1
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Orta AK, Riera N, Li YE, Tanaka S, Yun HG, Klaic L, Clemons WM. The mechanism of the phage-encoded protein antibiotic from ΦX174. Science 2023; 381:eadg9091. [PMID: 37440661 DOI: 10.1126/science.adg9091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/23/2023] [Indexed: 07/15/2023]
Abstract
The historically important phage ΦX174 kills its host bacteria by encoding a 91-residue protein antibiotic called protein E. Using single-particle electron cryo-microscopy, we demonstrate that protein E bridges two bacterial proteins to form the transmembrane YES complex [MraY, protein E, sensitivity to lysis D (SlyD)]. Protein E inhibits peptidoglycan biosynthesis by obstructing the MraY active site leading to loss of lipid I production. We experimentally validate this result for two different viral species, providing a clear model for bacterial lysis and unifying previous experimental data. Additionally, we characterize the Escherichia coli MraY structure-revealing features of this essential enzyme-and the structure of the chaperone SlyD bound to a protein. Our structures provide insights into the mechanism of phage-mediated lysis and for structure-based design of phage therapeutics.
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Affiliation(s)
- Anna K Orta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nadia Riera
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yancheng E Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shiho Tanaka
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hyun Gi Yun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lada Klaic
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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2
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Chromatin localization of nucleophosmin organizes ribosome biogenesis. Mol Cell 2022; 82:4443-4457.e9. [PMID: 36423630 PMCID: PMC9949351 DOI: 10.1016/j.molcel.2022.10.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 11/24/2022]
Abstract
Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin compartment and move to the outer granular component, where maturation occurs. We find that the Schizosaccharomyces pombe nucleophosmin-like protein Fkbp39 localizes to rDNA sites encoding the 60S subunit rRNA, and this localization contributes to its specific association with nascent 60S subunits. Fkbp39 dissociates from chromatin to bind nascent 60S subunits, causing the latter to partition away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. In vivo, Fkbp39 binding directs the translocation of nascent 60S subunits toward the nucleophosmin-rich granular component. This process increases the efficiency of 60S subunit assembly, facilitating the incorporation of 60S RNA domain III. Thus, chromatin localization determines the specificity of nucleophosmin in sorting nascent ribosomal subunits and coordinates their movement into specialized assembly compartments within the nucleolus.
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3
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Wassarman DR, Bankapalli K, Pallanck LJ, Shokat KM. Tissue-restricted inhibition of mTOR using chemical genetics. Proc Natl Acad Sci U S A 2022; 119:e2204083119. [PMID: 36095197 PMCID: PMC9499525 DOI: 10.1073/pnas.2204083119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/06/2022] [Indexed: 11/18/2022] Open
Abstract
Mammalian target of rapamycin (mTOR) is a highly conserved eukaryotic protein kinase that coordinates cell growth and metabolism, and plays a critical role in cancer, immunity, and aging. It remains unclear how mTOR signaling in individual tissues contributes to whole-organism processes because mTOR inhibitors, like the natural product rapamycin, are administered systemically and target multiple tissues simultaneously. We developed a chemical-genetic system, termed selecTOR, that restricts the activity of a rapamycin analog to specific cell populations through targeted expression of a mutant FKBP12 protein. This analog has reduced affinity for its obligate binding partner FKBP12, which reduces its ability to inhibit mTOR in wild-type cells and tissues. Expression of the mutant FKBP12, which contains an expanded binding pocket, rescues the activity of this rapamycin analog. Using this system, we show that selective mTOR inhibition can be achieved in Saccharomyces cerevisiae and human cells, and we validate the utility of our system in an intact metazoan model organism by identifying the tissues responsible for a rapamycin-induced developmental delay in Drosophila.
