakob RP, Koch JR, Burmann BM, Schmidpeter PAM, Hunkeler M, Hiller S, Schmid FX, Maier T. Dimeric Structure of the Bacterial Extracellular Foldase PrsA. J Biol Chem 2014; 290:3278-92. [PMID: 25525259 DOI: 10.1074/jbc.m114.622910] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Secretion of proteins into the membrane-cell wall space is essential for cell wall biosynthesis and pathogenicity in Gram-positive bacteria. Folding and maturation of many secreted proteins depend on a single extracellular foldase, the PrsA protein. PrsA is a 30-kDa protein, lipid anchored to the outer leaflet of the cell membrane. The crystal structure of Bacillus subtilis PrsA reveals a central catalytic parvulin-type prolyl isomerase domain, which is inserted into a larger composite NC domain formed by the N- and C-terminal regions. This domain architecture resembles, despite a lack of sequence conservation, both trigger factor, a ribosome-binding bacterial chaperone, and SurA, a periplasmic chaperone in Gram-negative bacteria. Two main structural differences are observed in that the N-terminal arm of PrsA is substantially shortened relative to the trigger factor and SurA and in that PrsA is found to dimerize in a unique fashion via its NC domain. Dimerization leads to a large, bowl-shaped crevice, which might be involved in vivo in protecting substrate proteins from aggregation. NMR experiments reveal a direct, dynamic interaction of both the parvulin and the NC domain with secretion propeptides, which have been implicated in substrate targeting to PrsA.
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Affiliation(s)
- Roman P Jakob
- From the Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland and
| | - Johanna R Koch
- the Laboratorium für Biochemie and Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Björn M Burmann
- From the Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland and
| | - Philipp A M Schmidpeter
- the Laboratorium für Biochemie and Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Moritz Hunkeler
- From the Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland and
| | - Sebastian Hiller
- From the Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland and
| | - Franz X Schmid
- the Laboratorium für Biochemie and Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Timm Maier
- From the Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland and
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9
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Generation of a Highly Active Folding Enzyme by Combining a Parvulin-Type Prolyl Isomerase from SurA with an Unrelated Chaperone Domain. J Mol Biol 2013; 425:4089-98. [DOI: 10.1016/j.jmb.2013.06.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 11/19/2022]
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10
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Linnert M, Lin YJ, Manns A, Haupt K, Paschke AK, Fischer G, Weiwad M, Lücke C. The FKBP-type domain of the human aryl hydrocarbon receptor-interacting protein reveals an unusual Hsp90 interaction. Biochemistry 2013; 52:2097-107. [PMID: 23418784 DOI: 10.1021/bi301649m] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aryl hydrocarbon receptor-interacting protein (AIP) has been predicted to consist of an N-terminal FKBP-type peptidyl-prolyl cis/trans isomerase (PPIase) domain and a C-terminal tetratricopeptide repeat (TPR) domain, as typically found in FK506-binding immunophilins. AIP, however, exhibited no inherent FK506 binding or PPIase activity. Alignment with the prototypic FKBP12 showed a high sequence homology but indicated inconsistencies with regard to the secondary structure prediction derived from chemical shift analysis of AIP(2-166). NMR-based structure determination of AIP(2-166) now revealed a typical FKBP fold with five antiparallel β-strands forming a half β-barrel wrapped around a central α-helix, thus permitting AIP to be also named FKBP37.7 according to FKBP nomenclature. This PPIase domain, however, features two structure elements that are unusual for FKBPs: (i) an N-terminal α-helix, which additionally stabilizes the domain, and (ii) a rather long insert, which connects the last two β-strands and covers the putative active site. Diminution of the latter insert did not generate PPIase activity or FK506 binding capability, indicating that the lack of catalytic activity in AIP is the result of structural differences within the PPIase domain. Compared to active FKBPs, a diverging conformation of the loop connecting β-strand C' and the central α-helix apparently is responsible for this inherent lack of catalytic activity in AIP. Moreover, Hsp90 was identified as potential physiological interaction partner of AIP, which revealed binding contacts not only at the TPR domain but uncommonly also at the PPIase domain.
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Affiliation(s)
- Miriam Linnert
- Max Planck Research Unit for Enzymology of Protein Folding , Weinbergweg 22, 06120 Halle (Saale), Germany
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11
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Zoldák G, Geitner AJ, Schmid FX. The Prolyl Isomerase SlyD Is a Highly Efficient Enzyme but Decelerates the Conformational Folding of a Client Protein. J Am Chem Soc 2013; 135:4372-9. [DOI: 10.1021/ja311775a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Gabriel Zoldák
- Laboratorium
für Biochemie und Bayreuther Zentrum
für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Anne-Juliane Geitner
- Laboratorium
für Biochemie und Bayreuther Zentrum
für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Franz X. Schmid
- Laboratorium
für Biochemie und Bayreuther Zentrum
für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
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12
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Kovermann M, Balbach J. Dynamic control of the prolyl isomerase function of the dual-domain SlyD protein. Biophys Chem 2013; 171:16-23. [DOI: 10.1016/j.bpc.2012.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/22/2012] [Accepted: 11/22/2012] [Indexed: 12/13/2022]
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13
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Arai K, Noguchi M, Singh BG, Priyadarsini KI, Fujio K, Kubo Y, Takayama K, Ando S, Iwaoka M. A water-soluble selenoxide reagent as a useful probe for the reactivity and folding of polythiol peptides. FEBS Open Bio 2012; 3:55-64. [PMID: 23772375 PMCID: PMC3668528 DOI: 10.1016/j.fob.2012.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/20/2012] [Accepted: 12/20/2012] [Indexed: 11/16/2022] Open
Abstract
A water-soluble selenoxide (DHSox) having a five-membered ring structure enables rapid and selective conversion of cysteinyl SH groups in a polypeptide chain into SS bonds in a wide pH and temperature range. It was previously demonstrated that the second-order rate constants for the SS formation with DHSox would be proportional to the number of the free SH groups present in the substrate if there is no steric congestion around the SH groups. In the present study, kinetics of the SS formation with DHSox was extensively studied at pH 4–10 and 25 °C by using reduced ribonuclease A, recombinant hirudin variant (CX-397), insulin A- and B-chains, and relaxin A-chain, which have two to eight cysteine residues, as polythiol substrates. The obtained rate constants showed stochastic SS formation behaviors under most conditions. However, the rate constants for CX-397 at pH 8.0 and 10.0 were not proportional to the number of the free SH groups, suggesting that the SS intermediate ensembles possess densely packed structures under weakly basic conditions. The high two-electron redox potential of DHSox (375 mV at 25 °C) compared to l-cystine supported the high ability of DHSox for SS formation in a polypeptide chain. Interestingly, the rate constants of the SS formation jumped up at a pH around the pKa value of the cysteinyl SH groups. The SS formation velocity was slightly decreased by addition of a denaturant due probably to the interaction between the denaturant and the peptide. The stochastic behaviors as well as the absolute values of the second-order rate constants in comparison to dithiothreitol (DTTred) are useful to probe the chemical reactivity and conformation, hence the folding, of polypeptide chains.
