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Moschidi D, Cantrelle FX, Boll E, Hanoulle X. Backbone NMR resonance assignment of the apo human Tsg101-UEV domain. Biomol NMR Assign 2023; 17:49-54. [PMID: 36740661 DOI: 10.1007/s12104-023-10119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/24/2023] [Indexed: 06/02/2023]
Abstract
The Endosomal Sorting Complex Required for Transport (ESCRT) pathway, through inverse topology membrane remodeling, is involved in many biological functions, such as ubiquitinated membrane receptor trafficking and degradation, multivesicular bodies (MVB) formation and cytokinesis. Dysfunctions in ESCRT pathway have been associated to several human pathologies, such as cancers and neurodegenerative diseases. The ESCRT machinery is also hijacked by many enveloped viruses to bud away from the plasma membrane of infected cells. Human tumor susceptibility gene 101 (Tsg101) protein is an important ESCRT-I complex component. The structure of the N-terminal ubiquitin E2 variant (UEV) domain of Tsg101 (Tsg101-UEV) comprises an ubiquitin binding pocket next to a late domain [P(S/T)AP] binding groove. These two binding sites have been shown to be involved both in the physiological roles of ESCRT-I and in the release of the viral particles, and thus are attractive targets for antivirals. The structure of the Tsg101-UEV domain has been characterized, using X-ray crystallography or NMR spectroscopy, either in its apo-state or bound to ubiquitin or late domains. In this study, we report the backbone NMR resonance assignments, including the proline signals, of the apo human Tsg101-UEV domain, that so far was not publicly available. These data, that are in good agreement with the crystallographic structure of Tsg101-UEV domain, can therefore be used for further NMR studies, including protein-protein interaction studies and drug discovery.
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Affiliation(s)
- Danai Moschidi
- CNRS EMR9002 Integrative Structural Biology, F-59000, Lille, France
| | | | - Emmanuelle Boll
- CNRS EMR9002 Integrative Structural Biology, F-59000, Lille, France
| | - Xavier Hanoulle
- CNRS EMR9002 Integrative Structural Biology, F-59000, Lille, France.
- Determinants of Aging-Related Diseases, Univ. Lille, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular, F-59000, Inserm, Lille, France.
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Brier L, Hassan H, Hanoulle X, Landry V, Moschidi D, Desmarets L, Rouillé Y, Dumont J, Herledan A, Warenghem S, Piveteau C, Carré P, Ikherbane S, Cantrelle FX, Dupré E, Dubuisson J, Belouzard S, Leroux F, Deprez B, Charton J. Novel dithiocarbamates selectively inhibit 3CL protease of SARS-CoV-2 and other coronaviruses. Eur J Med Chem 2023; 250:115186. [PMID: 36796300 PMCID: PMC9901219 DOI: 10.1016/j.ejmech.2023.115186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
Since end of 2019, the global and unprecedented outbreak caused by the coronavirus SARS-CoV-2 led to dramatic numbers of infections and deaths worldwide. SARS-CoV-2 produces two large viral polyproteins which are cleaved by two cysteine proteases encoded by the virus, the 3CL protease (3CLpro) and the papain-like protease, to generate non-structural proteins essential for the virus life cycle. Both proteases are recognized as promising drug targets for the development of anti-coronavirus chemotherapy. Aiming at identifying broad spectrum agents for the treatment of COVID-19 but also to fight emergent coronaviruses, we focused on 3CLpro that is well conserved within this viral family. Here we present a high-throughput screening of more than 89,000 small molecules that led to the identification of a new chemotype, potent inhibitor of the SARS-CoV-2 3CLpro. The mechanism of inhibition, the interaction with the protease using NMR and X-Ray, the specificity against host cysteine proteases and promising antiviral properties in cells are reported.
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Affiliation(s)
- Lucile Brier
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Haitham Hassan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Xavier Hanoulle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Valerie Landry
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Danai Moschidi
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Lowiese Desmarets
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Yves Rouillé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Julie Dumont
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Sandrine Warenghem
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Paul Carré
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Sarah Ikherbane
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - François-Xavier Cantrelle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Elian Dupré
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Jean Dubuisson
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Sandrine Belouzard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France.
