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Frade K, Silveira CM, Salgueiro BA, Mendes S, Martins LO, Frazão C, Todorovic S, Moe E. Biochemical, Biophysical, and Structural Analysis of an Unusual DyP from the Extremophile Deinococcus radiodurans. Molecules 2024; 29:358. [PMID: 38257271 PMCID: PMC10820274 DOI: 10.3390/molecules29020358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Dye-decolorizing peroxidases (DyPs) are heme proteins with distinct structural properties and substrate specificities compared to classical peroxidases. Here, we demonstrate that DyP from the extremely radiation-resistant bacterium Deinococcus radiodurans is, like some other homologues, inactive at physiological pH. Resonance Raman (RR) spectroscopy confirms that the heme is in a six-coordinated-low-spin (6cLS) state at pH 7.5 and is thus unable to bind hydrogen peroxide. At pH 4.0, the RR spectra of the enzyme reveal the co-existence of high-spin and low-spin heme states, which corroborates catalytic activity towards H2O2 detected at lower pH. A sequence alignment with other DyPs reveals that DrDyP possesses a Methionine residue in position five in the highly conserved GXXDG motif. To analyze whether the presence of the Methionine is responsible for the lack of activity at high pH, this residue is substituted with a Glycine. UV-vis and RR spectroscopies reveal that the resulting DrDyPM190G is also in a 6cLS spin state at pH 7.5, and thus the Methionine does not affect the activity of the protein. The crystal structures of DrDyP and DrDyPM190G, determined to 2.20 and 1.53 Å resolution, respectively, nevertheless reveal interesting insights. The high-resolution structure of DrDyPM190G, obtained at pH 8.5, shows that one hydroxyl group and one water molecule are within hydrogen bonding distance to the heme and the catalytic Asparagine and Arginine. This strong ligand most likely prevents the binding of the H2O2 substrate, reinforcing questions about physiological substrates of this and other DyPs, and about the possible events that can trigger the removal of the hydroxyl group conferring catalytic activity to DrDyP.
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Affiliation(s)
| | | | | | | | | | | | | | - Elin Moe
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da Republica (EAN), 2780-157 Oeiras, Portugal; (K.F.); (C.M.S.); (B.A.S.); (S.M.); (L.O.M.); (C.F.); (S.T.)
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2
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Engrola FSS, Paquete-Ferreira J, Santos-Silva T, Correia MAS, Leisico F, Santos MFA. Screening of Buffers and Additives for Protein Stabilization by Thermal Shift Assay: A Practical Approach. Methods Mol Biol 2023; 2652:199-213. [PMID: 37093477 DOI: 10.1007/978-1-0716-3147-8_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Thermal shift assay (TSA), also commonly designed by differential scanning fluorimetry (DSF) or ThermoFluor, is a technique relatively easy to implement and perform, useful in a myriad of applications. In addition to versatility, it is also rather inexpensive, making it suitable for high-throughput approaches. TSA uses a fluorescent dye to monitor the thermal denaturation of the protein under study and determine its melting temperature (Tm). One of its main applications is to identify the best buffers and additives that enhance protein stability.Understanding the TSA operating mode and the main methodological steps is a central key to designing effective experiments and retrieving meaningful conclusions. This chapter intends to present a straightforward TSA protocol, with different troubleshooting tips, to screen effective protein stabilizers such as buffers and additives, as well as data treatment and analysis. TSA results provide conditions in which the protein of interest is stable and therefore suitable to carry out further biophysical and structural characterization.
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Affiliation(s)
- Filipa S S Engrola
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - João Paquete-Ferreira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Teresa Santos-Silva
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Márcia A S Correia
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Francisco Leisico
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- Institut de Biologie Structurale, UMR 5075, University Grenoble Alpes, CNRS, CEA, Grenoble, France.