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Affiliation(s)
- Douglas R. Wassarman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- HHMI, University of California, San Francisco, CA 94158
| | | | - Leo J. Pallanck
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Kevan M. Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- HHMI, University of California, San Francisco, CA 94158
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4
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Joshi DC, Gosse C, Huang SY, Lin JH. A Curvilinear-Path Umbrella Sampling Approach to Characterizing the Interactions Between Rapamycin and Three FKBP12 Variants. Front Mol Biosci 2022; 9:879000. [PMID: 35874613 PMCID: PMC9304761 DOI: 10.3389/fmolb.2022.879000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Rapamycin is an immunosuppressant macrolide that exhibits anti-proliferative properties through inhibiting the mTOR kinase. In fact, the drug first associates with the FKBP12 enzyme before interacting with the FRB domain of its target. Despite the availability of structural and thermodynamic information on the interaction of FKBP12 with rapamycin, the energetic and mechanistic understanding of this process is still incomplete. We recently reported a multiple-walker umbrella sampling simulation approach to characterizing the protein–protein interaction energetics along curvilinear paths. In the present paper, we extend our investigations to a protein-small molecule duo, the FKBP12•rapamycin complex. We estimate the binding free energies of rapamycin with wild-type FKBP12 and two mutants in which a hydrogen bond has been removed, D37V and Y82F. Furthermore, the underlying mechanistic details are analyzed. The calculated standard free energies of binding agree well with the experimental data, and the roles of the hydrogen bonds are shown to be quite different for each of these two mutated residues. On one hand, removing the carboxylate group of D37 strongly destabilizes the association; on the other hand, the hydroxyl group of Y82 is nearly unnecessary for the stability of the complex because some nonconventional, cryptic, indirect interaction mechanisms seem to be at work.
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Affiliation(s)
| | - Charlie Gosse
- Institut de Biologie de l’Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Shu-Yu Huang
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Jung-Hsin Lin
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Biomedical Translation Research Center, National Biotechnology Research Park, Academia Sinica, Taipei, Taiwan
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
- College of Engineering Sciences, Chang Gung University, Taoyuan, Taiwan
- *Correspondence: Jung-Hsin Lin,
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5
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Anchal, Kaushik V, Goel M. Distribution of Peptidyl-Prolyl Isomerase (PPIase) in the Archaea. Front Microbiol 2021; 12:751049. [PMID: 34691003 PMCID: PMC8530231 DOI: 10.3389/fmicb.2021.751049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Cis-trans isomerization of the peptide bond prior to proline is an intrinsically slow process but plays an essential role in protein folding. In vivo cis-trans isomerization reaction is catalyzed by Peptidyl-prolyl isomerase (PPIases), a category of proteins widely distributed among all the three domains of life. The present study is majorly focused on the distribution of different types of PPIases in the archaeal domain. All the three hitherto known families of PPIases (namely FKBP, Cyclophilin and parvulin) were studied to identify the evolutionary conservation across the phylum archaea. The basic function of cyclophilin, FKBP and parvulin has been conserved whereas the sequence alignment suggested variations in each clade. The conserved residues within the predicted motif of each family are unique. The available protein structures of different PPIase across various domains were aligned to ascertain the structural variation in the catalytic site. The structural alignment of native PPIase proteins among various groups suggested that the apo-protein may have variable conformations but when bound to their specific inhibitors, they attain similar active site configuration. This is the first study of its kind which explores the distribution of archaeal PPIases, along with detailed structural and functional analysis of each type of PPIase found in archaea.
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Affiliation(s)
- Anchal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Vineeta Kaushik
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Manisha Goel
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
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6
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Caminati G, Procacci P. Mounting evidence of FKBP12 implication in neurodegeneration. Neural Regen Res 2020; 15:2195-2202. [PMID: 32594030 PMCID: PMC7749462 DOI: 10.4103/1673-5374.284980] [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: 02/03/2020] [Revised: 02/18/2020] [Accepted: 03/24/2020] [Indexed: 12/25/2022] Open
Abstract
Intrinsically disordered proteins, such as tau or α-synuclein, have long been associated with a dysfunctional role in neurodegenerative diseases. In Alzheimer's and Parkinson's' diseases, these proteins, sharing a common chemical-physical pattern with alternating hydrophobic and hydrophilic domains rich in prolines, abnormally aggregate in tangles in the brain leading to progressive loss of neurons. In this review, we present an overview linking the studies on the implication of the peptidyl-prolyl isomerase domain of immunophilins, and notably FKBP12, to a variety of neurodegenerative diseases, focusing on the molecular origin of such a role. The involvement of FKBP12 dysregulation in the aberrant aggregation of disordered proteins pinpoints this protein as a possible therapeutic target and, at the same time, as a predictive biomarker for early diagnosis in neurodegeneration, calling for the development of reliable, fast and cost-effective detection methods in body fluids for community-based screening campaigns.