| | - Julie Charton
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France
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Cantrelle F, Boll E, Brier L, Moschidi D, Belouzard S, Landry V, Leroux F, Dewitte F, Landrieu I, Dubuisson J, Deprez B, Charton J, Hanoulle X. NMR Spectroscopy of the Main Protease of SARS‐CoV‐2 and Fragment‐Based Screening Identify Three Protein Hotspots and an Antiviral Fragment. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- François‐Xavier Cantrelle
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Emmanuelle Boll
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Lucile Brier
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Danai Moschidi
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Sandrine Belouzard
- Univ. Lille CNRS INSERM, CHU Lille Institut Pasteur de Lille U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille 1 rue du Professeur Calmette F-59019 Lille France
| | - Valérie Landry
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Florence Leroux
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Frédérique Dewitte
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Isabelle Landrieu
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Jean Dubuisson
- Univ. Lille CNRS INSERM, CHU Lille Institut Pasteur de Lille U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille 1 rue du Professeur Calmette F-59019 Lille France
| | - Benoit Deprez
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Julie Charton
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Xavier Hanoulle
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
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4
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Cantrelle F, Boll E, Brier L, Moschidi D, Belouzard S, Landry V, Leroux F, Dewitte F, Landrieu I, Dubuisson J, Deprez B, Charton J, Hanoulle X. NMR Spectroscopy of the Main Protease of SARS-CoV-2 and Fragment-Based Screening Identify Three Protein Hotspots and an Antiviral Fragment. Angew Chem Int Ed Engl 2021; 60:25428-25435. [PMID: 34570415 PMCID: PMC8653025 DOI: 10.1002/anie.202109965] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/16/2021] [Indexed: 11/17/2022]
Abstract
The main protease (3CLp) of the SARS-CoV-2, the causative agent for the COVID-19 pandemic, is one of the main targets for drug development. To be active, 3CLp relies on a complex interplay between dimerization, active site flexibility, and allosteric regulation. The deciphering of these mechanisms is a crucial step to enable the search for inhibitors. In this context, using NMR spectroscopy, we studied the conformation of dimeric 3CLp from the SARS-CoV-2 and monitored ligand binding, based on NMR signal assignments. We performed a fragment-based screening that led to the identification of 38 fragment hits. Their binding sites showed three hotspots on 3CLp, two in the substrate binding pocket and one at the dimer interface. F01 is a non-covalent inhibitor of the 3CLp and has antiviral activity in SARS-CoV-2 infected cells. This study sheds light on the complex structure-function relationships of 3CLp and constitutes a strong basis to assist in developing potent 3CLp inhibitors.
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Affiliation(s)
- François‐Xavier Cantrelle
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Emmanuelle Boll
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Lucile Brier
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Danai Moschidi
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Sandrine Belouzard
- Univ. LilleCNRSINSERM, CHU LilleInstitut Pasteur de LilleU1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille1 rue du Professeur CalmetteF-59019LilleFrance
| | - Valérie Landry
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Florence Leroux
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Frédérique Dewitte
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Isabelle Landrieu
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Jean Dubuisson
- Univ. LilleCNRSINSERM, CHU LilleInstitut Pasteur de LilleU1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille1 rue du Professeur CalmetteF-59019LilleFrance
| | - Benoit Deprez
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Julie Charton
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Xavier Hanoulle
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
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McShan AC, Devlin CA, Morozov GI, Overall SA, Moschidi D, Akella N, Procko E, Sgourakis NG. TAPBPR promotes antigen loading on MHC-I molecules using a peptide trap. Nat Commun 2021; 12:3174. [PMID: 34039964 PMCID: PMC8154891 DOI: 10.1038/s41467-021-23225-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/16/2021] [Indexed: 11/08/2022] Open
Abstract
Chaperones Tapasin and TAP-binding protein related (TAPBPR) perform the important functions of stabilizing nascent MHC-I molecules (chaperoning) and selecting high-affinity peptides in the MHC-I groove (editing). While X-ray and cryo-EM snapshots of MHC-I in complex with TAPBPR and Tapasin, respectively, have provided important insights into the peptide-deficient MHC-I groove structure, the molecular mechanism through which these chaperones influence the selection of specific amino acid sequences remains incompletely characterized. Based on structural and functional data, a loop sequence of variable lengths has been proposed to stabilize empty MHC-I molecules through direct interactions with the floor of the groove. Using deep mutagenesis on two complementary expression systems, we find that important residues for the Tapasin/TAPBPR chaperoning activity are located on a large scaffolding surface, excluding the loop. Conversely, loop mutations influence TAPBPR interactions with properly conformed MHC-I molecules, relevant for peptide editing. Detailed biophysical characterization by solution NMR, ITC and FP-based assays shows that the loop hovers above the MHC-I groove to promote the capture of incoming peptides. Our results suggest that the longer loop of TAPBPR lowers the affinity requirements for peptide selection to facilitate peptide loading under conditions and subcellular compartments of reduced ligand concentration, and to prevent disassembly of high-affinity peptide-MHC-I complexes that are transiently interrogated by TAPBPR during editing.
