1
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Lindemeier D, Graubner W, Mehner-Breitfeld D, Malešević M, Brüser T. Positive charges promote the recognition of proteins by the chaperone SlyD from Escherichia coli. PLoS One 2024; 19:e0305823. [PMID: 38917203 PMCID: PMC11198818 DOI: 10.1371/journal.pone.0305823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
SlyD is a widely-occurring prokaryotic FKBP-family prolyl isomerase with an additional chaperone domain. Often, such as in Escherichia coli, a third domain is found at its C-terminus that binds nickel and provides it for nickel-enzyme biogenesis. SlyD has been found to bind signal peptides of proteins that are translocated by the Tat pathway, a system for the transport of folded proteins across membranes. Using peptide arrays to analyze these signal peptide interactions, we found that SlyD interacted only with positively charged peptides, with a preference for arginines over lysines, and large hydrophobic residues enhanced binding. Especially a twin-arginine motif was recognized, a pair of highly conserved arginines adjacent to a stretch of hydrophobic residues. Using isothermal titration calorimetry (ITC) with purified SlyD and a signal peptide-containing model Tat substrate, we could show that the wild type twin-arginine signal peptide was bound with higher affinity than an RR>KK mutated variant, confirming that positive charges are recognized by SlyD, with a preference of arginines over lysines. The specific role of negative charges of the chaperone domain surface and of hydrophobic residues in the chaperone active site was further analyzed by ITC of mutated SlyD variants. Our data show that the supposed key hydrophobic residues of the active site are indeed crucial for binding, and that binding is influenced by negative charges on the chaperone domain. Recognition of positive charges is likely achieved by a large negatively charged surface region of the chaperone domain, which is highly conserved although individual positions are variable.
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Affiliation(s)
- Daniel Lindemeier
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
| | - Wenke Graubner
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
| | | | - Miroslav Malešević
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Thomas Brüser
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
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2
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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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3
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Pazicky S, Werle ALA, Lei J, Löw C, Weininger U. Impact of distant peptide substrate residues on enzymatic activity of SlyD. Cell Mol Life Sci 2022; 79:138. [PMID: 35184231 PMCID: PMC8858294 DOI: 10.1007/s00018-022-04179-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 11/05/2022]
Abstract
Peptidyl-prolyl isomerases (PPIases) catalyze intrinsically slow and often rate-limiting isomerization of prolyl-peptide bonds in unfolded or partially folded proteins, thereby speeding up the folding process and preventing misfolding. They often possess binding and chaperone domains in addition to the domain carrying the isomerization activity. Although generally, their substrates display no identity in their amino acid sequence upstream and downstream of the proline with 20 possibilities for each residue, PPIases are efficient enzymes. SlyD is a highly efficient PPIase consisting of an isomerase domain and an additional chaperone domain. The binding of peptide substrates to SlyD and its enzymatic activity depend to some extend on the proline-proximal residues, however, the impact of proline-distant residues has not been investigated so far. Here, we introduce a label-free NMR-based method to measure SlyD activity on different peptide substrates and analysed the data in the context of obtained binding affinities and several co-crystal structures. We show that especially charged and aromatic residues up to eight positions downstream and three positions upstream of the proline and outside the canonical region of similar conformations affect the activity and binding, although they rarely display distinct conformations in our crystal structures. We hypothesize that these positions primarily influence the association reaction. In the absence of the chaperone domain the isomerase activity strongly correlates with substrate affinity, whereas additional factors play a role in its presence. The mutual orientation of isomerase and chaperone domains depends on the presence of substrates in both binding sites, implying allosteric regulation of enzymatic activity.
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4
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Scheuplein NJ, Bzdyl NM, Kibble EA, Lohr T, Holzgrabe U, Sarkar-Tyson M. Targeting Protein Folding: A Novel Approach for the Treatment of Pathogenic Bacteria. J Med Chem 2020; 63:13355-13388. [PMID: 32786507 DOI: 10.1021/acs.jmedchem.0c00911] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Infectious diseases are a major cause of morbidity and mortality worldwide, exacerbated by increasing antibiotic resistance in many bacterial species. The development of drugs with new modes of action is essential. A leading strategy is antivirulence, with the aim to target bacterial proteins that are important in disease causation and progression but do not affect growth, resulting in reduced selective pressure for resistance. Immunophilins, a superfamily of peptidyl-prolyl cis-trans isomerase (PPIase) enzymes have been shown to be important for virulence in a broad-spectrum of pathogenic bacteria. This Perspective will provide an overview of the recent advances made in understanding the role of each immunophilin family, cyclophilins, FK506 binding proteins (FKBPs), and parvulins in bacteria. Inhibitor design and medicinal chemistry strategies for development of novel drugs against bacterial FKBPs will be discussed. Furthermore, drugs against human cyclophilins and parvulins will be reviewed in their current indication as antiviral and anticancer therapies.