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Affiliation(s)
- Gabriella Caminati
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
- Center for Colloid and Surface Science (CSGI), University of Florence, Sesto Fiorentino, Italy
| | - Piero Procacci
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
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7
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Liu D, Wu Q, Chen W, Lin H, Liu Y, Liang H, Zhu F. Tacrolimus-loaded methoxy poly(ethylene glycol)-block-poly(D,L)-lactic–co-glycolic acid micelles self-assembled in aqueous solution for treating cornea immune rejection after allogenic penetrating keratoplasty in rats. Eur J Pharm Sci 2019; 133:104-114. [DOI: 10.1016/j.ejps.2019.03.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 03/07/2019] [Accepted: 03/26/2019] [Indexed: 01/12/2023]
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8
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Goh CKW, Silvester J, Wan Mahadi WNS, Chin LP, Ying LT, Leow TC, Kurahashi R, Takano K, Budiman C. Expression and characterization of functional domains of FK506-binding protein 35 from Plasmodium knowlesi. Protein Eng Des Sel 2018; 31:489-498. [PMID: 31120120 DOI: 10.1093/protein/gzz008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 12/24/2018] [Accepted: 04/06/2019] [Indexed: 11/13/2022] Open
Abstract
The FK506-binding protein of Plasmodium knowlesi (Pk-FKBP35) is considerably a viable antimalarial drug target, which belongs to the peptidyl-prolyl cis-trans isomerase (PPIase) protein family member. Structurally, this protein consists of an N-terminal FK506-binding domain (FKBD) and a C-terminal tetratricopeptide repeat domain (TPRD). This study aims to decipher functional properties of these domains as a platform for development of novel antimalarial drugs. Accordingly, full-length Pk-FKBP35 as well as its isolated domains, Pk-FKBD and Pk-TPRD were overexpressed, purified, and characterized. The results showed that catalytic PPIase activity was confined to the full-length Pk-FKBP35 and Pk-FKBD, suggesting that the catalytic activity is structurally regulated by the FKBD. Meanwhile, oligomerization analysis revealed that Pk-TPRD is essential for dimerization. Asp55, Arg60, Trp77 and Phe117 in the Pk-FKBD were considerably important for catalysis as underlined by significant reduction of PPIase activity upon mutations at these residues. Further, inhibition activity of Pk-FKBP35 towards calcineurin phosphatase activity revealed that the presence of FKBD is essential for the inhibitory property, while TPRD may be important for efficient binding to calcineurin. We then discussed possible roles of FKBP35 in Plasmodium cells and proposed mechanisms by which the immunosuppressive drug, FK506, interacts with the protein.
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Affiliation(s)
- Carlmond Kah Wun Goh
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Jovi Silvester
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | | | - Lee Ping Chin
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Lau Tiek Ying
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Malaysia
| | - Ryo Kurahashi
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Japan
| | - Kazufumi Takano
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Japan
| | - Cahyo Budiman
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
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9
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Kawagoe S, Nakagawa H, Kumeta H, Ishimori K, Saio T. Structural insight into proline cis/ trans isomerization of unfolded proteins catalyzed by the trigger factor chaperone. J Biol Chem 2018; 293:15095-15106. [PMID: 30093407 PMCID: PMC6166725 DOI: 10.1074/jbc.ra118.003579] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
Molecular chaperones often possess functional modules that are specialized in assisting the formation of specific structural elements, such as a disulfide bridges and peptidyl–prolyl bonds in cis form, in the client protein. A ribosome-associated molecular chaperone trigger factor (TF), which has a peptidyl–prolyl cis/trans isomerase (PPIase) domain, acts as a highly efficient catalyst in the folding process limited by peptidyl–prolyl isomerization. Herein we report a study on the mechanism through which TF recognizes the proline residue in the unfolded client protein during the cis/trans isomerization process. The solution structure of TF in complex with the client protein showed that TF recognizes the proline-aromatic motif located in the hydrophobic stretch of the unfolded client protein through its conserved hydrophobic cleft, which suggests that TF preferentially accelerates the isomerization of the peptidyl–prolyl bond that is eventually folded into the core of the protein in its native fold. Molecular dynamics simulation revealed that TF exploits the backbone amide group of Ile195 to form an intermolecular hydrogen bond with the carbonyl oxygen of the amino acid residue preceding the proline residue at the transition state, which presumably stabilizes the transition state and thus accelerates the isomerization. The importance of such intermolecular hydrogen-bond formation during the catalysis was further corroborated by the activity assay and NMR relaxation analysis.
