1
|
Prout-Holm RA, van Walstijn CC, Hitsman A, Rowley MJ, Olsen JE, Page BDG, Frankel A. Investigating Protein Binding with the Isothermal Ligand-induced Resolubilization Assay. Chembiochem 2024; 25:e202300773. [PMID: 38266114 DOI: 10.1002/cbic.202300773] [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: 11/13/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 01/26/2024]
Abstract
Target engagement assays typically detect and quantify the direct physical interaction of a protein of interest and its ligand through stability changes upon ligand binding. Commonly used target engagement methods detect ligand-induced stability by subjecting samples to thermal or proteolytic stress. Here we describe a new variation to these approaches called Isothermal Ligand-induced Resolubilization Assay (ILIRA), which utilizes lyotropic solubility stress to measure ligand binding through changes in target protein solubility. We identified distinct buffer systems and salt concentrations that compromised protein solubility for four diverse proteins: dihydrofolate reductase (DHFR), nucleoside diphosphate-linked moiety X motif 5 (NUDT5), poly [ADP-ribose] polymerase 1 (PARP1), and protein arginine N-methyltransferase 1 (PRMT1). Ligand-induced solubility rescue was demonstrated for these proteins, suggesting that ILIRA can be used as an additional target engagement technique. Differences in ligand-induced protein solubility were assessed by Coomassie blue staining for SDS-PAGE and dot blot, as well as by NanoOrange, Thioflavin T, and Proteostat fluorescence, thus offering flexibility for readout and assay throughput.
Collapse
Affiliation(s)
- Riley A Prout-Holm
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Cerissa C van Walstijn
- Faculty of Science, Utrecht University, Heidelberglaan 8, 3584 CS, Utrecht, The Netherlands
| | - Alana Hitsman
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Michael J Rowley
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jonas E Olsen
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Brent D G Page
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| |
Collapse
|
2
|
Bhojane PP, Joshi S, Sahoo SJ, Rathore AS. Unexplored Excipients in Biotherapeutic Formulations: Natural Osmolytes as Potential Stabilizers Against Thermally Induced Aggregation of IgG1 Biotherapeutics. AAPS PharmSciTech 2021; 23:26. [PMID: 34907498 PMCID: PMC8670780 DOI: 10.1208/s12249-021-02183-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/17/2021] [Indexed: 11/30/2022] Open
Abstract
Monoclonal antibodies (mAbs), while incredibly successful, are prone to a variety of degradation pathways, the most significant of which is aggregation. One of the most commonly used strategy to overcome protein aggregation is addition of excipients to the formulation. Osmolytes such as trehalose, sucrose, and glycine are widely used. In this paper, we explore potential use of naturally occurring osmolytes such as betaine, sarcosine, ectoine, and hydroxyectoine for reducing aggregation of mAb therapeutics. Experimentation has been performed on two IgG1 mAbs via accelerated stability studies. A variety of analytical tools have been used for monitoring the impact, dynamic light scattering (DLS) for colloidal stability, Fourier transform infrared (FTIR) spectroscopy and fluorescence spectroscopy for conformational stability and the higher order structure (HOS), and differential scanning calorimetry (DSC) for thermal stability. No significant impact of osmolyte addition was observed on protein structure, on comparative Fc receptor (FcRn) binding, and on biocompatibility as per our hemolytic assay. Our results rank the osmolytes’ stabilizing trend to be sarcosine > betaine > hydroxyectoine > ectoine. Sarcosine emerged as the most successful osmolyte rendering highest degree of protection against aggregation. Our data support the prospect of using these osmolytes as successful excipients for mAb formulations.
Collapse
|
3
|
|
4
|
Wood VE, Groves K, Cryar A, Quaglia M, Matejtschuk P, Dalby PA. HDX and In Silico Docking Reveal that Excipients Stabilize G-CSF via a Combination of Preferential Exclusion and Specific Hotspot Interactions. Mol Pharm 2020; 17:4637-4651. [PMID: 33112626 DOI: 10.1021/acs.molpharmaceut.0c00877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Assuring the stability of therapeutic proteins is a major challenge in the biopharmaceutical industry, and a better molecular understanding of the mechanisms through which formulations influence their stability is an ongoing priority. While the preferential exclusion effects of excipients are well known, the additional presence and impact of specific protein-excipient interactions have proven to be more elusive to identify and characterize. We have taken a combined approach of in silico molecular docking and hydrogen deuterium exchange-mass spectrometry (HDX-MS) to characterize the interactions between granulocyte colony-stimulating factor (G-CSF), and some common excipients. These interactions were related to their influence on the thermal-melting temperatures (Tm) for the nonreversible unfolding of G-CSF in liquid formulations. The residue-level interaction sites predicted in silico correlated well with those identified experimentally and highlighted the potential impact of specific excipient interactions on the Tm of G-CSF.