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Key Words
- 1S, 2S, 3S, and 4S, ensembles of SS intermediates with one, two, three, and four SS bonds, respectively
- 1S°, 2S°, and 3S°, ensembles of SS intermediates of CX-397 with one, two, and three kinetically formed SS bonds, respectively
- 4-Dihydroxyselenolane oxide
- AEMTS, 2-aminoethyl methanethiosulfonate
- CD, circular dichroism
- CX-397, recombinant hirudin variant CX-397
- DHSox, trans-3,4-dihydroxyselenolane oxide
- DHSred, reduced DHSox
- DTTox, oxidized dithiothreitol
- DTTred, dl-dithiothreitol
- Disulfide
- ESI, electron spray ionization
- GSSG, oxidized glutathione
- Gdn-HCl, guanidine hydrochloride
- HPLC, high-performance liquid chromatography
- HV-1, recombinant hirudin variant-1
- HV-3, recombinant hirudin variant-3
- Ins-A, insulin A-chain
- Ins-B, insulin B-chain
- N, native protein
- NHE, normal hydrogen electrode
- Oxidative folding
- R, reduced polypeptide
- RNase A, ribonuclease A
- Redox potential
- Rlx-A, relaxin A-chain
- R°, reduced CX-397 at acidic conditions
- SH, thiol
- SS, disulfide
- SeSe, diselenide
- S−, thiolate
- TFA, trifluoroacetic acid
- Tris, tris(hydroxymethyl)aminomethane.
- pI, isoelectric point
- trans-3
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Affiliation(s)
- Kenta Arai
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan
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Geitner AJ, Schmid FX. Combination of the Human Prolyl Isomerase FKBP12 with Unrelated Chaperone Domains Leads to Chimeric Folding Enzymes with High Activity. J Mol Biol 2012; 420:335-49. [DOI: 10.1016/j.jmb.2012.04.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 04/10/2012] [Accepted: 04/18/2012] [Indexed: 12/11/2022]
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15
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Arai K, Kumakura F, Iwaoka M. Kinetic and thermodynamic analysis of the conformational folding process of SS-reduced bovine pancreatic ribonuclease A using a selenoxide reagent with high oxidizing ability. FEBS Open Bio 2012; 2:60-70. [PMID: 23653890 PMCID: PMC3646284 DOI: 10.1016/j.fob.2012.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 04/10/2012] [Accepted: 04/10/2012] [Indexed: 11/18/2022] Open
Abstract
Redox-coupled folding pathways of bovine pancreatic ribonuclease A (RNase A) with four intramolecular disulfide (SS) bonds comprise three phases: (I) SS formation to generate partially oxidized intermediate ensembles with no rigid folded structure; (II) SS rearrangement from the three SS intermediate ensemble (3S) to the des intermediates having three native SS linkages; (III) final oxidation of the last native SS linkage to generate native RNase A. We previously demonstrated that DHSox, a water-soluble selenoxide reagent for rapid and quantitative SS formation, allows clear separation of the three folding phases. In this study, the main conformational folding phase (phase II) has been extensively analyzed at pH 8.0 under a wide range of temperatures (5–45 °C), and thermodynamic and kinetic parameters for the four des intermediates were determined. The free-energy differences (ΔG) as a function of temperature suggested that the each SS linkage has different thermodynamic and kinetic roles in stability of the native structure. On the other hand, comparison of the rate constants and the activation energies for 3S → des with those reported for the conformational folding of SS-intact RNase A suggested that unfolded des species (desU) having three native SS linkages but not yet being folded are involved in very small amounts (<1%) in the 3S intermediate ensemble and the desU species would gain the native-like structures via X-Pro isomerization like SS-intact RNase A. It was revealed that DHSox is useful for kinetic and thermodynamic analysis of the conformational folding process on the oxidative folding pathways of SS-reduced proteins.
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Key Words
- 1S, 2S, 3S, and 4S, ensembles of folding intermediates of RNase A with one, two, three, and four SS linkages, respectively
- AEMTS, 2-aminoethyl methanethiosulfonate
- BPTI, bovine pancreatic trypsin inhibitor
- DHSox, trans-3,4-dihydroxyselenolane oxide
- DTTox, oxidized DTT
- DTTred, dithiothreitol
- Disulfide bond
- EDTA, ethylenediaminetetraacetic acid
- ESI, electron spray ionization
- GSSG, oxidized glutathione
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- HPLC, high performance liquid chromatography
- N, native RNase A
- Oxidative protein folding
- R, reduced RNase A
- RNase A, bovine pancreatic ribonuclease A
- Ribonuclease A
- SH, thiol
- SS, disulfide
- Selenoxide
- TFA, trifluoroacetic acid
- Trans-3,4-dihydroxyselenolane oxide
- U, unfolded RNase A
- UV, ultraviolet
- X-Pro isomerization
- desN, folded des intermediate
- desU, unfolded des intermediate
- des[26–84], des[40–95], des[58–110], and des[65–72], structured 3S intermediates of RNase A having three native SS bonds but lacking one native SS bond specified
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Affiliation(s)
- Kenta Arai
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan
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Haupt C, Patzschke R, Weininger U, Gröger S, Kovermann M, Balbach J. Transient Enzyme–Substrate Recognition Monitored by Real-Time NMR. J Am Chem Soc 2011; 133:11154-62. [DOI: 10.1021/ja2010048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caroline Haupt
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Rica Patzschke
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Ulrich Weininger
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Stefan Gröger
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Michael Kovermann
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Jochen Balbach
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
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17
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Kale A, Phansopa C, Suwannachart C, Craven CJ, Rafferty JB, Kelly DJ. The virulence factor PEB4 (Cj0596) and the periplasmic protein Cj1289 are two structurally related SurA-like chaperones in the human pathogen Campylobacter jejuni. J Biol Chem 2011; 286:21254-65. [PMID: 21524997 PMCID: PMC3122185 DOI: 10.1074/jbc.m111.220442] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 04/08/2011] [Indexed: 11/06/2022] Open
Abstract
The PEB4 protein is an antigenic virulence factor implicated in host cell adhesion, invasion, and colonization in the food-borne pathogen Campylobacter jejuni. peb4 mutants have defects in outer membrane protein assembly and PEB4 is thought to act as a periplasmic chaperone. The crystallographic structure of PEB4 at 2.2-Å resolution reveals a dimer with distinct SurA-like chaperone and peptidyl-prolyl cis/trans isomerase (PPIase) domains encasing a large central cavity. Unlike SurA, the chaperone domain is formed by interlocking helices from each monomer, creating a domain-swapped architecture. PEB4 stimulated the rate of proline isomerization limited refolding of denatured RNase T(1) in a juglone-sensitive manner, consistent with parvulin-like PPIase domains. Refolding and aggregation of denatured rhodanese was significantly retarded in the presence of PEB4 or of an engineered variant specifically lacking the PPIase domain, suggesting the chaperone domain possesses a holdase activity. Using bioinformatics approaches, we identified two other SurA-like proteins (Cj1289 and Cj0694) in C. jejuni. The 2.3-Å structure of Cj1289 does not have the domain-swapped architecture of PEB4 and thus more resembles SurA. Purified Cj1289 also enhanced RNase T(1) refolding, although poorly compared with PEB4, but did not retard the refolding of denatured rhodanese. Structurally, Cj1289 is the most similar protein to SurA in C. jejuni, whereas PEB4 has most structural similarity to the Par27 protein of Bordetella pertussis. Our analysis predicts that Cj0694 is equivalent to the membrane-anchored chaperone PpiD. These results provide the first structural insights into the periplasmic assembly of outer membrane proteins in C. jejuni.