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Affiliation(s)
- Andrew C McShan
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christine A Devlin
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - Giora I Morozov
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah A Overall
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Danai Moschidi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Neha Akella
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA.
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Wei KY, Moschidi D, Bick MJ, Nerli S, McShan AC, Carter LP, Huang PS, Fletcher DA, Sgourakis NG, Boyken SE, Baker D. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. Proc Natl Acad Sci U S A 2020; 117:7208-7215. [PMID: 32188784 PMCID: PMC7132107 DOI: 10.1073/pnas.1914808117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320-327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol. 13, 1280-1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149-21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations-one short (∼66 Å height) and the other long (∼100 Å height)-reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.
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Affiliation(s)
- Kathy Y Wei
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of California, Berkeley, CA 94720
| | - Danai Moschidi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Santrupti Nerli
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
- Department of Computer Science, University of California, Santa Cruz, CA 95064
| | - Andrew C McShan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Lauren P Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, CA 94720
- Joint UC Berkeley-UC San Francisco Graduate Group in Bioengineering, Berkeley, CA 94720
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
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7
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Zarafeta D, Moschidi D, Ladoukakis E, Gavrilov S, Chrysina ED, Chatziioannou A, Kublanov I, Skretas G, Kolisis FN. Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. Sci Rep 2016; 6:38886. [PMID: 27991516 PMCID: PMC5171882 DOI: 10.1038/srep38886] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/14/2016] [Indexed: 11/09/2022] Open
Abstract
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Evangelia D. Chrysina
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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Zarafeta D, Szabo Z, Moschidi D, Phan H, Chrysina ED, Peng X, Ingham CJ, Kolisis FN, Skretas G. EstDZ3: A New Esterolytic Enzyme Exhibiting Remarkable Thermostability. Front Microbiol 2016; 7:1779. [PMID: 27899916 PMCID: PMC5110521 DOI: 10.3389/fmicb.2016.01779] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/24/2016] [Indexed: 11/25/2022] Open
Abstract
Lipolytic enzymes that retain high levels of catalytic activity when exposed to a variety of denaturing conditions are of high importance for a number of biotechnological applications. In this study, we aimed to identify new lipolytic enzymes, which are highly resistant to prolonged exposure to elevated temperatures. To achieve this, we searched for genes encoding for such proteins in the genomes of a microbial consortium residing in a hot spring located in China. After performing functional genomic screening on a bacterium of the genus Dictyoglomus, which was isolated from this hot spring following in situ enrichment, we identified a new esterolytic enzyme, termed EstDZ3. Detailed biochemical characterization of the recombinant enzyme, revealed that it constitutes a slightly alkalophilic and highly active esterase against esters of fatty acids with short to medium chain lengths. Importantly, EstDZ3 exhibits remarkable thermostability, as it retains high levels of catalytic activity after exposure to temperatures as high as 95°C for several hours. Furthermore, it exhibits very good stability against exposure to high concentrations of a variety of organic solvents. Interestingly, EstDZ3 was found to have very little similarity to previously characterized esterolytic enzymes. Computational modeling of the three-dimensional structure of this new enzyme predicted that it exhibits a typical α/β hydrolase fold that seems to include a “subdomain insertion”, which is similar to the one present in its closest homolog of known function and structure, the cinnamoyl esterase Lj0536 from Lactobacillus johnsonii. As it was found in the case of Lj0536, this structural feature is expected to be an important determinant of the catalytic properties of EstDZ3. The high levels of esterolytic activity of EstDZ3, combined with its remarkable thermostability and good stability against a range of organic solvents and other denaturing agents, render this new enzyme a candidate biocatalyst for high-temperature biotechnological applications.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research FoundationAthens, Greece; Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of AthensAthens, Greece
| | | | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Hien Phan
- Danish Archaea Centre, Department of Biology, Copenhagen University Copenhagen, Denmark
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation Athens, Greece
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, Copenhagen University Copenhagen, Denmark
| | | | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation Athens, Greece
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