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Affiliation(s)
- Nicolas J Scheuplein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Nicole M Bzdyl
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 6009 Perth, Australia
| | - Emily A Kibble
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 6009 Perth, Australia.,School of Veterinary and Life Sciences, Murdoch University, 6150 Murdoch, Australia
| | - Theresa Lohr
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 6009 Perth, Australia
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5
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Identification of Substrates of Cytoplasmic Peptidyl-Prolyl Cis/Trans Isomerases and Their Collective Essentiality in Escherichia Coli. Int J Mol Sci 2020; 21:ijms21124212. [PMID: 32545723 PMCID: PMC7353009 DOI: 10.3390/ijms21124212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 11/16/2022] Open
Abstract
Protein folding often requires molecular chaperones and folding catalysts, such as peptidyl-prolyl cis/trans isomerases (PPIs). The Escherichia coli cytoplasm contains six well-known PPIs, although a requirement of their PPIase activity, the identity of their substrates and relative enzymatic contribution is unknown. Thus, strains lacking all periplasmic and one of the cytoplasmic PPIs were constructed. Measurement of their PPIase activity revealed that PpiB is the major source of PPIase activity in the cytoplasm. Furthermore, viable Δ6ppi strains could be constructed only on minimal medium in the temperature range of 30-37 °C, but not on rich medium. To address the molecular basis of essentiality of PPIs, proteins that aggregate in their absence were identified. Next, wild-type and putative active site variants of FkpB, FklB, PpiB and PpiC were purified and in pull-down experiments substrates specific to each of these PPIs identified, revealing an overlap of some substrates. Substrates of PpiC were validated by immunoprecipitations using extracts from wild-type and PpiC-H81A strains carrying a 3xFLAG-tag appended to the C-terminal end of the ppiC gene on the chromosome. Using isothermal titration calorimetry, RpoE, RseA, S2, and AhpC were established as FkpB substrates and PpiC's PPIase activity was shown to be required for interaction with AhpC.
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6
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Lee D, Yoon S, Lee J, Lim D, Yoon C, Im H, Lee K. Amyloid Fibril Formation of α‐Synuclein Is Modulated via the Estrogen Receptor Ligand Binding Domain of Estrogen Receptor α Bound with Tamoxifen‐based Small Molecules. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.11956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Dawon Lee
- Department of ChemistrySejong University Seoul 05006 South Korea
| | - Soyoung Yoon
- Department of ChemistrySejong University Seoul 05006 South Korea
| | - Jinwoo Lee
- Department of ChemistrySejong University Seoul 05006 South Korea
| | - Dongyeol Lim
- Department of ChemistrySejong University Seoul 05006 South Korea
| | - Chun Yoon
- Department of ChemistrySejong University Seoul 05006 South Korea
| | - Hana Im
- Department of Integrative Bioscience and BiotechnologySejong University Seoul 05006 South Korea
| | - Kyunghee Lee
- Department of ChemistrySejong University Seoul 05006 South Korea
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7
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Peeß C, Scholz C, Casagolda D, Düfel H, Gerg M, Kowalewsky F, Bocola M, von Proff L, Goller S, Klöppel-Swarlik H, Hoppe A, Schräml M. A novel epitope-presenting thermostable scaffold for the development of highly specific insulin-like growth factor-1/2 antibodies. J Biol Chem 2019; 294:13434-13444. [PMID: 31337703 PMCID: PMC6737233 DOI: 10.1074/jbc.ra119.007654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/12/2019] [Indexed: 11/24/2022] Open
Abstract
High sequence and structural homology between mature human insulin-like growth factors IGF-1 and IGF-2 makes serological discrimination by immunodiagnostic IGF tests a challenging task. There is an urgent need for highly specific IGF-1 and IGF-2 antibodies, yet only a short sequence element, i.e. the IGF loop, provides enough difference in sequence to discriminate between the two molecules. We sought to address this unmet demand by investigating novel chimeric immunogens as carriers for recombinant peptide motif grafting. We found Thermus thermophilus sensitive to lysis D (SlyD) and Thermococcus gammatolerans SlyD FK-506–binding protein (FKBP) domains suitable for presentation of the predefined epitopes, namely the IGF-1 and IGF-2 loops. Chimeric SlyD-IGF proteins allowed for the development of exceptionally specific IGF-1 and IGF-2 monoclonal antibodies. The selected antibodies bound with high affinity to the distinct IGF epitopes displayed on the protein scaffolds, as well as on the mature human IGF isoforms. The respective SlyD scaffolds display favorable engineering properties in that they are small, monomeric, and cysteine-free and can be produced in high yields in a prokaryotic host, such as Escherichia coli. In conclusion, FKBP domains from thermostable SlyD proteins are highly suitable as a generic scaffold platform for epitope grafting.
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Affiliation(s)
- Carmen Peeß
- Antibody Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | | | - David Casagolda
- Enzyme & Protein Technologies, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Hartmut Düfel
- Antibody Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Michael Gerg
- Antibody Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Frank Kowalewsky
- Antibody Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University, 52074 Aachen, Germany
| | - Leopold von Proff
- Enzyme & Protein Technologies, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Sabine Goller
- Enzyme & Protein Technologies, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Heidi Klöppel-Swarlik
- Endocrinological Diseases III, Centralized and Point of Care, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Alessandra Hoppe
- Endocrinological Diseases III, Centralized and Point of Care, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Michael Schräml
- Enzyme & Protein Technologies, Roche Diagnostics GmbH, 82377 Penzberg, Germany.
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8
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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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9
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Yoon S, Kim S, Im H, Lee K. Regulation of Amyloid Fibril Formation from Human Islet Amyloid Polypeptide by a Ligand Binding to the Fusion of FK506-binding Protein and the Insertion-in-Flap Domain. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Soyoung Yoon
- Department of Chemistry; Sejong University; Seoul 143-747 Korea
| | - Soohyun Kim
- Department of Chemistry; Sejong University; Seoul 143-747 Korea
| | - Hana Im
- Department of Molecular Biology; Sejong University; Seoul 143-747 Korea
| | - Kyunghee Lee
- Department of Chemistry; Sejong University; Seoul 143-747 Korea
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10
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Kumar A, Balbach J. Targeting the molecular chaperone SlyD to inhibit bacterial growth with a small molecule. Sci Rep 2017; 7:42141. [PMID: 28176839 PMCID: PMC5296862 DOI: 10.1038/srep42141] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/03/2017] [Indexed: 12/23/2022] Open
Abstract
Molecular chaperones are essential molecules for cell growth, whereby they maintain protein homeostasis. Because of their central cellular function, bacterial chaperones might be potential candidates for drug targets. Antimicrobial resistance is currently one of the greatest threats to human health, with gram-negative bacteria being of major concern. We found that a Cu2+ complex readily crosses the bacterial cell wall and inhibits SlyD, which is a molecular chaperone, cis/trans peptidyl prolyl isomerise (PPIase) and involved in various other metabolic pathways. The Cu2+ complex binds to the active sites of SlyD, which suppresses its PPIase and chaperone activities. Significant cell growth retardation could be observed for pathogenic bacteria (e.g., Staphylococcus aureus and Pseudomonas aeruginosa). We anticipate that rational development of drugs targeting molecular chaperones might help in future control of pathogenic bacterial growth, in an era of rapidly increasing antibiotic resistance.