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Affiliation(s)
- Avinash Kale
- From the Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Chatchawal Phansopa
- From the Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Chatrudee Suwannachart
- From the Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - C. Jeremy Craven
- From the Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - John B. Rafferty
- From the Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - David J. Kelly
- From the Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
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18
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Kahra D, Kovermann M, Löw C, Hirschfeld V, Haupt C, Balbach J, Hübner CG. Conformational plasticity and dynamics in the generic protein folding catalyst SlyD unraveled by single-molecule FRET. J Mol Biol 2011; 411:781-90. [PMID: 21596048 DOI: 10.1016/j.jmb.2011.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 04/29/2011] [Accepted: 05/02/2011] [Indexed: 11/15/2022]
Abstract
The relation between conformational dynamics and chemistry in enzyme catalysis recently has received increasing attention. While, in the past, the mechanochemical coupling was mainly attributed to molecular motors, nowadays, it seems that this linkage is far more general. Single-molecule fluorescence methods are perfectly suited to directly evidence conformational flexibility and dynamics. By labeling the enzyme SlyD, a member of peptidyl-prolyl cis-trans isomerases of the FK506 binding protein type with an inserted chaperone domain, with donor and acceptor fluorophores for single-molecule fluorescence resonance energy transfer, we directly monitor conformational flexibility and conformational dynamics between the chaperone domain and the FK506 binding protein domain. We find a broad distribution of distances between the labels with two main maxima, which we attribute to an open conformation and to a closed conformation of the enzyme. Correlation analysis demonstrates that the conformations exchange on a rate in the 100 Hz range. With the aid from Monte Carlo simulations, we show that there must be conformational flexibility beyond the two main conformational states. Interestingly, neither the conformational distribution nor the dynamics is significantly altered upon binding of substrates or other known binding partners. Based on these experimental findings, we propose a model where the conformational dynamics is used to search the conformation enabling the chemical step, which also explains the remarkable substrate promiscuity connected with a high efficiency of this class of peptidyl-prolyl cis-trans isomerases.
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Affiliation(s)
- Dana Kahra
- Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23564 Lübeck, Germany
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19
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Zoldák G, Schmid FX. Cooperation of the prolyl isomerase and chaperone activities of the protein folding catalyst SlyD. J Mol Biol 2010; 406:176-94. [PMID: 21147124 DOI: 10.1016/j.jmb.2010.12.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 10/29/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
The SlyD (sensitive to lysis D) protein of Escherichia coli is a folding enzyme with a chaperone domain and a prolyl isomerase domain of the FK506 binding protein type. Here we investigated how the two domains and their interplay are optimized for function in protein folding. Unfolded protein molecules initially form a highly dynamic complex with the chaperone domain of SlyD, and they are then transferred to the prolyl isomerase domain. The turnover number of the prolyl isomerase site is very high and guarantees that, after transfer, prolyl peptide bonds in substrate proteins are isomerized very rapidly. The Michaelis constant of catalyzed folding reflects the substrate affinity of the chaperone domain, and the turnover number is presumably determined by the rate of productive substrate transfer from the chaperone to the prolyl isomerase site and by the intrinsic propensity of the refolding protein chain to leave the active site with the native prolyl isomer. The efficiency of substrate transfer is high because dissociation from the chaperone site is very fast and because the two sites are close to each other. Protein molecules that left the prolyl isomerase site with an incorrect prolyl isomer can rapidly be re-bound by the chaperone domain because the association rate is very high as well.
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Affiliation(s)
- Gabriel Zoldák
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth,D-95440 Bayreuth, Germany
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20
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Weininger U, Jakob RP, Kovermann M, Balbach J, Schmid FX. The prolyl isomerase domain of PpiD from Escherichia coli shows a parvulin fold but is devoid of catalytic activity. Protein Sci 2010; 19:6-18. [PMID: 19866485 DOI: 10.1002/pro.277] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
PpiD is a periplasmic folding helper protein of Escherichia coli. It consists of an N-terminal helix that anchors PpiD in the inner membrane near the SecYEG translocon, followed by three periplasmic domains. The second domain (residues 264-357) shows homology to parvulin-like prolyl isomerases. This domain is a well folded, stable protein and follows a simple two-state folding mechanism. In its solution structure, as determined by NMR spectroscopy, it resembles most closely the first parvulin domain of the SurA protein, which resides in the periplasm of E. coli as well. A previously reported prolyl isomerase activity of PpiD could not be reproduced when using improved protease-free peptide assays or assays with refolding proteins as substrates. The parvulin domain of PpiD interacts, however, with a proline-containing tetrapeptide, and the binding site, as identified by NMR resonance shift analysis, colocalized with the catalytic sites of other parvulins. In its structure, the parvulin domain of PpiD resembles most closely the inactive first parvulin domain of SurA, which is part of the chaperone unit of this protein and presumably involved in substrate recognition.
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Affiliation(s)
- Ulrich Weininger
- Institut für Physik, Biophysik, and Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle(Saale), Germany
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21
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Löw C, Neumann P, Tidow H, Weininger U, Haupt C, Friedrich-Epler B, Scholz C, Stubbs MT, Balbach J. Crystal structure determination and functional characterization of the metallochaperone SlyD from Thermus thermophilus. J Mol Biol 2010; 398:375-90. [PMID: 20230833 DOI: 10.1016/j.jmb.2010.03.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 02/25/2010] [Accepted: 03/04/2010] [Indexed: 11/27/2022]
Abstract
SlyD (sensitive to lysis D; product of the slyD gene) is a prolyl isomerase [peptidyl-prolyl cis/trans isomerase (PPIase)] of the FK506 binding protein (FKBP) type with chaperone properties. X-ray structures derived from three different crystal forms reveal that SlyD from Thermus thermophilus consists of two domains representing two functional units. PPIase activity is located in a typical FKBP domain, whereas chaperone function is associated with the autonomously folded insert-in-flap (IF) domain. The two isolated domains are stable and functional in solution, but the presence of the IF domain increases the PPIase catalytic efficiency of the FKBP domain by 2 orders of magnitude, suggesting that the two domains act synergistically to assist the folding of polypeptide chains. The substrate binding surface of SlyD from T. thermophilus was mapped by NMR chemical shift perturbations to hydrophobic residues of the IF domain, which exhibits significantly reduced thermodynamic stability according to NMR hydrogen/deuterium exchange and fluorescence equilibrium transition experiments. Based on structural homologies, we hypothesize that this is due to the absence of a stabilizing beta-strand, suggesting in turn a mechanism for chaperone activity by 'donor-strand complementation.' Furthermore, we identified a conserved metal (Ni(2+)) binding site at the C-terminal SlyD-specific helical appendix of the FKBP domain, which may play a role in metalloprotein assembly.