| | - Marino F A Santos
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
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Sanjaya RE, Putri KDA, Kurniati A, Rohman A, Puspaningsih NNT. In silico characterization of the GH5-cellulase family from uncultured microorganisms: physicochemical and structural studies. J Genet Eng Biotechnol 2021; 19:143. [PMID: 34591195 PMCID: PMC8484414 DOI: 10.1186/s43141-021-00236-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 08/29/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Hydrolysis of cellulose-based biomass by cellulases produce fermented sugar for making biofuels, such as bioethanol. Cellulases hydrolyze the β-1,4-glycosidic linkage of cellulose and can be obtained from cultured and uncultured microorganisms. Uncultured microorganisms are a source for exploring novel cellulase genes through the metagenomic approach. Metagenomics concerns the extraction, cloning, and analysis of the entire genetic complement of a habitat without cultivating microbes. The glycoside hydrolase 5 family (GH5) is a cellulase family, as the largest group of glycoside hydrolases. Numerous variants of GH5-cellulase family have been identified through the metagenomic approach, including CelGH5 in this study. University-CoE-Research Center for Biomolecule Engineering, Universitas Airlangga successfully isolated CelGH5 from waste decomposition of oil palm empty fruit bunches (OPEFB) soil by metagenomics approach. The properties and structural characteristics of GH5-cellulases from uncultured microorganisms can be studied using computational tools and software. RESULTS The GH5-cellulase family from uncultured microorganisms was characterized using standard computational-based tools. The amino acid sequences and 3D-protein structures were retrieved from the GenBank Database and Protein Data Bank. The physicochemical analysis revealed the sequence length was roughly 332-751 amino acids, with the molecular weight range around 37-83 kDa, dominantly negative charges with pI values below 7. Alanine was the most abundant amino acid making up the GH5-cellulase family and the percentage of hydrophobic amino acids was more than hydrophilic. Interestingly, ten endopeptidases with the highest average number of cleavage sites were found. Another uniqueness demonstrated that there was also a difference in stability between in silico and wet lab. The II values indicated CelGH5 and ACA61162.1 as unstable enzymes, while the wet lab showed they were stable at broad pH range. The program of SOPMA, PDBsum, ProSA, and SAVES provided the secondary and tertiary structure analysis. The predominant secondary structure was the random coil, and tertiary structure has fulfilled the structure quality of QMEAN4, ERRAT, Ramachandran plot, and Z score. CONCLUSION This study can afford the new insights about the physicochemical and structural properties of the GH5-cellulase family from uncultured microorganisms. Furthermore, in silico analysis could be valuable in selecting a highly efficient cellulases for enhanced enzyme production.
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Affiliation(s)
- Rahmat Eko Sanjaya
- Mathematics and Natural Science Study Program, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Chemistry Education Study Program, Faculty of Teacher Training and Education, Universitas Lambung Mangkurat, Jl. Brigjend. H. Hasan Basry, Banjarmasin, Kalimantan, 70123, Indonesia
| | - Kartika Dwi Asni Putri
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
| | - Anita Kurniati
- Mathematics and Natural Science Study Program, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Department of Health, Faculty of Vocational Studies, Kampus B Universitas Airlangga, Surabaya, East Java, 60286, Indonesia
| | - Ali Rohman
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Department of Chemistry, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
| | - Ni Nyoman Tri Puspaningsih
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia.
- Department of Chemistry, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia.
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4
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Barroca-Ferreira J, Cruz-Vicente P, Santos MFA, Rocha SM, Santos-Silva T, Maia CJ, Passarinha LA. Enhanced Stability of Detergent-Free Human Native STEAP1 Protein from Neoplastic Prostate Cancer Cells upon an Innovative Isolation Procedure. Int J Mol Sci 2021; 22:10012. [PMID: 34576175 PMCID: PMC8472055 DOI: 10.3390/ijms221810012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The STEAP1 is a cell-surface antigen over-expressed in prostate cancer, which contributes to tumor progression and aggressiveness. However, the molecular mechanisms underlying STEAP1 and its structural determinants remain elusive. METHODS The fraction capacity of Butyl- and Octyl-Sepharose matrices on LNCaP lysates was evaluated by manipulating the ionic strength of binding and elution phases, followed by a Co-Immunoprecipitation (Co-IP) polishing. Several potential stabilizing additives were assessed, and the melting temperature (Tm) values ranked the best/worst compounds. The secondary structure of STEAP1 was identified by circular dichroism. RESULTS The STEAP1 was not fully captured with 1.375 M (Butyl), in contrast with interfering heterologous proteins, which were strongly retained and mostly eluted with water. This single step demonstrated higher selectivity of Butyl-Sepharose for host impurities removal from injected crude samples. Co-IP allowed recovering a purified fraction of STEAP1 and contributed to unveil potential physiologically interacting counterparts with the target. A Tm of ~55 °C was determined, confirming STEAP1 stability in the purification buffer. A predominant α-helical structure was identified, ensuring the protein's structural stability. CONCLUSIONS A method for successfully isolating human STEAP1 from LNCaP cells was provided, avoiding the use of detergents to achieve stability, even outside a membrane-mimicking environment.