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Affiliation(s)
- Soichiro Kawagoe
- From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Hiroshi Nakagawa
- the Materials Sciences Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Hiroyuki Kumeta
- the Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 011-0021, Japan
| | - Koichiro Ishimori
- From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan, .,the Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan, and
| | - Tomohide Saio
- From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan, .,the Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan, and.,PRESTO, Japan Science and Technology Agency, Tokyo 102-0076, Japan
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10
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Weininger U, Modig K, Geitner AJ, Schmidpeter PAM, Koch JR, Akke M. Dynamics of Aromatic Side Chains in the Active Site of FKBP12. Biochemistry 2016; 56:334-343. [DOI: 10.1021/acs.biochem.6b01157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ulrich Weininger
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
- Institute
of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Kristofer Modig
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
| | - Anne-Juliane Geitner
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Philipp A. M. Schmidpeter
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Johanna R. Koch
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Mikael Akke
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
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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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Abstract
Invasive fungal infections remain difficult to treat and require novel targeting strategies. The 12-kDa FK506-binding protein (FKBP12) is a ubiquitously expressed peptidyl-prolyl isomerase with considerable homology between fungal pathogens and is thus a prime candidate for future targeting efforts to generate a panfungal strategy. Despite decades of research on FKBPs, their substrates and mechanisms of action remain unclear. Here we describe structural, biochemical, and in vivo analyses of FKBP12s from the pathogenic fungi Candida albicans, Candida glabrata, and Aspergillus fumigatus. Strikingly, multiple apo A. fumigatus and C. albicans FKBP12 crystal structures revealed a symmetric, intermolecular interaction involving the deep insertion of an active-site loop proline into the active-site pocket of an adjacent subunit. Such interactions have not been observed in previous FKBP structures. This finding indicates the possibility that this is a self-substrate interaction unique to the A. fumigatus and C. albicans fungal proteins that contain this central proline. Structures obtained with the proline in the cis and trans states provide more data in support of self-catalysis. Moreover, cysteine cross-linking experiments captured the interacting dimer, supporting the idea that it forms in solution. Finally, genetic studies exploring the impact of mutations altering the central proline and an adjacent residue provide evidence that any dimeric state formed in vivo, where FKBP12 concentrations are low, is transient. Taken together, these findings suggest a unique mechanism of self-substrate regulation by fungal FKBP12s, lending further novel understanding of this protein for future drug-targeting efforts. FKBP12 is a cis-trans peptidyl-prolyl isomerase that plays key roles in cellular protein homeostasis. FKBP12s also bind the immunosuppressive drug FK506 to inhibit the phosphatase calcineurin (CaN). CaN is required for virulence of A. fumigatus, C. albicans, C. glabrata, and other deadly fungal pathogens, marking FKBP12 and CaN as potential broad-spectrum drug targets. Here we describe structures of fungal FKBP12s. Multiple apo A. fumigatus and C. albicans FKBP12 structures reveal the insertion of a proline, conspicuously conserved in these proteins, into the active sites of adjacent molecules. This suggests that these proteins might serve as their own substrates. Cysteine disulfide trapping experiments provide support for this self-interaction and hence possible intermolecular catalysis by these enzymes.