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Affiliation(s)
- Christian Löw
- Institut für Physik, Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
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22
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Weininger U, Haupt C, Schweimer K, Graubner W, Kovermann M, Brüser T, Scholz C, Schaarschmidt P, Zoldak G, Schmid FX, Balbach J. NMR solution structure of SlyD from Escherichia coli: spatial separation of prolyl isomerase and chaperone function. J Mol Biol 2009; 387:295-305. [PMID: 19356587 DOI: 10.1016/j.jmb.2009.01.034] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 01/19/2009] [Accepted: 01/20/2009] [Indexed: 10/21/2022]
Abstract
SlyD (sensitive to lysis D) is a putative folding helper from the bacterial cytosol and harbors prolyl isomerase and chaperone activities. We determined the solution NMR structure of a truncated version of SlyD (1-165) from Escherichia coli (SlyD*) that lacks the presumably unstructured C-terminal tail. SlyD* consists of two well-separated domains: the FKBP domain, which harbors the prolyl isomerase activity, and the insert-in-flap (IF) domain, which harbors the chaperone activity. The IF domain is inserted into a loop of the FKBP domain near the prolyl isomerase active site. The NMR structure of SlyD* showed no distinct orientation of the two domains relative to each other. In the FKBP domain, Tyr68 points into the active site, which might explain the lowered intrinsic prolyl isomerase activity and the much lower FK506 binding affinity of the protein compared with archetype human FKBP12 (human FK506 binding protein with 12 kDa). The thermodynamics and kinetics of substrate binding by SlyD* were quantified by fluorescence resonance energy transfer. NMR titration experiments revealed that the IF domain recognizes and binds unfolded or partially folded proteins and peptides. Insulin aggregation is markedly slowed by SlyD* as evidenced by two-dimensional NMR spectroscopy in real time, probably due to SlyD* binding to denatured insulin. The capacity of the IF domain to establish an initial encounter-collision complex, together with the flexible orientation of the two interacting domains, makes SlyD* a very powerful catalyst of protein folding.
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Affiliation(s)
- Ulrich Weininger
- Institut für Physik, Fachgruppe Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
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23
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Tremmel D, Tropschug M. Neurospora crassa FKBP22 Is a Novel ER Chaperone and Functionally Cooperates with BiP. J Mol Biol 2007; 369:55-68. [PMID: 17428499 DOI: 10.1016/j.jmb.2007.01.092] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 01/09/2007] [Accepted: 01/11/2007] [Indexed: 11/30/2022]
Abstract
FK506 binding proteins (FKBPs) belong to the family of peptidyl prolyl cis-trans isomerases (PPIases) catalyzing the cis/trans isomerisation of Xaa-Pro bonds in oligopeptides and proteins. FKBPs are involved in folding, assembly and trafficking of proteins. However, only limited knowledge is available about the roles of FKBPs in the endoplasmic reticulum (ER) and their interaction with other proteins. Here we show the ER located Neurospora crassa FKBP22 to be a dimeric protein with PPIase and a novel chaperone activity. While the homodimerization of FKBP22 is mediated by its carboxy-terminal domain, the amino-terminal domain is a functional FKBP domain. The chaperone activity is mediated by the FKBP domain but is exhibited only by the full-length protein. We further demonstrate a direct interaction between FKBP22 and BiP, the major Hsp70 chaperone in the ER. The binding to BiP is mediated by the FKBP domain of FKBP22. Interestingly BiP enhances the chaperone activity of FKBP22. Both proteins form a stable complex with an unfolded substrate protein and thereby prevent its aggregation. These results suggest that BiP and FKBP22 form a folding helper complex with a high chaperoning capacity in the ER of Neurospora crassa.
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Affiliation(s)
- Dirk Tremmel
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und molekulare Zellforschung, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 7, D-79104 Freiburg, Germany
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24
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Knappe TA, Eckert B, Schaarschmidt P, Scholz C, Schmid FX. Insertion of a Chaperone Domain Converts FKBP12 into a Powerful Catalyst of Protein Folding. J Mol Biol 2007; 368:1458-68. [PMID: 17397867 DOI: 10.1016/j.jmb.2007.02.097] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Accepted: 02/28/2007] [Indexed: 11/28/2022]
Abstract
The catalytic activity of human FKBP12 as a prolyl isomerase is high towards short peptides, but very low in proline-limited protein folding reactions. In contrast, the SlyD proteins, which are members of the FKBP family, are highly active as folding enzymes. They contain an extra "insert-in-flap" or IF domain near the prolyl isomerase active site. The excision of this domain did not affect the prolyl isomerase activity of SlyD from Escherichia coli towards short peptide substrates but abolished its catalytic activity in proline-limited protein folding reactions. The reciprocal insertion of the IF domain of SlyD into human FKBP12 increased its folding activity 200-fold and generated a folding catalyst that is more active than SlyD itself. The IF domain binds to refolding protein chains and thus functions as a chaperone module. A prolyl isomerase catalytic site and a separate chaperone site with an adapted affinity for refolding protein chains are the key elements for a productive coupling between the catalysis of prolyl isomerization and conformational folding in the enzymatic mechanisms of SlyD and other prolyl isomerases, such as trigger factor and FkpA.
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Affiliation(s)
- Thomas A Knappe
- Laboratorium für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany
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25
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Weiwad M, Werner A, Rücknagel P, Schierhorn A, Küllertz G, Fischer G. Catalysis of proline-directed protein phosphorylation by peptidyl-prolyl cis/trans isomerases. J Mol Biol 2004; 339:635-46. [PMID: 15147846 DOI: 10.1016/j.jmb.2004.04.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Revised: 04/01/2004] [Accepted: 04/01/2004] [Indexed: 11/25/2022]
Abstract
Proline-directed protein phosphorylation was shown to depend on the capacity of the targeted Ser(Thr)-Pro bond to exhibit conformational polymorphism. The cis/trans isomer specificity underlying ERK2-catalyzed phosphate transfer leads to a complete discrimination of the cis Ser(Thr)-Pro conformer of oligopeptide substrates. We investigated in vitro the ERK2-catalyzed phosphorylation of Aspergillus oryzae RNase T1 containing two Ser-Pro bonds both of which share high stabilization energy in their respective native state conformation, the cis Ser54-Pro and the trans Ser72-Pro moiety. Despite trans isomer specificity of ERK2, a doubly phosphorylated RNase T1 was found as the final reaction product. Similarly, the RNase T1 S54G/P55N and RNase T1 P73V variants, which retain the prolyl bond conformations of the RNase T1-wt, were both monophosphorylated with a catalytic efficiency kcat/KM of 425 M(-1) s(-1) and 1228 M(-1) s(-1), respectively. However, initial phosphorylation rates did not depend linearly on the ERK2 concentration. The phosphorylation rate of the resulting plateau region at high ERK2 concentrations can be increased up to threefold for the RNase T1 P73V variant in the presence of the peptidyl-prolyl cis/trans isomerase Cyclophilin 18, indicating a conformational interconversion as the rate limiting step in the catalyzed phosphate group transfer. Using peptidyl-prolyl cis/trans isomerases with different substrate specificity, we identified a native state conformational equilibrium of the Ser54-Pro bond with the minor trans Ser54-Pro bond as the phosphorylation-sensitive moiety. This technique can therefore be used for a determination of the ratio and the interconversion rates of prolyl bond isomers in the native state of proteins.