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Affiliation(s)
- Amit Kumar
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Physics, Biophysics, Martin Luther University, Halle, Wittenberg, Germany
| | - Jochen Balbach
- Institute of Physics, Biophysics, Martin Luther University, Halle, Wittenberg, Germany
- Centre for Structure und Dynamics of Proteins (MZP), Martin Luther University Halle, Wittenberg, Germany
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11
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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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12
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Batra J, Tjong H, Zhou HX. Electrostatic effects on the folding stability of FKBP12. Protein Eng Des Sel 2016; 29:301-308. [PMID: 27381026 PMCID: PMC4955870 DOI: 10.1093/protein/gzw014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 03/28/2016] [Accepted: 04/15/2016] [Indexed: 01/17/2023] Open
Abstract
The roles of electrostatic interactions in protein folding stability have been a matter of debate, largely due to the complexity in the theoretical treatment of these interactions. We have developed computational methods for calculating electrostatic effects on protein folding stability. To rigorously test and further refine these methods, here we carried out experimental studies into electrostatic effects on the folding stability of the human 12-kD FK506 binding protein (FKBP12). This protein has a close homologue, FKBP12.6, with amino acid substitutions in only 18 of their 107 residues. Of the 18 substitutions, 8 involve charged residues. Upon mutating FKBP12 residues at these 8 positions individually into the counterparts in FKBP12.6, the unfolding free energy (ΔGu) of FKBP12 changed by -0.3 to 0.7 kcal/mol. Accumulating stabilizing substitutions resulted in a mutant with a 0.9 kcal/mol increase in stability. Additional charge mutations were grafted from a thermophilic homologue, MtFKBP17, which aligns to FKBP12 with 31% sequence identity over 89 positions. Eleven such charge mutations were studied, with ΔΔGu varying from -2.9 to 0.1 kcal/mol. The predicted electrostatic effects by our computational methods with refinements herein had a root-mean-square deviation of 0.9 kcal/mol from the experimental ΔΔGu values on 16 single mutations of FKBP12. The difference in ΔΔGu between mutations grafted from FKBP12.6 and those from MtFKBP17 suggests that more distant homologues are less able to provide guidance for enhancing folding stability.
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Affiliation(s)
- Jyotica Batra
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Present address: Department of Chemistry and Physics, Bellarmine University, 2001 Newburg Road, Louisville, KY40205, USA
| | - Harianto Tjong
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Present address: Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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13
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Reuten R, Nikodemus D, Oliveira MB, Patel TR, Brachvogel B, Breloy I, Stetefeld J, Koch M. Maltose-Binding Protein (MBP), a Secretion-Enhancing Tag for Mammalian Protein Expression Systems. PLoS One 2016; 11:e0152386. [PMID: 27029048 PMCID: PMC4814134 DOI: 10.1371/journal.pone.0152386] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/14/2016] [Indexed: 01/07/2023] Open
Abstract
Recombinant proteins are commonly expressed in eukaryotic expression systems to ensure the formation of disulfide bridges and proper glycosylation. Although many proteins can be expressed easily, some proteins, sub-domains, and mutant protein versions can cause problems. Here, we investigated expression levels of recombinant extracellular, intracellular as well as transmembrane proteins tethered to different polypeptides in mammalian cell lines. Strikingly, fusion of proteins to the prokaryotic maltose-binding protein (MBP) generally enhanced protein production. MBP fusion proteins consistently exhibited the most robust increase in protein production in comparison to commonly used tags, e.g., the Fc, Glutathione S-transferase (GST), SlyD, and serum albumin (ser alb) tag. Moreover, proteins tethered to MBP revealed reduced numbers of dying cells upon transient transfection. In contrast to the Fc tag, MBP is a stable monomer and does not promote protein aggregation. Therefore, the MBP tag does not induce artificial dimerization of tethered proteins and provides a beneficial fusion tag for binding as well as cell adhesion studies. Using MBP we were able to secret a disease causing laminin β2 mutant protein (congenital nephrotic syndrome), which is normally retained in the endoplasmic reticulum. In summary, this study establishes MBP as a versatile expression tag for protein production in eukaryotic expression systems.