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13
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Nerattini F, Chelli R, Procacci P. II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands. Phys Chem Chem Phys 2016; 18:15005-18. [DOI: 10.1039/c5cp05521k] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fast switch double annihilation method (FS-DAM) provides an effective mean to the compute the binding free energies in drug-receptor systems. Here we present an application to the FK506-related ligands of the FKBP12 protein.
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14
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Jo GA, Lee JM, No G, Kang DS, Kim SH, Ahn SH, Kong IS. Isolation and characterization of a 17-kDa FKBP-type peptidyl-prolyl cis/trans isomerase from Vibrio anguillarum. Protein Expr Purif 2015; 110:130-7. [DOI: 10.1016/j.pep.2015.02.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/29/2022]
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15
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Procacci P, Bizzarri M, Marsili S. Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations. J Chem Theory Comput 2013; 10:439-50. [DOI: 10.1021/ct400809n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Piero Procacci
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Marco Bizzarri
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Simone Marsili
- Centro Nacional de Investigaciones Oncologicas, Calle de Melchor Fernández Almagro, 3, E-28029 Madrid, Spain
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16
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Noncanonical FK506-binding protein BDBT binds DBT to enhance its circadian function and forms foci at night. Neuron 2013; 80:984-96. [PMID: 24210908 DOI: 10.1016/j.neuron.2013.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2013] [Indexed: 11/22/2022]
Abstract
The kinase DOUBLETIME is a master regulator of the Drosophila circadian clock, yet the mechanisms regulating its activity remain unclear. A proteomic analysis of DOUBLETIME interactors led to the identification of an unstudied protein designated CG17282. RNAi-mediated knockdown of CG17282 produced behavioral arrhythmicity and long periods and high levels of hypophosphorylated nuclear PERIOD and phosphorylated DOUBLETIME. Overexpression of DOUBLETIME in flies suppresses these phenotypes and overexpression of CG17282 in S2 cells enhances DOUBLETIME-dependent PERIOD degradation, indicating that CG17282 stimulates DOUBLETIME's circadian function. In photoreceptors, CG17282 accumulates rhythmically in PERIOD- and DOUBLETIME-dependent cytosolic foci. Finally, structural analyses demonstrated CG17282 is a noncanonical FK506-binding protein with an inactive peptide prolyl-isomerase domain that binds DOUBLETIME and tetratricopeptide repeats that may promote assembly of larger protein complexes. We have named CG17282 BRIDE OF DOUBLETIME and established it as a mediator of DOUBLETIME's effects on PERIOD, most likely in cytosolic foci that regulate PERIOD nuclear accumulation.
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17
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Ikura T, Ito N. Peptidyl-prolyl isomerase activity of FK506 binding protein 12 prevents tau peptide from aggregating. Protein Eng Des Sel 2013; 26:539-46. [DOI: 10.1093/protein/gzt033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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18
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Structural insights into substrate binding by PvFKBP35, a peptidylprolyl cis-trans isomerase from the human malarial parasite Plasmodium vivax. EUKARYOTIC CELL 2013; 12:627-34. [PMID: 23435727 DOI: 10.1128/ec.00016-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The immunosuppressive drug FK506 binding proteins (FKBPs), an immunophilin family with the immunosuppressive drug FK506 binding property, exhibit peptidylprolyl cis-trans isomerase (PPIase) activity. While the cyclophilin-catalyzed peptidylprolyl isomerization of X-Pro peptide bonds has been extensively studied, the mechanism of the FKBP-mediated peptidylprolyl isomerization remains uncharacterized. Thus, to investigate the binding of FKBP with its substrate and the underlying catalytic mechanism of the FKBP-mediated proline isomerization, here we employed the FK506 binding domain (FKBD) of the human malarial parasite Plasmodium vivax FK506 binding protein 35 (PvFKBP35) and examined the details of the molecular interaction between the isomerase and a peptide substrate. The crystallographic structures of apo PvFKBD35 and its complex with the tetrapeptide substrate succinyl-Ala-Leu-Pro-Phe-p-nitroanilide (sALPFp) determined at 1.4 Å and 1.65 Å resolutions, respectively, showed that the substrate binds to PvFKBD35 in a cis conformation. Nuclear magnetic resonance (NMR) studies demonstrated the chemical shift perturbations of D55, H67, V73, and I74 residues upon the substrate binding. In addition, the X-ray crystal structure, along with the mutational studies, shows that Y100 is a key residue for the catalytic activity. Taken together, our results provide insights into the catalytic mechanism of PvFKBP35-mediated cis-trans isomerization of substrate and ultimately might aid designing substrate mimetic inhibitors targeting the malarial parasite FKBPs.