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Affiliation(s)
- Matthias Weiwad
- Research Unit Enzymology of Protein Folding, Max-Planck Society, Weinbergweg 22, D-06120 Halle/Saale, Germany
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26
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Hainzl O, Wegele H, Richter K, Buchner J. Cns1 Is an Activator of the Ssa1 ATPase Activity. J Biol Chem 2004; 279:23267-73. [PMID: 15044454 DOI: 10.1074/jbc.m402189200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hsp90 is a key mediator in the folding process of a growing number of client proteins. The molecular chaperone cooperates with many co-chaperones and partner proteins to fulfill its task. In Saccharomyces cerevisiae, several co-chaperones of Hsp90 interact with Hsp90 via a tetratricopeptide repeat (TPR) domain. Here we show that one of these proteins, Cns1, binds both to Hsp90 and to the yeast Hsp70 protein Ssa1 with comparable affinities. This is reminiscent of Sti1, another TPR-containing co-chaperone. Unlike Sti1, Cns1 exhibits no influence on the ATPase of Hsp90. However, it activates the ATPase of Ssa1 up to 30-fold by accelerating the rate-limiting ATP hydrolysis step. This stimulating effect is mediated by the N-terminal TPR-containing part of Cns1, whereas the C-terminal part showed no effect. Competition experiments allow the conclusion that Hsp90 and Ssa1 compete for binding to the single TPR domain of Cns1. Taken together, Cns1 is a potent cochaperone of Ssa1. Our findings highlight the importance of the regulation of Hsp70 function in the context of the Hsp90 chaperone cycle.
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Affiliation(s)
- Otmar Hainzl
- Institut für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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27
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Affiliation(s)
- F X Schmid
- Biochemisches Laboratorium, Universität Bayreuth, D-95440 Bayreuth, Germany
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28
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Abstract
Trigger factor is a ribosome-bound folding helper, which, apparently, combines two functions, chaperoning of nascent proteins and catalyzing prolyl isomerization in their folding. Immediate chaperone binding at the ribosome might interfere with rapid protein folding reactions, and we find that trigger factor indeed retards the in vitro folding of a protein with native prolyl isomers. The kinetic analysis of trigger factor binding to a refolding protein reveals that the adverse effects of trigger factor on conformational folding are minimized by rapid binding and release. The complex between trigger factor and a substrate protein is thus very short-lived, and fast-folding proteins can escape efficiently from an accidental interaction with trigger factor. Protein chains with incorrect prolyl isomers cannot complete folding and therefore can rebind for further rounds of catalysis. Unlike DnaK, trigger factor interacts with substrate proteins in a nucleotide-independent binding reaction, which seems to be optimized for high catalytic activity rather than for chaperone function. The synthetic lethality, observed when the genes for both DnaK and trigger factor are disrupted, might result from an indirect linkage. In the absence of trigger factor, folding is retarded and more aggregates form, which can neither be prevented nor disposed of when DnaK is lacking as well.
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Affiliation(s)
- R Maier
- Laboratorium für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany
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29
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Ramm K, Plückthun A. High enzymatic activity and chaperone function are mechanistically related features of the dimeric E. coli peptidyl-prolyl-isomerase FkpA. J Mol Biol 2001; 310:485-98. [PMID: 11428902 DOI: 10.1006/jmbi.2001.4747] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have recently described the existence of a chaperone activity for the dimeric peptidyl-prolyl cis/trans isomerase FkpA from the periplasm of Escherichia coli that is independent of its isomerase activity. We have now investigated the molecular mechanism of these two activities in vitro in greater detail. The isomerase activity with a protein substrate (RNaseT1) is characterized by a 100-fold higher k(cat)/K(M) value than with a short tetrapeptide substrate. This enhanced activity with a protein is due to an increased affinity towards the protein substrate mediated by a polypeptide-binding site that is distinct from the active site. The chaperone activity is also mediated by interaction of folding and unfolding intermediates with a binding site that is most likely identical to the polypeptide-binding site which enhances catalysis. Both activities are thus mechanistically related, being based on the transient interaction with this high-affinity polypeptide-binding site. Only the isomerase activity, but not the chaperone activity, with the substrate citrate synthase can be inhibited by FK520. Experiments with the isolated domains of FkpA imply that both the isomerase and the chaperone site are located on the highly conserved FKBP domain. The additional amino-terminal domain mediates the dimerization and thus places the two active sites of the FKBP domains in juxtaposition, such that they can simultaneously interact with a protein, and this is required for full catalytic activity.
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Affiliation(s)
- K Ramm
- Biochemisches Institut, Universität Zürich, Winterthurerstr. 190, Zürich, CH-8057, Switzerland
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30
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Behrens S, Maier R, de Cock H, Schmid FX, Gross CA. The SurA periplasmic PPIase lacking its parvulin domains functions in vivo and has chaperone activity. EMBO J 2001; 20:285-94. [PMID: 11226178 PMCID: PMC140197 DOI: 10.1093/emboj/20.1.285] [Citation(s) in RCA: 183] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Escherichia coli periplasmic peptidyl-prolyl isomerase (PPIase) SurA is involved in the maturation of outer membrane porins. SurA consists of a substantial N-terminal region, two iterative parvulin-like domains and a C-terminal tail. Here we show that a variant of SurA lacking both parvulin-like domains exhibits a PPIase-independent chaperone-like activity in vitro and almost completely complements the in vivo function of intact SurA. SurA interacts preferentially (>50-fold) with in vitro synthesized porins over other similarly sized proteins, leading us to suggest that the chaperone-like function of SurA preferentially facilitates maturation of outer membrane proteins.