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Affiliation(s)
- Jorge Barroca-Ferreira
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Pedro Cruz-Vicente
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Marino F. A. Santos
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Sandra M. Rocha
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
| | - Teresa Santos-Silva
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Cláudio J. Maia
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
| | - Luís A. Passarinha
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- Laboratório de Fármaco-Toxicologia-UBIMedical, University of Beira Interior, 6201-284 Covilhã, Portugal
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5
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Fernandes A, Piotrowski Y, Williamson A, Frade K, Moe E. Studies of multifunctional DNA polymerase I from the extremely radiation resistant Deinococcus radiodurans: Recombinant expression, purification and characterization of the full-length protein and its large fragment. Protein Expr Purif 2021; 187:105925. [PMID: 34175440 DOI: 10.1016/j.pep.2021.105925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 11/19/2022]
Abstract
Deinococcus radiodurans is a bacterium with extreme resistance to desiccation and radiation. Although the origins of this extreme resistance have not been fully elucidated, an efficient DNA repair machinery that includes the enzyme DNA polymerase I, is potentially crucial as part of a protection mechanism. Here we have cloned and performed small, medium, and large-scale expression of full-length D. radiodurans DNA polymerase I (DrPolI) as well as the large/Klenow fragment (DrKlenow). We then carried out functional characterization of 5' exonuclease, DNA strand displacement and polymerase activities of these proteins using gel-based and molecular beacon-based biochemical assays. With the same expression and purification strategy, we got higher yield in the production of DrKlenow than of the full-length protein, approximately 2.5 mg per liter of culture. Moreover, we detected a prominent 5' exonuclease activity of DrPolI in vitro. This activity and, DrKlenow strand displacement and DNA polymerase activities are preferentially stimulated at pH 8.0-8.5 and are reduced by addition of NaCl. Interestingly, both protein variants are more thermostable at pH 6.0-6.5. The characterization of DrPolI's multiple functions provides new insights into the enzyme's role in DNA repair pathways, and how the modulation of these functions is potentially used by D. radiodurans as a survival strategy.
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Affiliation(s)
- A Fernandes
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Y Piotrowski
- UiT - The Artic University of Norway, Tromsø, Norway
| | - A Williamson
- UiT - The Artic University of Norway, Tromsø, Norway; University of Waikato, Hamilton, New Zealand
| | - K Frade
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - E Moe
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal; UiT - The Artic University of Norway, Tromsø, Norway.
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6
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Borges PT, Romão CV, Saraiva LM, Gonçalves VL, Carrondo MA, Teixeira M, Frazão C. Analysis of a new flavodiiron core structural arrangement in Flv1-ΔFlR protein from Synechocystis sp. PCC6803. J Struct Biol 2019; 205:91-102. [DOI: 10.1016/j.jsb.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/24/2018] [Accepted: 11/09/2018] [Indexed: 12/11/2022]
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7
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Booth W, Schlachter CR, Pote S, Ussin N, Mank NJ, Klapper V, Offermann LR, Tang C, Hurlburt BK, Chruszcz M. Impact of an N-terminal Polyhistidine Tag on Protein Thermal Stability. ACS OMEGA 2018; 3:760-768. [PMID: 29399652 PMCID: PMC5793033 DOI: 10.1021/acsomega.7b01598] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/05/2018] [Indexed: 05/15/2023]
Abstract
For years, the use of polyhistidine tags (His-tags) has been a staple in the isolation of recombinant proteins in immobilized metal affinity chromatography experiments. Their usage has been widely beneficial in increasing protein purity from crude cell lysates. For some recombinant proteins, a consequence of His-tag addition is that it can affect protein function and stability. Functional proteins are essential in the elucidation of their biological, kinetic, structural, and thermodynamic properties. In this study, we determine the effect of N-terminal His-tags on the thermal stability of select proteins using differential scanning fluorimetry and identify that the removal of the His-tag can have both beneficial and deleterious effects on their stability.