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Affiliation(s)
- Raphael Reuten
- Institute for Dental Research and Oral Musculoskeletal Biology, Medical Faculty, University of Cologne, Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
- * E-mail: (MK); (RR)
| | - Denise Nikodemus
- Institute for Dental Research and Oral Musculoskeletal Biology, Medical Faculty, University of Cologne, Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Maria B. Oliveira
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Trushar R. Patel
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba RT3 2N2, Canada
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, United Kingdom
| | - Bent Brachvogel
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
- Experimental Neonatology, Department of Pediatrics and Adolescent Medicine, Medical Faculty, University of Cologne, Cologne, Germany
| | - Isabelle Breloy
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba RT3 2N2, Canada
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Medical Faculty, University of Cologne, Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- * E-mail: (MK); (RR)
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14
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Kim S, Shin E, Im H, Lee K. Expression of Chaperone-Synuclein Fusion Proteins and Their Regulatory Effects on Amyloid Fibril Formation. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Soohyun Kim
- Department of Chemistry; Sejong University; Seoul 143-747 Korea
| | - Eunsook Shin
- Department of Chemistry; Sejong University; Seoul 143-747 Korea
| | - Hana Im
- Department of Molecular Biology; Sejong University; Seoul 143-747 Korea
| | - Kyunghee Lee
- Department of Chemistry; Sejong University; Seoul 143-747 Korea
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15
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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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16
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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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17
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Ishikawa Y, Boudko S, Bächinger HP. Ziploc-ing the structure: Triple helix formation is coordinated by rough endoplasmic reticulum resident PPIases. Biochim Biophys Acta Gen Subj 2015; 1850:1983-93. [PMID: 25583561 DOI: 10.1016/j.bbagen.2014.12.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/26/2014] [Accepted: 12/29/2014] [Indexed: 11/18/2022]
Abstract
BACKGROUND Protein folding is crucial for proteins' specific functions and is facilitated by various types of enzymes and molecular chaperones. The peptidyl prolyl cis/trans isomerases (PPIase) are one of these families of enzymes. They ubiquitously exist inside the cell and there are eight PPIases in the rough endoplasmic reticulum (rER), a compartment where the folding of most secreted proteins occurs. SCOPE OF REVIEW We review the functional and structural aspects of individual rER resident PPIases. Furthermore, we specifically discuss the role of these PPIases during collagen biosynthesis, since collagen is the most abundant protein in humans, is synthesized in the rER, and contains a proportionally high number of proline residues. MAJOR CONCLUSIONS The rER resident PPIases recognize different sets of substrates and facilitate their folding. Although they are clearly catalysts for protein folding, they also have more broad and multifaceted functions. We propose that PPIases coordinate collagen biosynthesis in the rER. GENERAL SIGNIFICANCE This review expands our understanding of collagen biosynthesis by explaining the influence of novel indirect mechanisms of regulating folding and this is also explored for PPIases. We also suggest future directions of research to obtain a better understanding of collagen biosynthesis and functions of PPIases in the rER. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Yoshihiro Ishikawa
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA; Shriners Hospital for Children, Research Department, Portland, OR 97239, USA
| | - Sergei Boudko
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA; Shriners Hospital for Children, Research Department, Portland, OR 97239, USA
| | - Hans Peter Bächinger
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA; Shriners Hospital for Children, Research Department, Portland, OR 97239, USA.
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18
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Schmidpeter PAM, Koch JR, Schmid FX. Control of protein function by prolyl isomerization. Biochim Biophys Acta Gen Subj 2014; 1850:1973-82. [PMID: 25542300 DOI: 10.1016/j.bbagen.2014.12.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 01/12/2023]
Abstract
BACKGROUND Prolyl cis/trans isomerizations have long been known as critical and rate-limiting steps in protein folding. RESULTS Now it is clear that they are also used as slow conformational switches and molecular timers in the regulation of protein activity. Here we describe several such proline switches and how they are regulated. CONCLUSIONS AND GENERAL SIGNIFICANCE Prolyl isomerizations can function as attenuators and provide allosteric systems with a molecular memory. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Philipp A M Schmidpeter
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Johanna R Koch
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Franz X Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95440 Bayreuth, Germany.
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19
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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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20
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Reinstein J. Proximity effects on the protein domain level: engineering prolyl isomerases through combinatorial biochemistry. J Mol Biol 2013; 425:4065-6. [PMID: 23911550 DOI: 10.1016/j.jmb.2013.07.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Jochen Reinstein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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21
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Monneau YR, Soufari H, Nelson CJ, Mackereth CD. Structure and activity of the peptidyl-prolyl isomerase domain from the histone chaperone Fpr4 toward histone H3 proline isomerization. J Biol Chem 2013; 288:25826-25837. [PMID: 23888048 DOI: 10.1074/jbc.m113.479964] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The FK506-binding protein (FKBP) family of peptidyl-prolyl isomerases (PPIases) is characterized by a common catalytic domain that binds to the inhibitors FK506 and rapamycin. As one of four FKBPs within the yeast Saccharomyces cerevisiae, Fpr4 has been described as a histone chaperone, and is in addition implicated in epigenetic function in part due to its mediation of cis-trans conversion of proline residues within histone tails. To better understand the molecular details of this activity, we have determined the solution structure of the Fpr4 C-terminal PPIase domain by using NMR spectroscopy. This canonical FKBP domain actively increases the rate of isomerization of three decapeptides derived from the N terminus of yeast histone H3, whereas maintaining intrinsic cis and trans populations. Observation of the uncatalyzed and Fpr4-catalyzed isomerization rates at equilibrium demonstrate Pro(16) and Pro(30) of histone H3 as the major proline targets of Fpr4, with little activity shown against Pro(38). This alternate ranking of the three target prolines, as compared with affinity determination or the classical chymotrypsin-based fluorescent assay, reveals the mechanistic importance of substrate residues C-terminal to the peptidyl-prolyl bond.
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Affiliation(s)
- Yoan R Monneau
- From the Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Heddy Soufari
- From the Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France,; the INSERM U869, University of Bordeaux, 33076 Bordeaux, France, and
| | - Christopher J Nelson
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Cameron D Mackereth
- From the Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France,; the INSERM U869, University of Bordeaux, 33076 Bordeaux, France, and.
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22
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Abstract
In this article, we will cover the folding of proteins in the lumen of the endoplasmic reticulum (ER), including the role of three types of covalent modifications: signal peptide removal, N-linked glycosylation, and disulfide bond formation, as well as the function and importance of resident ER folding factors. These folding factors consist of classical chaperones and their cochaperones, the carbohydrate-binding chaperones, and the folding catalysts of the PDI and proline cis-trans isomerase families. We will conclude with the perspective of the folding protein: a comparison of characteristics and folding and exit rates for proteins that travel through the ER as clients of the ER machinery.