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Affiliation(s)
- Susanne Behrens
- Departments of Stomatology and Microbiology, University of California, San Francisco, 513 Parnassus Avenue, CA 94143, USA, Abteilung Molekulare Genetik und Präparative Molekularbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Laboratorium für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany and Department of Molecular Cell Biology, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Corresponding author e-mail:
| | - Raimund Maier
- Departments of Stomatology and Microbiology, University of California, San Francisco, 513 Parnassus Avenue, CA 94143, USA, Abteilung Molekulare Genetik und Präparative Molekularbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Laboratorium für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany and Department of Molecular Cell Biology, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Corresponding author e-mail:
| | - Hans de Cock
- Departments of Stomatology and Microbiology, University of California, San Francisco, 513 Parnassus Avenue, CA 94143, USA, Abteilung Molekulare Genetik und Präparative Molekularbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Laboratorium für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany and Department of Molecular Cell Biology, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Corresponding author e-mail:
| | - Franz X. Schmid
- Departments of Stomatology and Microbiology, University of California, San Francisco, 513 Parnassus Avenue, CA 94143, USA, Abteilung Molekulare Genetik und Präparative Molekularbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Laboratorium für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany and Department of Molecular Cell Biology, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Corresponding author e-mail:
| | - Carol A. Gross
- Departments of Stomatology and Microbiology, University of California, San Francisco, 513 Parnassus Avenue, CA 94143, USA, Abteilung Molekulare Genetik und Präparative Molekularbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Laboratorium für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany and Department of Molecular Cell Biology, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Corresponding author e-mail:
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31
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Scholz C, Mücke M, Rape M, Pecht A, Pahl A, Bang H, Schmid FX. Recognition of protein substrates by the prolyl isomerase trigger factor is independent of proline residues. J Mol Biol 1998; 277:723-32. [PMID: 9533890 DOI: 10.1006/jmbi.1997.1604] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The trigger factor is associated with bacterial ribosomes and catalyzes proline-limited protein folding reactions. Its folding activity is very high and conserved in evolution, as shown for the homologous enzymes from Escherichia coli and Mycoplasma genitalium. The folding protein substrate (a variant of ribonuclease T1) binds with high affinity to the trigger factors, and permanently unfolded proteins are strong, competitive inhibitors. We used this inhibition to characterize the substrate binding sites of the trigger factors. Unfolded alpha-lactalbumin binds very tightly and inhibits the trigger factor from M. genitalium with a KI value of 50 nM. The binding of inhibitory proteins is independent of proline residues, as shown for unfolded tendamistat, which binds to the trigger factor with equal affinity in the presence and in the absence of its three proline residues. The good inhibition by a non-folding variant of ribonuclease T1 that lacks Pro39 showed that this proline, at which the catalysis of folding occurs, is dispensable for substrate binding. The trigger factors cannot catalyze prolyl isomerization when proteins are partially folded already. They preferentially recognize unstructured protein chains, which bind with high affinity to a site distinct from the catalytic prolyl isomerase center in the FKBP domain.
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Affiliation(s)
- C Scholz
- Biochemisches Laboratorium, Universität Bayreuth, Bayreuth, D-95440, Germany
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32
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Scholz C, Scherer G, Mayr LM, Schindler T, Fischer G, Schmid FX. Prolyl isomerases do not catalyze isomerization of non-prolyl peptide bonds. Biol Chem 1998; 379:361-5. [PMID: 9563833 DOI: 10.1515/bchm.1998.379.3.361] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Prolyl isomerases accelerate the cis <--> trans isomerization of prolyl peptide bonds during protein folding and probably also in folded proteins. We asked whether this catalytic function is in fact restricted to prolyl bonds or whether the isomerizations of 'normal' non-prolyl peptide bonds are catalyzed as well. By using the P39A variant of ribonuclease T1 as a substrate we find that the trans --> cis isomerization of the Tyr38-Ala39 bond in the refolding of this protein is not catalyzed by prolyl isomerases of the cyclophilin, FKBP and parvulin families. These enzymes are neither able to catalyze amide bond isomerizations in the proline-free model peptide Ala-Ala-Tyr-Ala-Ala.
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Affiliation(s)
- C Scholz
- Laboratorium für Biochemie, Universität Bayreuth, Germany
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33
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Dolinski K, Scholz C, Muir RS, Rospert S, Schmid FX, Cardenas ME, Heitman J. Functions of FKBP12 and mitochondrial cyclophilin active site residues in vitro and in vivo in Saccharomyces cerevisiae. Mol Biol Cell 1997; 8:2267-80. [PMID: 9362068 PMCID: PMC25707 DOI: 10.1091/mbc.8.11.2267] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/1997] [Accepted: 08/15/1997] [Indexed: 02/05/2023] Open
Abstract
Cyclophilin and FK506 binding protein (FKBP) accelerate cis-trans peptidyl-prolyl isomerization and bind to and mediate the effects of the immunosuppressants cyclosporin A and FK506. The normal cellular functions of these proteins, however, are unknown. We altered the active sites of FKBP12 and mitochondrial cyclophilin from the yeast Saccharomyces cerevisiae by introducing mutations previously reported to inactivate these enzymes. Surprisingly, most of these mutant enzymes were biologically active in vivo. In accord with previous reports, all of the mutant enzymes had little or no detectable prolyl isomerase activity in the standard peptide substrate-chymotrypsin coupled in vitro assay. However, in a variation of this assay in which the protease is omitted, the mutant enzymes exhibited substantial levels of prolyl isomerase activity (5-20% of wild-type), revealing that these mutations confer sensitivity to protease digestion and that the classic in vitro assay for prolyl isomerase activity may be misleading. In addition, the mutant enzymes exhibited near wild-type activity with two protein substrates, dihydrofolate reductase and ribonuclease T1, whose folding is accelerated by prolyl isomerases. Thus, a number of cyclophilin and FKBP12 "active-site" mutants previously identified are largely active but protease sensitive, in accord with our findings that these mutants display wild-type functions in vivo. One mitochondrial cyclophilin mutant (R73A), and also the wild-type human FKBP12 enzyme, catalyze protein folding in vitro but lack biological activity in vivo in yeast. Our findings provide evidence that both prolyl isomerase activity and other structural features are linked to FKBP and cyclophilin in vivo functions and suggest caution in the use of these active-site mutations to study FKBP and cyclophilin functions.
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Affiliation(s)
- K Dolinski
- Department of Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
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34
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Abstract
Recently a new family of prolyl isomerases was discovered, which is unrelated with the cyclophilins or the FK-506 binding proteins. Parvulin, the smallest member of this new family, is a protein with only 92 residues, but parvulin-like domains occur in several large proteins that are apparently involved in protein folding or activation processes. We show here that, in addition to its activity in assays with proline-containing tetrapeptides, parvulin catalyzes the proline-limited folding of a variant of ribonuclease T1 with a kcat/Km value of 30,000 M-1 s-1. This value is much smaller than the kcat/Km value of 1.1x10(7) M-1 s-1 determined for the parvulin-catalyzed prolyl isomerization in the tetrapeptide succinyl-Ala-Leu-Pro-Phe-4-nitroanilide. Parvulin itself unfolds and refolds reversibly in a simple two-state reaction with a Gibbs free energy of stabilization of 28 kJ/mol at 10 degrees C. Most of the unfolded parvulin molecules refold in a slow reaction that involves prolyl isomerization and is catalyzed by cyclophilin, another prolyl isomerase. Moreover, parvulin accelerates its own refolding in an autocatalytic fashion, and the rate of refolding increases tenfold when the concentration of parvulin is increased from 0.5 to 3.0 microM. Apparently, small single-domain prolyl isomerases catalyze prolyl isomerization much better in short peptides than in protein folding reactions, presumably because the prolyl bonds are less accessible in refolding protein chains. It is possible that the additional domains of the large prolyl isomerases improve the affinity for protein substrates.