Collapse
Affiliation(s)
- Victoria E Wood
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Kate Groves
- National Measurement Laboratory at LGC Ltd., Queens Road, Teddington TW11 0LY, United Kingdom
| | - Adam Cryar
- National Measurement Laboratory at LGC Ltd., Queens Road, Teddington TW11 0LY, United Kingdom
| | - Milena Quaglia
- National Measurement Laboratory at LGC Ltd., Queens Road, Teddington TW11 0LY, United Kingdom
| | - Paul Matejtschuk
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
| |
Collapse
|
5
|
Yanykin DV, Malferrari M, Rapino S, Venturoli G, Semenov AY, Mamedov MD. Hydroxyectoine protects Mn-depleted photosystem II against photoinhibition acting as a source of electrons. PHOTOSYNTHESIS RESEARCH 2019; 141:165-179. [PMID: 30701483 DOI: 10.1007/s11120-019-00617-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
In the present study, we have investigated the effect of hydroxyectoine (Ect-OH), a heterocyclic amino acid, on oxygen evolution in photosystem II (PS II) membrane fragments and on photoinhibition of Mn-depleted PS II (apo-WOC-PS II) preparations. The degree of photoinhibition of apo-WOC-PS II preparations was estimated by the loss of the capability of exogenous electron donor (sodium ascorbate) to restore the amplitude of light-induced changes of chlorophyll fluorescence yield (∆F). It was found that Ect-OH (i) stimulates the oxygen-evolving activity of PS II, (ii) accelerates the electron transfer from exogenous electron donors (K4[Fe(CN)6], DPC, TMPD, Fe2+, and Mn2+) to the reaction center of apo-WOC-PS II, (iii) enhances the protective effect of exogenous electron donors against donor-side photoinhibition of apo-WOC-PS II preparations. It is assumed that Ect-OH can serve as an artificial electron donor for apo-WOC-PS II, which does not directly interact with either the donor or acceptor side of the reaction center. We suggest that the protein conformation in the presence of Ect-OH, which affects the extent of hydration, becomes favorable for accepting electrons from exogenous donors. To our knowledge, this is the first study dealing with redox activity of Ect-OH towards photosynthetic pigment-protein complexes.
Collapse
Affiliation(s)
- D V Yanykin
- Institute of Basic Biological Problems, FRC PSCBR RAS, Pushchino, Moscow Region, Russia, 142290.
| | - M Malferrari
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126, Bologna, Italy
| | - S Rapino
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126, Bologna, Italy
| | - G Venturoli
- Laboratory of Biochemistry and Molecular Biophysics, Department of Pharmacy and Biotechnology, FaBiT, University of Bologna, 40126, Bologna, Italy
| | - A Yu Semenov
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1-40, Moscow, Russia, 119992
| | - M D Mamedov
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1-40, Moscow, Russia, 119992
| |
Collapse
|
6
|
Wang W, Ohtake S. Science and art of protein formulation development. Int J Pharm 2019; 568:118505. [PMID: 31306712 DOI: 10.1016/j.ijpharm.2019.118505] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 02/07/2023]
Abstract
Protein pharmaceuticals have become a significant class of marketed drug products and are expected to grow steadily over the next decade. Development of a commercial protein product is, however, a rather complex process. A critical step in this process is formulation development, enabling the final product configuration. A number of challenges still exist in the formulation development process. This review is intended to discuss these challenges, to illustrate the basic formulation development processes, and to compare the options and strategies in practical formulation development.
Collapse
Affiliation(s)
- Wei Wang
- Biological Development, Bayer USA, LLC, 800 Dwight Way, Berkeley, CA 94710, United States.
| | - Satoshi Ohtake
- Pharmaceutical Research and Development, Pfizer Biotherapeutics Pharmaceutical Sciences, Chesterfield, MO 63017, United States
| |
Collapse
|
7
|
Boroujeni MB, Nayeri H. Stabilization of bovine lactoperoxidase in the presence of ectoine. Food Chem 2018; 265:208-215. [PMID: 29884374 DOI: 10.1016/j.foodchem.2018.05.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 10/16/2022]
Abstract
Lactoperoxidase (LPO) is a heme peroxidase with various applications in industry and medicine. In this study, the effects of ectoine, as a compatible solute, on the structure, thermal stability, thermodynamic parameters, activity, and stability of LPO have been investigated. The results showed that the catalytic activity of LPO was improved by increasing ectoine concentration. The UV-visible absorption spectroscopy and FTIR spectra studies indicated that ectoine could bind to the LPO spontaneously. Moreover, ectoine increased the enzyme Tm and Gibbs free energy. The fluorescence measurements showed that LPO fluorescence was quenched in the presence of ectoine. The quenching mechanism was probably a static quenching by forming a ground state complex. The thermodynamic parameters indicated that hydrogen bonding and Vander Waals forces played a key role in the LPO-ectoine interaction process. The findings suggest that ectoine could be used as a lactoperoxidase stabilizing agent for industrial or medical purposes.