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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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20
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Gollan PJ, Bhave M, Aro EM. The FKBP families of higher plants: Exploring the structures and functions of protein interaction specialists. FEBS Lett 2012; 586:3539-47. [PMID: 22982859 DOI: 10.1016/j.febslet.2012.09.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 08/31/2012] [Accepted: 09/03/2012] [Indexed: 01/24/2023]
Abstract
The FK506-binding proteins (FKBPs) are known both as the receptors for immunosuppressant drugs and as prolyl isomerase (PPIase) enzymes that catalyse rotation of prolyl bonds. FKBPs are characterised by the inclusion of at least one FK506-binding domain (FKBd), the receptor site for proline and the active site for PPIase catalysis. The FKBPs form large and diverse families in most organisms, with the largest FKBP families occurring in higher plants. Plant FKBPs are molecular chaperones that interact with specific protein partners to regulate a diversity of cellular processes. Recent studies have found that plant FKBPs operate in intricate and coordinated mechanisms for regulating stress response and development processes, and discoveries of new interaction partners expand their cellular influences to gene expression and photosynthetic adaptations. This review presents an examination of the molecular and structural features and functional roles of the higher plant FKBP family within the context of these recent findings, and discusses the significance of domain conservation and variation for the development of a diverse, versatile and complex chaperone family.
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Affiliation(s)
- Peter J Gollan
- Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, P.O. Box 218, Hawthorn, VIC 3122, Australia.
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21
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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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22
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A Burkholderia pseudomallei macrophage infectivity potentiator-like protein has rapamycin-inhibitable peptidylprolyl isomerase activity and pleiotropic effects on virulence. Infect Immun 2011; 79:4299-307. [PMID: 21859853 DOI: 10.1128/iai.00134-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Macrophage infectivity potentiators (Mips) are a group of virulence factors encoded by pathogenic bacteria such as Legionella, Chlamydia, and Neisseria species. Mips are part of the FK506-binding protein (FKBP) family, whose members typically exhibit peptidylprolyl cis-trans isomerase (PPIase) activity which is inhibitable by the immunosuppressants FK506 and rapamycin. Here we describe the identification and characterization of BPSS1823, a Mip-like protein in the intracellular pathogen Burkholderia pseudomallei. Recombinant BPSS1823 protein has rapamycin-inhibitable PPIase activity, indicating that it is a functional FKBP. A mutant strain generated by deletion of BPSS1823 in B. pseudomallei exhibited a reduced ability to survive within cells and significant attenuation in vivo, suggesting that BPSS1823 is important for B. pseudomallei virulence. In addition, pleiotropic effects were observed with a reduction in virulence mechanisms, including resistance to host killing mechanisms, swarming motility, and protease production.