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Affiliation(s)
- Ineke Braakman
- Cellular Protein Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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23
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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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24
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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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25
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Shin E, Im H, Lee K. Accelerated Fibril Formation of α-Synuclein by an IF-Inserted F36V Mutant. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.2.665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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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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27
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Higgins KA, Carr CE, Maroney MJ. Specific metal recognition in nickel trafficking. Biochemistry 2012; 51:7816-32. [PMID: 22970729 DOI: 10.1021/bi300981m] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nickel is an essential metal for a number of bacterial species that have developed systems for acquiring, delivering, and incorporating the metal into target enzymes and controlling the levels of nickel in cells to prevent toxic effects. As with other transition metals, these trafficking systems must be able to distinguish between the desired metal and other transition metal ions with similar physical and chemical properties. Because there are few enzymes (targets) that require nickel for activity (e.g., Escherichia coli transports nickel for hydrogenases made under anaerobic conditions, and Helicobacter pylori requires nickel for hydrogenase and urease that are essential for acid viability), the "traffic pattern" for nickel is relatively simple, and nickel trafficking therefore presents an opportunity to examine a system for the mechanisms that are used to distinguish nickel from other metals. In this review, we describe the details known for examples of uptake permeases, metallochaperones and proteins involved in metallocenter assembly, and nickel metalloregulators. We also illustrate a variety of mechanisms, including molecular recognition in the case of NikA protein and examples of allosteric regulation for HypA, NikR, and RcnR, employed to generate specific biological responses to nickel ions.
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Affiliation(s)
- Khadine A Higgins
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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28
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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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29
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Quistgaard EM, Nordlund P, Löw C. High‐resolution insights into binding of unfolded polypeptides by the PPIase chaperone SlpA. FASEB J 2012; 26:4003-13. [DOI: 10.1096/fj.12-208397] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Esben M. Quistgaard
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Pär Nordlund
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- School of Biological SciencesNanyang Technological UniversitySingapore
| | - Christian Löw
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
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30
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Jansen G, Määttänen P, Denisov AY, Scarffe L, Schade B, Balghi H, Dejgaard K, Chen LY, Muller WJ, Gehring K, Thomas DY. An interaction map of endoplasmic reticulum chaperones and foldases. Mol Cell Proteomics 2012; 11:710-23. [PMID: 22665516 DOI: 10.1074/mcp.m111.016550] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Chaperones and foldases in the endoplasmic reticulum (ER) ensure correct protein folding. Extensive protein-protein interaction maps have defined the organization and function of many cellular complexes, but ER complexes are under-represented. Consequently, chaperone and foldase networks in the ER are largely uncharacterized. Using complementary ER-specific methods, we have mapped interactions between ER-lumenal chaperones and foldases and describe their organization in multiprotein complexes. We identify new functional chaperone modules, including interactions between protein-disulfide isomerases and peptidyl-prolyl cis-trans-isomerases. We have examined in detail a novel ERp72-cyclophilin B complex that enhances the rate of folding of immunoglobulin G. Deletion analysis and NMR reveal a conserved surface of cyclophilin B that interacts with polyacidic stretches of ERp72 and GRp94. Mutagenesis within this highly charged surface region abrogates interactions with its chaperone partners and reveals a new mechanism of ER protein-protein interaction. This ability of cyclophilin B to interact with different partners using the same molecular surface suggests that ER-chaperone/foldase partnerships may switch depending on the needs of different substrates, illustrating the flexibility of multichaperone complexes of the ER folding machinery.
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Affiliation(s)
- Gregor Jansen
- Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada
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31
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Budiman C, Tadokoro T, Angkawidjaja C, Koga Y, Kanaya S. Role of polar and nonpolar residues at the active site for PPIase activity of FKBP22 from Shewanella sp. SIB1. FEBS J 2012; 279:976-86. [PMID: 22244380 DOI: 10.1111/j.1742-4658.2012.08483.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
FKBP22 from the psychotropic bacterium Shewanella sp. SIB1 is a homodimeric protein with peptidyl prolyl cis-trans isomerase (PPIase) activity. According to a tertiary model, several nonpolar residues including Trp157 and Phe197 form a substrate-binding cavity, and Asp137 and Arg142, which form a salt bridge, are located at the edge of this cavity. To analyze the role of these residues, nine single (D137A, R142A, W157A/F/Y, F197A/L/Y/W) and one double (D137A/R142A) mutant protein of SIB1 FKBP22 were constructed. The far- and near-UV CD spectra of these mutant proteins suggest that the mutations at Asp137 and Arg142 do not seriously affect the protein structure, while those at Trp157 and Phe197 cause a local conformational change around the mutation site. Each mutation decreased the PPIase activities of SIB1 FKBP22 for peptide and protein substrates similarly without seriously affecting chaperone function. This result indicates that SIB1 FKBP22 does not require PPIase activity for chaperone function. The PPIase activities of R142A, D137A and D137A/R142A decreased in this order, suggesting that Asp137 and Arg142 play a principal and auxiliary role in catalytic function, respectively, but Arg142 can function as a substitute of Asp137. Because the PPIase activity of SIB1 FKBP22 was not fully lost by the removal of all polar residues around the active site, the desolvation effect may also contribute to the enzymatic activity. However, the mutations of Trp157 to Phe or Phe197 to Leu greatly decrease the enzymatic activity, suggesting that the shape of the substrate-binding cavity is also important for enzymatic activity.