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Affiliation(s)
- C Scholz
- Laboratorium für Biochemie, Universität Bayreuth, Bayreuth, D-95440, Germany
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35
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Zarnt T, Tradler T, Stoller G, Scholz C, Schmid FX, Fischer G. Modular structure of the trigger factor required for high activity in protein folding. J Mol Biol 1997; 271:827-37. [PMID: 9299330 DOI: 10.1006/jmbi.1997.1206] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The Escherichia coli trigger factor is a peptidyl-prolyl cis/trans isomerase (PPIase) which catalyzes proline-limited protein folding extremely well. It has been found associated with nascent protein chains as well as with the chaperone GroEL. The trigger factor utilizes protein regions outside the central catalytic domain for catalyzing refolding of unfolded proteins efficiently. Here we produced several fragments which encompass individual domains or combinations of the middle FKBP-like domain (M) with the N-terminal (N) and C-terminal (C) regions, respectively. These fragments appear to be stably folded. They show ordered structure and cooperative urea-induced unfolding transitions, and the far-UV CD spectrum of the intact trigger factor is well represented by the sum of the spectra of the fragments. This suggests that the native trigger factor shows a modular structure, which is composed of three fairly independent folding units. In the intact protein there is a slight mutual stabilization of these units. The high enzymatic activity in protein folding could not be restored by fusing alternatively the N or the C-terminal regions to the catalytic domain (in NM and MC constructs, respectively). Surprisingly, the high folding activity of the intact trigger factor has been regained partially by functional complementation of the overlapping NM and MC constructs.
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Affiliation(s)
- T Zarnt
- Forschungsstelle "Enzymologie der Proteinfaltung", Max-Planck-Gesellschaft, Kurt-Mothes-Str. 3, Halle/Saale, D-06120, Germany
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36
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Scholz C, Schindler T, Dolinski K, Heitman J, Schmid FX. Cyclophilin active site mutants have native prolyl isomerase activity with a protein substrate. FEBS Lett 1997; 414:69-73. [PMID: 9305734 DOI: 10.1016/s0014-5793(97)00979-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The prolyl isomerase activity of cyclophilins is traditionally measured by an assay in which prolyl cis/trans isomerization in a chromogenic tetrapeptide is coupled with its isomer-specific cleavage by chymotrypsin. Two variants of mitochondrial cyclophilin with substitutions in the presumed active site (R73A and H144Q) are inactive in the protease-coupled assay, but show almost wild-type activity in an assay that is based on the catalysis of a proline-limited protein folding reaction. This prolyl isomerase assay is preferable, both because coupling with proteolysis is avoided and because an intact protein instead of a short peptide is used as a substrate. Possibly, some earlier conclusions about the catalytic mechanism and the involvement of the prolyl isomerase activity in the cellular function of immunophilins may need reevaluation.
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Affiliation(s)
- C Scholz
- Biochemisches Laboratorium, Universität Bayreuth, Germany
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37
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Vanhove M, Guillaume G, Ledent P, Richards JH, Pain RH, Frère JM. Kinetic and thermodynamic consequences of the removal of the Cys-77-Cys-123 disulphide bond for the folding of TEM-1 beta-lactamase. Biochem J 1997; 321 ( Pt 2):413-7. [PMID: 9020874 PMCID: PMC1218084 DOI: 10.1042/bj3210413] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Class A beta-lactamases of the TEM family contain a single disulphide bond which connects cysteine residues 77 and 123. To clarify the possible role of the disulphide bond in the stability and folding kinetics of the TEM-1 beta-lactamase, this bond was removed by introducing a Cys-77-->Ser mutation, and the enzymically active mutant protein was studied by reversible guanidine hydrochloride-induced denaturation. The unfolding and refolding rates were monitored using tryptophan fluorescence. At low guanidine hydrochloride concentrations, the refolding of the wild-type and mutant enzymes followed biphasic time courses. The characteristics of the two phases were not significantly affected by the mutation. Double-jump experiments, in which the protein was unfolded in a high concentration of guanidine hydrochloride for a short time period and then refolded by diluting out the denaturant, indicated that, for both the wild-type and mutant enzymes, the two refolding phases could be ascribed to proline isomerization reactions. Equilibrium unfolding experiments monitored by fluorescence spectroscopy and far-UV CD indicated a three-state mechanism (N<-->H<--U). Both the folded mutant protein (N) and, to a lesser extent the thermodynamically stable intermediate, H. were destabilized relative to the fully unfolded state, U. Removal of the disulphide bond resulted in a decrease of 14.2 kJ/mol (3.4 kcal/mol) in the global free energy of stabilization. Similarly, the mutation also induced a drastic increase in the rate of thermal inactivation.
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Affiliation(s)
- M Vanhove
- Laboratoire d'Enzymologie, Institut de Chimie B6, Université de Liège, Belgium
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38
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Balbach J, Forge V, Lau WS, van Nuland NA, Brew K, Dobson CM. Protein folding monitored at individual residues during a two-dimensional NMR experiment. Science 1996; 274:1161-3. [PMID: 8895458 DOI: 10.1126/science.274.5290.1161] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
An approach is described to monitor directly at the level of individual residues the formation of structure during protein folding. A two-dimensional heteronuclear nuclear magnetic resonance (NMR) spectrum was recorded after the rapid initiation of the refolding of a protein labeled with nitrogen-15. The intensities and line shapes of the cross peaks in the spectrum reflected the kinetic time course of the folding events that occurred during the spectral accumulation. The method was used to demonstrate the cooperative nature of the acquisition of the native main chain fold of apo bovine alpha-lactalbumin. The general approach, however, should be applicable to the investigation of a wide range of chemical reactions.
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Affiliation(s)
- J Balbach
- Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QT, UK
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39
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Quimby BB, Wells L, Wilkinson KD, Fridovich-Keil JL. Functional requirements of the active site position 185 in the human enzyme galactose-1-phosphate uridylyltransferase. J Biol Chem 1996; 271:26835-42. [PMID: 8900165 DOI: 10.1074/jbc.271.43.26835] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The active site of galactose-1-phosphate uridylyltransferase (GALT) includes a HPH sequence that has been conserved in all species examined from Escherichia coli to humans. The crystal structure of the E. coli enzyme suggests that this proline is important in positioning the active site histidine (His-166) near the substrate. To examine the role of this proline in the homologous human sequence, we have performed saturating mutagenesis at Pro-185 within human GALT and characterized each resultant mutant enzyme using a yeast expression system. Activity analyses in crude lysates indicated that only proline at position 185 produced wild-type levels of activity, although five other amino acids, Ala, Gly, Ser, Gln, and Glu, all produced partially active enzymes. Western blot analyses of the GALT proteins in these lysates demonstrated that abundance varied from 9-118% of wild-type and was independent of activity. All five active mutant proteins were purified and characterized with regard to specific activity, apparent Km for both substrates, and temperature-dependence of activity. Finally, modeling of these mutations onto the conserved E. coli active site structure was performed. Together, these results provide functional evidence demonstrating the critical role of Pro-185 in facilitating the transferase reaction.
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Affiliation(s)
- B B Quimby
- Graduate Program in Genetics and Molecular Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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40
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Schindler T, Mayr LM, Landt O, Hahn U, Schmid FX. The role of a trans-proline in the folding mechanism of ribonuclease T1. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 241:516-24. [PMID: 8917450 DOI: 10.1111/j.1432-1033.1996.00516.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Protein folding is often retarded by the cis reversible trans isomerizations of prolyl peptide bonds both in vitro and in vivo. An important role for the folding mechanism is well established for the prolyl peptide bonds that are cis in the native protein, but not for those that are trans. Here we investigated the role of trans-Pro73 for the folding of ribonuclease T1 (which additionally contains two cis-prolines) by comparing the wild-type protein with the Pro73-->Val variant. The Pro-->Val substitution led to a destabilization of the folded protein by 8.5 kJ/mol, which is explained by the strong, 25-fold increase in the rate of unfolding. In contrast, the rates and amplitudes of the fast and slow refolding reactions were virtually unchanged. trans-Proline residues remain largely trans after unfolding, and therefore their contributions to the observed folding kinetics should indeed be insignificant for proteins which also contain one or more cis prolines. The cis-proline residues dominate the kinetics of refolding, because almost all slow-folding molecules contain the respective incorrect (trans) isomers, and because trans-->cis isomerizations are slower than cis-->trans isomerizations. The inability to detect contributions from a trans-proline to the kinetics of folding does not imply that this proline is non-essential for folding in the sense that its cis reversible trans isomerization is energetically uncoupled from conformational folding.