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Affiliation(s)
- William
T. Booth
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Caleb R. Schlachter
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Swanandi Pote
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Nikita Ussin
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Nicholas J. Mank
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Vincent Klapper
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Lesa R. Offermann
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
- Department
of Chemistry, Davidson College, Davidson, North Carolina 28035, United States
| | - Chuanbing Tang
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Barry K. Hurlburt
- United
States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124, United States
| | - Maksymilian Chruszcz
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
- E-mail: . Tel: (803) 777-7399. Fax: (803) 777-9521
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8
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Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets. Nat Commun 2017; 8:2244. [PMID: 29269835 PMCID: PMC5740061 DOI: 10.1038/s41467-017-02098-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/07/2017] [Indexed: 12/17/2022] Open
Abstract
Protein:protein interactions are among the most difficult to treat molecular mechanisms of disease pathology. Cystine-dense peptides have the potential to disrupt such interactions, and are used in drug-like roles by every clade of life, but their study has been hampered by a reputation for being difficult to produce, owing to their complex disulfide connectivity. Here we describe a platform for identifying target-binding cystine-dense peptides using mammalian surface display, capable of interrogating high quality and diverse scaffold libraries with verifiable folding and stability. We demonstrate the platform’s capabilities by identifying a cystine-dense peptide capable of inhibiting the YAP:TEAD interaction at the heart of the oncogenic Hippo pathway, and possessing the potency and stability necessary for consideration as a drug development candidate. This platform provides the opportunity to screen cystine-dense peptides with drug-like qualities against targets that are implicated for the treatment of diseases, but are poorly suited for conventional approaches. Pathologies related to protein:protein interaction are hard to treat but cystine-dense peptides have the potential to disrupt such interactions. Here the authors develop a high-diversity mammalian cell screen for cystine-dense peptides with drug potential and use it to identify a YAP:TEAD inhibitor.
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9
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Qian X, Hamid FM, El Sahili A, Darwis DA, Wong YH, Bhushan S, Makeyev EV, Lescar J. Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases. J Biol Chem 2016; 291:9295-309. [PMID: 26907693 PMCID: PMC4861493 DOI: 10.1074/jbc.m115.685933] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Indexed: 12/15/2022] Open
Abstract
Many eukaryotic organisms encode more than one RNA-dependent RNA polymerase (RdRP) that probably emerged as a result of gene duplication. Such RdRP paralogs often participate in distinct RNA silencing pathways and show characteristic repertoires of enzymatic activities in vitro However, to what extent members of individual paralogous groups can undergo functional changes during speciation remains an open question. We show that orthologs of QDE-1, an RdRP component of the quelling pathway in Neurospora crassa, have rapidly diverged in evolution at the amino acid sequence level. Analyses of purified QDE-1 polymerases from N. crassa (QDE-1(Ncr)) and related fungi, Thielavia terrestris (QDE-1(Tte)) and Myceliophthora thermophila (QDE-1(Mth)), show that all three enzymes can synthesize RNA, but the precise modes of their action differ considerably. Unlike their QDE-1(Ncr) counterpart favoring processive RNA synthesis, QDE-1(Tte) and QDE-1(Mth) produce predominantly short RNA copies via primer-independent initiation. Surprisingly, a 3.19 Å resolution crystal structure of QDE-1(Tte) reveals a quasisymmetric dimer similar to QDE-1(Ncr) Further electron microscopy analyses confirm that QDE-1(Tte) occurs as a dimer in solution and retains this status upon interaction with a template. We conclude that divergence of orthologous RdRPs can result in functional innovation while retaining overall protein fold and quaternary structure.
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Affiliation(s)
- Xinlei Qian
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Fursham M Hamid
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Abbas El Sahili
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Dina Amallia Darwis
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Yee Hwa Wong
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Shashi Bhushan
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Eugene V Makeyev
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore, the Medical Research Council Centre for Developmental Neurobiology, King's College, London SE1 1UL, United Kingdom, and
| | - Julien Lescar
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore, UPMC UMRS CR7-CNRS ERL 8255-INSERM U1135 Centre d' Immunologie et des Maladies Infectieuses, Faculté de Médecine Pierre et Marie Curie, Centre Hospitalier Universitaire Pitié-Salpêtrière, 75031 Paris, France
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10
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Sousa CM, Carpentier P, Matias PM, Testa F, Pinho F, Sarti P, Giuffrè A, Bandeiras TM, Romão CV. Superoxide reductase from Giardia intestinalis: structural characterization of the first SOR from a eukaryotic organism shows an iron centre that is highly sensitive to photoreduction. ACTA ACUST UNITED AC 2015; 71:2236-47. [PMID: 26527141 DOI: 10.1107/s1399004715015825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/24/2015] [Indexed: 11/11/2022]
Abstract
Superoxide reductase (SOR), which is commonly found in prokaryotic organisms, affords protection from oxidative stress by reducing the superoxide anion to hydrogen peroxide. The reaction is catalyzed at the iron centre, which is highly conserved among the prokaryotic SORs structurally characterized to date. Reported here is the first structure of an SOR from a eukaryotic organism, the protozoan parasite Giardia intestinalis (GiSOR), which was solved at 2.0 Å resolution. By collecting several diffraction data sets at 100 K from the same flash-cooled protein crystal using synchrotron X-ray radiation, photoreduction of the iron centre was observed. Reduction was monitored using an online UV-visible microspectrophotometer, following the decay of the 647 nm absorption band characteristic of the iron site in the glutamate-bound, oxidized state. Similarly to other 1Fe-SORs structurally characterized to date, the enzyme displays a tetrameric quaternary-structure arrangement. As a distinctive feature, the N-terminal loop of the protein, containing the characteristic EKHxP motif, revealed an unusually high flexibility regardless of the iron redox state. At variance with previous evidence collected by X-ray crystallography and Fourier transform infrared spectroscopy of prokaryotic SORs, iron reduction did not lead to dissociation of glutamate from the catalytic metal or other structural changes; however, the glutamate ligand underwent X-ray-induced chemical changes, revealing high sensitivity of the GiSOR active site to X-ray radiation damage.