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Affiliation(s)
- Cahyo Budiman
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Japan
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32
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Shin ES, Lee KH. Insertion of IF (insertion-in-flap) Domain into F36V to Provide Higher Activity of Peptidyl-propyl cis-trans Isomerase. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.1.281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Kaluarachchi H, Siebel JF, Kaluarachchi-Duffy S, Krecisz S, Sutherland DEK, Stillman MJ, Zamble DB. Metal selectivity of the Escherichia coli nickel metallochaperone, SlyD. Biochemistry 2011; 50:10666-77. [PMID: 22047179 DOI: 10.1021/bi2014882] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
SlyD is a Ni(II)-binding protein that contributes to nickel homeostasis in Escherichia coli. The C-terminal domain of SlyD contains a rich variety of metal-binding amino acids, suggesting broader metal binding capabilities, and previous work demonstrated that the protein can coordinate several types of first-row transition metals. However, the binding of SlyD to metals other than Ni(II) has not been previously characterized. To improve our understanding of the in vitro metal-binding activity of SlyD and how it correlates with the in vivo function of this protein, the interactions between SlyD and the series of biologically relevant transition metals [Mn(II), Fe(II), Co(II), Cu(I), and Zn(II)] were examined by using a combination of optical spectroscopy and mass spectrometry. Binding of SlyD to Mn(II) or Fe(II) ions was not detected, but the protein coordinates multiple ions of Co(II), Zn(II), and Cu(I) with appreciable affinity (K(D) values in or below the nanomolar range), highlighting the promiscuous nature of this protein. The order of affinities of SlyD for the metals examined is as follows: Mn(II) and Fe(II) < Co(II) < Ni(II) ~ Zn(II) ≪ Cu(I). Although the purified protein is unable to overcome the large thermodynamic preference for Cu(I) and exclude Zn(II) chelation in the presence of Ni(II), in vivo studies reveal a Ni(II)-specific function for the protein. Furthermore, these latter experiments support a specific role for SlyD as a [NiFe]-hydrogenase enzyme maturation factor. The implications of the divergence between the metal selectivity of SlyD in vitro and the specific activity in vivo are discussed.
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Affiliation(s)
- Harini Kaluarachchi
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
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Cheng T, Li H, Xia W, Sun H. Multifaceted SlyD from Helicobacter pylori: implication in [NiFe] hydrogenase maturation. J Biol Inorg Chem 2011; 17:331-43. [PMID: 22045417 PMCID: PMC3292732 DOI: 10.1007/s00775-011-0855-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 10/07/2011] [Indexed: 12/31/2022]
Abstract
SlyD belongs to the FK506-binding protein (FKBP) family with both peptidylprolyl isomerase (PPIase) and chaperone activities, and is considered to be a ubiquitous cytosolic protein-folding facilitator in bacteria. It possesses a histidine- and cysteine-rich C-terminus binding to selected divalent metal ions (e.g., Ni2+, Zn2+), which is important for its involvement in the maturation processes of metalloenzymes. We have determined the solution structure of C-terminus-truncated SlyD from Helicobacter pylori (HpSlyDΔC). HpSlyDΔC folds into two well-separated, orientation-independent domains: the PPIase-active FKBP domain and the chaperone-active insert-in-flap (IF) domain. The FKBP domain consists of a four-stranded antiparallel β-sheet with an α-helix on one side, whereas the IF domain folds into a four-stranded antiparallel β-sheet accompanied by a short α-helix. Intact H. pylori SlyD binds both Ni2+ and Zn2+, with dissociation constants of 2.74 and 3.79 μM respectively. Intriguingly, binding of Ni2+ instead of Zn2+ induces protein conformational changes around the active sites of the FKBP domain, implicating a regulatory role of nickel. The twin-arginine translocation (Tat) signal peptide from the small subunit of [NiFe] hydrogenase (HydA) binds the protein at the IF domain. Nickel binding and the recognition of the Tat signal peptide by the protein suggest that SlyD participates in [NiFe] hydrogenase maturation processes.
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Affiliation(s)
- Tianfan Cheng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Hongyan Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Wei Xia
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Hongzhe Sun
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
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35
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Budiman C, Koga Y, Takano K, Kanaya S. FK506-Binding protein 22 from a psychrophilic bacterium, a cold shock-inducible peptidyl prolyl isomerase with the ability to assist in protein folding. Int J Mol Sci 2011; 12:5261-84. [PMID: 21954357 PMCID: PMC3179164 DOI: 10.3390/ijms12085261] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/28/2011] [Accepted: 08/09/2011] [Indexed: 11/23/2022] Open
Abstract
Adaptation of microorganisms to low temperatures remains to be fully elucidated. It has been previously reported that peptidyl prolyl cis-trans isomerases (PPIases) are involved in cold adaptation of various microorganisms whether they are hyperthermophiles, mesophiles or phsycrophiles. The rate of cis-trans isomerization at low temperatures is much slower than that at higher temperatures and may cause problems in protein folding. However, the mechanisms by which PPIases are involved in cold adaptation remain unclear. Here we used FK506-binding protein 22, a cold shock protein from the psychrophilic bacterium Shewanella sp. SIB1 (SIB1 FKBP22) as a model protein to decipher the involvement of PPIases in cold adaptation. SIB1 FKBP22 is homodimer that assumes a V-shaped structure based on a tertiary model. Each monomer consists of an N-domain responsible for dimerization and a C-catalytic domain. SIB1 FKBP22 is a typical cold-adapted enzyme as indicated by the increase of catalytic efficiency at low temperatures, the downward shift in optimal temperature of activity and the reduction in the conformational stability. SIB1 FKBP22 is considered as foldase and chaperone based on its ability to catalyze refolding of a cis-proline containing protein and bind to a folding intermediate protein, respectively. The foldase and chaperone activites of SIB1 FKBP22 are thought to be important for cold adaptation of Shewanella sp. SIB1. These activities are also employed by other PPIases for being involved in cold adaptation of various microorganisms. Despite other biological roles of PPIases, we proposed that foldase and chaperone activities of PPIases are the main requirement for overcoming the cold-stress problem in microorganisms due to folding of proteins.
