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Žoldák G, Knappe TA, Geitner AJ, Scholz C, Dobbek H, Schmid FX, Jakob RP. Bacterial Chaperone Domain Insertions Convert Human FKBP12 into an Excellent Protein-Folding Catalyst-A Structural and Functional Analysis. Molecules 2024; 29:1440. [PMID: 38611720 PMCID: PMC11013033 DOI: 10.3390/molecules29071440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Many folding enzymes use separate domains for the binding of substrate proteins and for the catalysis of slow folding reactions such as prolyl isomerization. FKBP12 is a small prolyl isomerase without a chaperone domain. Its folding activity is low, but it could be increased by inserting the chaperone domain from the homolog SlyD of E. coli near the prolyl isomerase active site. We inserted two other chaperone domains into human FKBP12: the chaperone domain of SlpA from E. coli, and the chaperone domain of SlyD from Thermococcus sp. Both stabilized FKBP12 and greatly increased its folding activity. The insertion of these chaperone domains had no influence on the FKBP12 and the chaperone domain structure, as revealed by two crystal structures of the chimeric proteins. The relative domain orientations differ in the two crystal structures, presumably representing snapshots of a more open and a more closed conformation. Together with crystal structures from SlyD-like proteins, they suggest a path for how substrate proteins might be transferred from the chaperone domain to the prolyl isomerase domain.
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Affiliation(s)
- Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, Pavol Jozef Šafárik University in Košice, 040 11 Kosice, Slovakia
| | - Thomas A. Knappe
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Anne-Juliane Geitner
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | | | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany;
| | - Franz X. Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Roman P. Jakob
- Departement Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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2
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Abstract
The marvel of X-ray crystallography is the beauty and precision of the atomic structures deduced from diffraction patterns. Since these patterns record only amplitudes, phases for the diffracted waves must also be evaluated for systematic structure determination. Thus, we have the phase problem as a central complication, both intellectually for the field and practically so for many analyses. Here, I discuss how we - myself, my laboratory and the diffraction community - have faced the phase problem, considering the evolution of methods for phase evaluation as structural biology developed to the present day. During the explosive growth of macromolecular crystallography, practice in diffraction analysis evolved from a universal reliance on isomorphous replacement to the eventual domination of anomalous diffraction for de novo structure determination. As the Protein Data Bank (PDB) grew and familial relationships among proteins became clear, molecular replacement overtook all other phasing methods; however, experimental phasing remained essential for molecules without obvious precedents, with multi- and single-wavelength anomalous diffraction (MAD and SAD) predominating. While the mathematics-based direct methods had proved to be inadequate for typical macromolecules, they returned to crack substantial selenium substructures in SAD analyses of selenomethionyl proteins. Native SAD, exploiting the intrinsic S and P atoms of biomolecules, has become routine. Selenomethionyl SAD and MAD were the mainstays of structural genomics efforts to populate the PDB with novel proteins. A recent dividend has been paid in the success of PDB-trained artificial intelligence approaches for protein structure prediction. Currently, molecular replacement with AlphaFold models often obviates the need for experimental phase evaluation. For multiple reasons, we are now unfazed by the phase problem. Cryo-EM analysis is an attractive alternative to crystallography for many applications faced by today's structural biologists. It simply finesses the phase problem; however, the principles and procedures of diffraction analysis remain pertinent and are adopted in single-particle cryo-EM studies of biomolecules.
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Affiliation(s)
- Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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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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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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Lee SH, Kim YH, Lee K, Im H. Peptidyl-Prolyl Isomerase Cpr7p of Yeast Prevents Protein Aggregation Upon Freezing. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Seung Hyun Lee
- Department of Integrative Bioscience and Biotechnology; Sejong University; Seoul 05006 Korea
| | - Yang-Hee Kim
- Department of Integrative Bioscience and Biotechnology; Sejong University; Seoul 05006 Korea
| | - Kyunghee Lee
- Department of Chemistry; Sejong University; Seoul 05006 Korea
| | - Hana Im
- Department of Integrative Bioscience and Biotechnology; Sejong University; Seoul 05006 Korea
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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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Lee KY, Lee BJ. Solution NMR studies on Helicobacter pylori proteins for antibiotic target discovery. Expert Opin Drug Discov 2016; 11:681-93. [PMID: 27216839 DOI: 10.1080/17460441.2016.1189411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Helicobacter pylori (H. pylori) is a well-known widespread pathogenic bacterium that survives in the extremely acidic conditions of the human gastric mucosa. The global prevalence of H. pylori-resistant antibiotics has become an emerging issue in the 21st century and has necessitated the development of novel antibiotic drugs. Many efforts have aimed to discover antibiotic target proteins of H. pylori based on its genome of more than 1600 genes. AREAS COVERED This article highlights NMR spectroscopy as a valuable tool for determining the structure and dynamics of potential antibiotic-targeted proteins of H. pylori and evaluating their modes of interaction with native or synthetic binding partners. The residue-specific information on binding in solution provides a structural basis to identify and optimize lead compounds. EXPERT OPINION NMR spectroscopy is a powerful method for obtaining details of biomolecular interactions with a broad range of binding affinities. This strength facilitates the identification of the binding interface of the encounter complex that plays an integral role in a variety of biological functions. This low-affinity complex is difficult to crystallize, which impedes structure determination using X-ray crystallography. Additionally, the relative binding affinities can be predicted from the type of spectral change upon binding. High-resolution NMR spectroscopy in combination with advanced computer simulation would provide more confidence in complex structures. The application of NMR to studies of the H. pylori protein could contribute to the development of these targeted novel antibiotics.
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Affiliation(s)
- Ki-Young Lee
- a Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul , Korea
| | - Bong-Jin Lee
- a Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul , Korea
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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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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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