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Affiliation(s)
- Cristiana M Sousa
- Instituto de Tecnologia Química e Biológica, António Xavier Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Philippe Carpentier
- Structural Biology Group, ESRF - The European Synchrotron, CS40220, 38043 Grenoble CEDEX 9, France
| | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica, António Xavier Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Fabrizio Testa
- Department of Biochemical Sciences, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Filipa Pinho
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Paolo Sarti
- Department of Biochemical Sciences, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Tiago M Bandeiras
- Instituto de Tecnologia Química e Biológica, António Xavier Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica, António Xavier Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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11
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Zheng Y, Yang Y, Xu Y. Purification and characterization of Cyclin-H1 from Arabidopsis thaliana. Protein Expr Purif 2015; 114:9-14. [PMID: 26073096 DOI: 10.1016/j.pep.2015.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 06/03/2015] [Indexed: 12/01/2022]
Abstract
Cyclin H (CycH), a member of the large cyclin family, participates in every process of cell division. Its biological functions and importance have received wide attention in mammalians, but not in higher plants. This work reports a protein purification protocol for obtaining Arabidopsis CycH;1 (AtCycH;1) from prokaryotic expression system, followed by characterization of its biophysical properties. The protein was constructed with a His-tag at its N-terminus. One-step nickel-affinity purification yielded high pure target protein, which behaved as a monomer in the testing condition. Circular Dichroism spectrum revealed that AtCycH;1 is a helical protein containing a significant amount of disordered structures. Further assays indicated that AtCycH;1 exhibits poor heat-resistance and can be easily degraded in room temperature, suggesting low stability for the protein. The flexible and unstable properties may be intrinsic to the protein in vivo as it has to bind with different partners during the cell cycle and be promptly degraded to meet the phase transition. The instability, however, can be improved by adding SO4(2-) ion in the protein buffer. The presence of a high concentration of SO4(2-) is capable of increasing the thermal stability and inhibiting the degradation. Irrespective of whether the association of SO4(2-) with AtCycH;1 drives the protein into more compact form or not, the current results may provide clues for a successful crystallization of AtCycH;1 and its subsequent structural analysis in the future.
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Affiliation(s)
- Yawen Zheng
- The Nurturing Station for the State Key Laboratory of Subtropical Sylviculture, Zhejiang Agriculture and Forestry University, Lin'an, Zhejiang 311300, China
| | - Yiyi Yang
- The Nurturing Station for the State Key Laboratory of Subtropical Sylviculture, Zhejiang Agriculture and Forestry University, Lin'an, Zhejiang 311300, China
| | - Yingwu Xu
- The Nurturing Station for the State Key Laboratory of Subtropical Sylviculture, Zhejiang Agriculture and Forestry University, Lin'an, Zhejiang 311300, China.
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12
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Giegé R. A historical perspective on protein crystallization from 1840 to the present day. FEBS J 2013; 280:6456-97. [DOI: 10.1111/febs.12580] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/30/2013] [Accepted: 09/27/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire; Université de Strasourg et CNRS; France
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13
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Boivin S, Kozak S, Meijers R. Optimization of protein purification and characterization using Thermofluor screens. Protein Expr Purif 2013; 91:192-206. [DOI: 10.1016/j.pep.2013.08.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/29/2013] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
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14
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Auld D, Lea W, Davis MI, Simeonov A. Literature Search and Review. Assay Drug Dev Technol 2012. [DOI: 10.1089/adt.2012.1002.lr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Doug Auld
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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