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Affiliation(s)
- Cahyo Budiman
- Department of Material and Life Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mails: (C.B.); (Y.K.); (S.K.)
| | - Yuichi Koga
- Department of Material and Life Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mails: (C.B.); (Y.K.); (S.K.)
| | - Kazufumi Takano
- Department of Material and Life Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mails: (C.B.); (Y.K.); (S.K.)
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-Cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Shigenori Kanaya
- Department of Material and Life Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mails: (C.B.); (Y.K.); (S.K.)
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36
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Haupt C, Weininger U, Kovermann M, Balbach J. Local and Coupled Thermodynamic Stability of the Two-Domain and Bifunctional Enzyme SlyD from Escherichia coli. Biochemistry 2011; 50:7321-9. [DOI: 10.1021/bi2000627] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Caroline Haupt
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Ulrich Weininger
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Michael Kovermann
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Jochen Balbach
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
- Mitteldeutsches Zentrum für
Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
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37
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Robichon C, Luo J, Causey TB, Benner JS, Samuelson JC. Engineering Escherichia coli BL21(DE3) derivative strains to minimize E. coli protein contamination after purification by immobilized metal affinity chromatography. Appl Environ Microbiol 2011; 77:4634-46. [PMID: 21602383 PMCID: PMC3127686 DOI: 10.1128/aem.00119-11] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 05/04/2011] [Indexed: 11/20/2022] Open
Abstract
Recombinant His-tagged proteins expressed in Escherichia coli and purified by immobilized metal affinity chromatography (IMAC) are commonly coeluted with native E. coli proteins, especially if the recombinant protein is expressed at a low level. The E. coli contaminants display high affinity to divalent nickel or cobalt ions, mainly due to the presence of clustered histidine residues or biologically relevant metal binding sites. To improve the final purity of expressed His-tagged protein, we engineered E. coli BL21(DE3) expression strains in which the most recurring contaminants are either expressed with an alternative tag or mutated to decrease their affinity to divalent cations. The current study presents the design, engineering, and characterization of two E. coli BL21(DE3) derivatives, NiCo21(DE3) and NiCo22(DE3), which express the endogenous proteins SlyD, Can, ArnA, and (optionally) AceE fused at their C terminus to a chitin binding domain (CBD) and the protein GlmS, with six surface histidines replaced by alanines. We show that each E. coli CBD-tagged protein remains active and can be efficiently eliminated from an IMAC elution fraction using a chitin column flowthrough step, while the modification of GlmS results in loss of affinity for nickel-containing resin. The "NiCo" strains uniquely complement existing methods for improving the purity of recombinant His-tagged protein.
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Affiliation(s)
- Carine Robichon
- New England BioLabs, Inc., Gene Expression Division, 240 County Road, Ipswich, Massachusetts 01938
| | - Jianying Luo
- New England BioLabs, Inc., Gene Expression Division, 240 County Road, Ipswich, Massachusetts 01938
| | - Thomas B. Causey
- New England BioLabs, Inc., Gene Expression Division, 240 County Road, Ipswich, Massachusetts 01938
| | - Jack S. Benner
- New England BioLabs, Inc., Gene Expression Division, 240 County Road, Ipswich, Massachusetts 01938
| | - James C. Samuelson
- New England BioLabs, Inc., Gene Expression Division, 240 County Road, Ipswich, Massachusetts 01938
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38
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Kovermann M, Zierold R, Haupt C, Löw C, Balbach J. NMR relaxation unravels interdomain crosstalk of the two domain prolyl isomerase and chaperone SlyD. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:873-81. [DOI: 10.1016/j.bbapap.2011.03.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/18/2011] [Accepted: 03/25/2011] [Indexed: 11/26/2022]
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39
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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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40
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Norville IH, Breitbach K, Eske-Pogodda K, Harmer NJ, Sarkar-Tyson M, Titball RW, Steinmetz I. A novel FK-506-binding-like protein that lacks peptidyl-prolyl isomerase activity is involved in intracellular infection and in vivo virulence of Burkholderia pseudomallei. MICROBIOLOGY-SGM 2011; 157:2629-2638. [PMID: 21680634 DOI: 10.1099/mic.0.049163-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Burkholderia pseudomallei is a facultative intracellular bacterial pathogen causing melioidosis, an often fatal infectious disease that is endemic in several tropical and subtropical areas around the world. We previously described a Ptk2 cell-based plaque assay screening system of B. pseudomallei transposon mutants that led to the identification of several novel virulence determinants. Using this approach we identified a mutant with reduced plaque formation in which the BPSL0918 gene was disrupted. BPSL0918 encodes a putative FK-506-binding protein (FKBP) representing a family of proteins that typically possess peptidyl-prolyl isomerase (PPIase) activity. A B. pseudomallei ΔBPSL0918 mutant showed a severely impaired ability to resist intracellular killing and to replicate within primary macrophages. Complementation of the mutant fully restored its ability to grow intracellularly. Moreover, B. pseudomallei ΔBPSL0918 was significantly attenuated in a murine model of infection. Structural modelling confirmed a modified FKBP fold of the BPSL0918-encoded protein but unlike virulence-associated FKBPs from other pathogenic bacteria, recombinant BPSL0918 protein did not possess PPIase activity in vitro. In accordance with this observation BPSL0918 exhibits several mutations in residues that have been proposed to mediate PPIase activity in other FKBPs. To our knowledge this B. pseudomallei FKBP represents the first example of this protein family which lacks PPIase activity but is important in intracellular infection of a bacterial pathogen.