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Affiliation(s)
- T Schindler
- Laboratorium für Biochemie, Universität Bayreuth, Germany
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41
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Walter S, Lorimer GH, Schmid FX. A thermodynamic coupling mechanism for GroEL-mediated unfolding. Proc Natl Acad Sci U S A 1996; 93:9425-30. [PMID: 8790346 PMCID: PMC38444 DOI: 10.1073/pnas.93.18.9425] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Chaperonins prevent the aggregation of partially folded or misfolded forms of a protein and, thus, keep it competent for productive folding. It was suggested that GroEL, the chaperonin of Escherichia coli, exerts this function 1 unfolding such intermediates, presumably in a catalytic fashion. We investigated the kinetic mechanism of GroEL-induced protein unfolding by using a reduced and carbamidomethylated variant of RNase T1, RCAM-T1, as a substrate. RCAM-T1 cannot fold to completion, because the two disulfide bonds are missing, and it is, thus, a good model for long-lived folding intermediates. RCAM-T1 unfolds when GroEL is added, but GroEL does not change the microscopic rate constant of unfolding, ruling out that it catalyzes unfolding. GroEL unfolds RCAM-T1 because it binds with high affinity to the unfolded form of the protein and thereby shifts the overall equilibrium toward the unfolded state. GroEL can unfold a partially folded or misfolded intermediate by this thermodynamic coupling mechanism when the Gibbs free energy of the binding to GroEL is larger than the conformational stability of the intermediate and when the rate of its unfolding is high.
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Affiliation(s)
- S Walter
- Laboratorium für Biochemie, Universität Bayreuth, Germany
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42
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O'Neal KD, Chari MV, Mcdonald CH, Cook RG, Yu-Lee LY, Morrisett JD, Shearer WT. Multiple cis-trans conformers of the prolactin receptor proline-rich motif (PRM) peptide detected by reverse-phase HPLC, CD and NMR spectroscopy. Biochem J 1996; 315 ( Pt 3):833-44. [PMID: 8645165 PMCID: PMC1217282 DOI: 10.1042/bj3150833] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
An eight-amino-acid synthetic peptide (IIe1-Phe2-Pro3-Pro4-Val5-Pro6-Gly7-Pro8) corresponding to the conserved proline-rich motif (PRM) of the intracellular domain of the prolactin receptor (PRL-R) was studied by one- and two-dimensional (1D and 2D) proton NMR spectroscopy in water and DMSO in order to characterize its conformational dynamics. The purified PRL-R PRM peptide eluted as two partially resolved peaks in equilibrium on reverse-phase HPLC (RP-HPLC) at 20 degrees C with a ratio of 60:40. At 30 degrees C, the two peaks coalesced into a single peak The two RP-HPLC peaks correspond to two peptide conformers resulting from the slow cis-trans isomerization of one of the four proline amide bonds. Although the peptide has only three amide (NH) protons, its ID NMR spectrum in water contains approximately 15 discernible NH region peaks, providing evidence for multiple conformers. The amide resonances were assigned on the basis of 2D-COSY spectra, chemical shift values resonance splitting patterns and temperature coefficients. The cis:trans ratio for each proline in water, calculated from integrated intensities and/or peak heights of the appropriate resonances, were Phe2-Pro3 (35:65), Pro3-Pro4 (40:60), Val5-Pro6 (70:30), and Gly7-Pro8 (30:70). Temperature studies (25-70 degrees C) were used to semi-quantitatively estimate the rates of isomerization for the different prolines. In water, Pro8 undergoes rapid isomerization; Pro3 isomerizes at an intermediate rate; while Pro4 and Pro6 both appear to isomerize very slowly since no coalescence of amide resonances was observed. In DMSO, only Pro4 displayed slow isomerization. Slow kinetics combined with a similar 60:40 ratio of conformers determined by RP-HPLC and NMR suggests that isomerization of the Pro3-Pro4 bond generates the two RP-HPLC peaks. Both proximal and distal proline isomerization effects were observed in NMR experiments. All of the 16 theoretical (24 = 16) proline configurations appear to exist in equilibrium in water The predominant (19%) conformation, trans3-trans4-cis6-trans8, may reflect the configuration of the PRM prolines in the native PRL-R. Isomerization of Pro6 from cis to trans generates an interaction between the peptide N-and C-termini, suggesting an overall pseudo-cyclic conformation. This all-trans proline configuration may play an important biochemical role in the function of cytokine/haematopoietin receptors. A model is proposed which suggests that isomerization of the PRM by an immunophilin such as the FK 506-binding protein (FKBP) serves as an on-off switch for cytokine receptor activation.
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Affiliation(s)
- K D O'Neal
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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43
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44
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Frech C, Schmid FX. DsbA-mediated disulfide bond formation and catalyzed prolyl isomerization in oxidative protein folding. J Biol Chem 1995; 270:5367-74. [PMID: 7890650 DOI: 10.1074/jbc.270.10.5367] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The interrelationship between the acquisition of ordered structure, prolyl isomerization, and the formation of the disulfide bonds in assisted protein folding was investigated by using a variant of ribonuclease T1 (C2S/C10N-RNase T1) with a single disulfide bond and two cis-prolyl bonds as a model protein. The thiol-disulfide oxidoreductase DsbA served as the oxidant for forming the disulfide bond and prolyl isomerase A as the catalyst of prolyl isomerization. Both enzymes are from the periplasm of Escherichia coli. Reduced C2S/C10N-RNase T1 is unfolded in 0 M NaCl, but native-like folded in > or = 2 M NaCl. Oxidation of 5 microM C2S/C10N-RNase T1 by 8 microM DsbA (at pH 7.0, 25 degrees C) is very rapid with a t1/2 of about 10 s (the second-order rate constant is 7 x 10(3) s-1 M-1), irrespective of whether the reduced molecules are unfolded or folded. When they are folded, the product of oxidation is the native protein. When they are denatured, first the disulfide bond is formed in the unfolded protein chains and then the native structure is acquired. This slow reaction is limited in rate by prolyl isomerization and catalyzed by prolyl isomerase. The efficiency of this catalysis is strongly decreased by the presence of the disulfide bond. Apparently, the rank order of chain folding, prolyl isomerization, and disulfide bond formation can vary in the oxidative folding of ribonuclease T1. Such a degeneracy could generally be an advantage for protein folding both in vitro and in vivo.
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Affiliation(s)
- C Frech
- Biochemisches Laboratorium, Universität Bayreuth, Federal Republic of Germany
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