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23
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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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Olivieri L, Gardebien F. Molecular Dynamics Simulations of a Binding Intermediate between FKBP12 and a High-Affinity Ligand. J Chem Theory Comput 2011; 7:725-41. [DOI: 10.1021/ct100394d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lilian Olivieri
- DSIMB, INSERM, U665, Paris, F-75015, France, DSIMB, INSERM, U665, Faculté des Sciences et Technologies, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France, INTS, Paris, F-75015, France, and Laboratoire de Biochimie et Génétique Moléculaire, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France
| | - Fabrice Gardebien
- DSIMB, INSERM, U665, Paris, F-75015, France, DSIMB, INSERM, U665, Faculté des Sciences et Technologies, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France, INTS, Paris, F-75015, France, and Laboratoire de Biochimie et Génétique Moléculaire, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France
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Peptide Bond cis/trans Isomerases: A Biocatalysis Perspective of Conformational Dynamics in Proteins. Top Curr Chem (Cham) 2011; 328:35-67. [DOI: 10.1007/128_2011_151] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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26
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Jacques DA, Langley DB, Hynson RMG, Whitten AE, Kwan A, Guss JM, Trewhella J. A novel structure of an antikinase and its inhibitor. J Mol Biol 2010; 405:214-26. [PMID: 21050859 DOI: 10.1016/j.jmb.2010.10.047] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/22/2010] [Accepted: 10/26/2010] [Indexed: 01/27/2023]
Abstract
In Bacillus subtilis, the KipI protein is a regulator of the phosphorelay governing the onset of sporulation. KipI binds the relevant sensor histidine kinase, KinA, and inhibits the autophosphorylation reaction. Gene homologues of kipI are found almost ubiquitously throughout the bacterial kingdom and are usually located adjacent to, and often fused with, kipA gene homologues. In B. subtilis, the KipA protein inhibits the antikinase activity of KipI thereby permitting sporulation. We have used a combination of biophysical techniques in order to understand the domain structure and shape of the KipI-KipA complex and probe the nature of the interaction. We also have solved the crystal structure of TTHA0988, a Thermus thermophilus protein of unknown function that is homologous to a KipI-KipA fusion. This structure, which is the first to be described for this class of proteins, provides unique insight into the nature of the KipI-KipA complex. The structure confirms that KipI and KipA are proteins with two domains, and the C-terminal domains belong to the cyclophilin family. These cyclophilin domains are positioned in the complex such that their conserved surfaces face each other to form a large "bicyclophilin" cleft. We discuss the sequence conservation and possible roles across species of this near-ubiquitous protein family, which is poorly understood in terms of function.
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Affiliation(s)
- David A Jacques
- School of Molecular Bioscience, University of Sydney, NSW 2006, Australia
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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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28
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Weininger U, Haupt C, Schweimer K, Graubner W, Kovermann M, Brüser T, Scholz C, Schaarschmidt P, Zoldak G, Schmid FX, Balbach J. NMR solution structure of SlyD from Escherichia coli: spatial separation of prolyl isomerase and chaperone function. J Mol Biol 2009; 387:295-305. [PMID: 19356587 DOI: 10.1016/j.jmb.2009.01.034] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 01/19/2009] [Accepted: 01/20/2009] [Indexed: 10/21/2022]
Abstract
SlyD (sensitive to lysis D) is a putative folding helper from the bacterial cytosol and harbors prolyl isomerase and chaperone activities. We determined the solution NMR structure of a truncated version of SlyD (1-165) from Escherichia coli (SlyD*) that lacks the presumably unstructured C-terminal tail. SlyD* consists of two well-separated domains: the FKBP domain, which harbors the prolyl isomerase activity, and the insert-in-flap (IF) domain, which harbors the chaperone activity. The IF domain is inserted into a loop of the FKBP domain near the prolyl isomerase active site. The NMR structure of SlyD* showed no distinct orientation of the two domains relative to each other. In the FKBP domain, Tyr68 points into the active site, which might explain the lowered intrinsic prolyl isomerase activity and the much lower FK506 binding affinity of the protein compared with archetype human FKBP12 (human FK506 binding protein with 12 kDa). The thermodynamics and kinetics of substrate binding by SlyD* were quantified by fluorescence resonance energy transfer. NMR titration experiments revealed that the IF domain recognizes and binds unfolded or partially folded proteins and peptides. Insulin aggregation is markedly slowed by SlyD* as evidenced by two-dimensional NMR spectroscopy in real time, probably due to SlyD* binding to denatured insulin. The capacity of the IF domain to establish an initial encounter-collision complex, together with the flexible orientation of the two interacting domains, makes SlyD* a very powerful catalyst of protein folding.
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Affiliation(s)
- Ulrich Weininger
- Institut für Physik, Fachgruppe Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
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Jacques DA, Langley DB, Jeffries CM, Cunningham KA, Burkholder WF, Guss JM, Trewhella J. Histidine Kinase Regulation by a Cyclophilin-like Inhibitor. J Mol Biol 2008; 384:422-35. [DOI: 10.1016/j.jmb.2008.09.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 10/21/2022]
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