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Affiliation(s)
- Isobel H Norville
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Katrin Breitbach
- Friedrich Loeffler Institute of Medical Microbiology, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Kristin Eske-Pogodda
- Friedrich Loeffler Institute of Medical Microbiology, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | | | - Mitali Sarkar-Tyson
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | | | - Ivo Steinmetz
- Friedrich Loeffler Institute of Medical Microbiology, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
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41
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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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42
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Schmidpeter PAM, Jahreis G, Geitner AJ, Schmid FX. Prolyl Isomerases Show Low Sequence Specificity toward the Residue Following the Proline. Biochemistry 2011; 50:4796-803. [DOI: 10.1021/bi200442q] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Philipp A. M. Schmidpeter
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Günther Jahreis
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, D-06120 Halle/Saale, 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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43
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Martinez-Hackert E, Hendrickson WA. Structural analysis of protein folding by the long-chain archaeal chaperone FKBP26. J Mol Biol 2011; 407:450-64. [PMID: 21262232 DOI: 10.1016/j.jmb.2011.01.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 01/05/2011] [Accepted: 01/12/2011] [Indexed: 11/17/2022]
Abstract
In the cell, protein folding is mediated by folding catalysts and chaperones. The two functions are often linked, especially when the catalytic module forms part of a multidomain protein, as in Methanococcus jannaschii peptidyl-prolyl cis/trans isomerase FKBP26. Here, we show that FKBP26 chaperone activity requires both a 50-residue insertion in the catalytic FKBP domain, also called 'Insert-in-Flap' or IF domain, and an 80-residue C-terminal domain. We determined FKBP26 structures from four crystal forms and analyzed chaperone domains in light of their ability to mediate protein-protein interactions. FKBP26 is a crescent-shaped homodimer. We reason that folding proteins are bound inside the large crescent cleft, thus enabling their access to inward-facing peptidyl-prolyl cis/trans isomerase catalytic sites and ipsilateral chaperone domain surfaces. As these chaperone surfaces participate extensively in crystal lattice contacts, we speculate that the observed lattice contacts reflect a proclivity for protein associations and represent substrate interactions by FKBP26 chaperone domains. Finally, we find that FKBP26 is an exceptionally flexible molecule, suggesting a mechanism for nonspecific substrate recognition.
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Affiliation(s)
- Erik Martinez-Hackert
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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44
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Chung KCC, Zamble DB. The Escherichia coli metal-binding chaperone SlyD interacts with the large subunit of [NiFe]-hydrogenase 3. FEBS Lett 2010; 585:291-4. [PMID: 21185288 DOI: 10.1016/j.febslet.2010.12.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/10/2010] [Accepted: 12/14/2010] [Indexed: 11/30/2022]
Abstract
The multi-step biosynthesis of the [NiFe]-hydrogenase enzyme involves a variety of accessory proteins. To further understand this process, a Strep-tag II variant of the large subunit of Escherichia coli hydrogenase 3, HycE, was constructed to enable isolation of protein complexes. A complex with SlyD, a chaperone protein implicated in hydrogenase production through association with the nickel-binding accessory protein HypB, was observed. A SlyD-HycE interaction preceding both iron and nickel insertion to the enzyme was detected, mediated by the chaperone domain of SlyD, and independent of HypB. These results support a model of several roles for SlyD during hydrogenase maturation.
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Affiliation(s)
- Kim C Chan Chung
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
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45
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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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46
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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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47
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Määttänen P, Gehring K, Bergeron JJM, Thomas DY. Protein quality control in the ER: the recognition of misfolded proteins. Semin Cell Dev Biol 2010; 21:500-11. [PMID: 20347046 DOI: 10.1016/j.semcdb.2010.03.006] [Citation(s) in RCA: 191] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 03/16/2010] [Accepted: 03/18/2010] [Indexed: 02/08/2023]
Abstract
The mechanism, in molecular terms of protein quality control, specifically of how the cell recognizes and discriminates misfolded proteins, remains a challenge. In the secretory pathway the folding status of glycoproteins passing through the endoplasmic reticulum is marked by the composition of the N-glycan. The different glycoforms are recognized by specialized lectins. The folding sensor UGGT acts as an unusual molecular chaperone and covalently modifies the Man9 N-glycan of a misfolded protein by adding a glucose moiety and converts it to Glc1Man9 that rebinds the lectin calnexin. However, further links between the folding status of a glycoprotein and the composition of the N-glycan are unclear. There is little unequivocal evidence for other proteins in the ER recognizing the N-glycan and also acting as molecular chaperones. Nevertheless, based upon a few examples, we suggest that this function is carried out by individual proteins in several different complexes. Thus, calnexin binds the protein disulfide isomerase ERp57, that acts upon Glc1Man9 glycoproteins. In another example the protein disulfide isomerase ERdj5 binds specifically to EDEM (which is probably a mannosidase) and a lectin OS9, and reduces the disulfide bonds of bound glycoproteins destined for ERAD. Thus the glycan recognition is performed by a lectin and the chaperone function performed by a specific partner protein that can recognize misfolded proteins. We predict that this will be a common arrangement of proteins in the ER and that members of protein foldase families such as PDI and PPI will bind specifically to lectins in the ER. Molecular chaperones BiP and GRp94 will assist in the folding of proteins bound in these complexes as well as in the folding of non-glycoproteins.
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Affiliation(s)
- Pekka Määttänen
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
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48
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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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Martino L, Kelly G, Conte MR. Letter to the Editor: resonance assignment of SlyD from E. coli. BIOMOLECULAR NMR ASSIGNMENTS 2009; 3:235-237. [PMID: 19760519 DOI: 10.1007/s12104-009-9183-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 09/05/2009] [Indexed: 05/28/2023]
Abstract
SlyD from Escherichia coli is a peptidyl-prolyl cis-trans isomerase involved in [Ni-Fe] hydrogenase metallocentre assembly in bacteria. We present here the backbone and side chain assignments for E. coli SlyD.
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