Collapse
Affiliation(s)
- Marziyeh Borjian Boroujeni
- Department of Biochemistry, Falavarjan Branch, Islamic Azad University, P.O.Box 81465-1148, Isfahan, Iran
| | - Hashem Nayeri
- Department of Biochemistry, Falavarjan Branch, Islamic Azad University, P.O.Box 81465-1148, Isfahan, Iran.
| |
Collapse
|
8
|
Robinson MJ, Matejtschuk P, Bristow AF, Dalby PA. Tm-Values and Unfolded Fraction Can Predict Aggregation Rates for Granulocyte Colony Stimulating Factor Variant Formulations but Not under Predominantly Native Conditions. Mol Pharm 2017; 15:256-267. [DOI: 10.1021/acs.molpharmaceut.7b00876] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mathew J. Robinson
- Department
of Biochemical Engineering, University College London, London WC1E 7JE, U.K
| | - Paul Matejtschuk
- National Institute
of Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Hertfordshire EN6 3QG, U.K
| | - Adrian F. Bristow
- National Institute
of Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Hertfordshire EN6 3QG, U.K
| | - Paul A. Dalby
- Department
of Biochemical Engineering, University College London, London WC1E 7JE, U.K
| |
Collapse
|
9
|
Salmannejad F, Nafissi-Varcheh N. Ectoine and hydroxyectoine inhibit thermal-induced aggregation and increase thermostability of recombinant human interferon Alfa2b. Eur J Pharm Sci 2017; 97:200-207. [DOI: 10.1016/j.ejps.2016.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/20/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
|
10
|
Zbacnik TJ, Holcomb RE, Katayama DS, Murphy BM, Payne RW, Coccaro RC, Evans GJ, Matsuura JE, Henry CS, Manning MC. Role of Buffers in Protein Formulations. J Pharm Sci 2016; 106:713-733. [PMID: 27894967 DOI: 10.1016/j.xphs.2016.11.014] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/25/2016] [Accepted: 11/17/2016] [Indexed: 12/19/2022]
Abstract
Buffers comprise an integral component of protein formulations. Not only do they function to regulate shifts in pH, they also can stabilize proteins by a variety of mechanisms. The ability of buffers to stabilize therapeutic proteins whether in liquid formulations, frozen solutions, or the solid state is highlighted in this review. Addition of buffers can result in increased conformational stability of proteins, whether by ligand binding or by an excluded solute mechanism. In addition, they can alter the colloidal stability of proteins and modulate interfacial damage. Buffers can also lead to destabilization of proteins, and the stability of buffers themselves is presented. Furthermore, the potential safety and toxicity issues of buffers are discussed, with a special emphasis on the influence of buffers on the perceived pain upon injection. Finally, the interaction of buffers with other excipients is examined.
Collapse
Affiliation(s)
| | - Ryan E Holcomb
- LegacyBioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Derrick S Katayama
- LegacyBioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Brian M Murphy
- LegacyBioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Robert W Payne
- LegacyBioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | | | | | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Mark Cornell Manning
- LegacyBioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523.
| |
Collapse
|
11
|
Hahn MB, Solomun T, Wellhausen R, Hermann S, Seitz H, Meyer S, Kunte HJ, Zeman J, Uhlig F, Smiatek J, Sturm H. Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA. J Phys Chem B 2015; 119:15212-20. [PMID: 26555929 DOI: 10.1021/acs.jpcb.5b09506] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations to study the local hydration shell around ectoine and its influence on the binding of a gene-5-protein (G5P) to a single-stranded DNA (dT25). Due to the very high hygroscopicity of ectoine, it was possible to analyze the highly stable hydration shell by confocal Raman spectroscopy. Corresponding molecular dynamics simulation results revealed a significant change of the water dielectric constant in the presence of a high molar ectoine concentration as compared to pure water. The SPR data showed that the amount of protein bound to DNA decreases in the presence of ectoine, and hence, the protein-DNA dissociation constant increases in a concentration-dependent manner. Concomitantly, the Raman spectra in terms of the amide I region revealed large changes in the protein secondary structure. Our results indicate that ectoine strongly affects the molecular recognition between the protein and the oligonucleotide, which has important consequences for osmotic regulation mechanisms.
Collapse
Affiliation(s)
- Marc Benjamin Hahn
- Federal Institute for Materials Research and Testing , D-12205 Berlin, Germany.,Department of Physics, Free University Berlin , D-14195 Berlin, Germany
| | - Tihomir Solomun
- Federal Institute for Materials Research and Testing , D-12205 Berlin, Germany
| | - Robert Wellhausen
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytic and Bioprocesses , D-14476 Potsdam-Golm, Germany
| | - Sabrina Hermann
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytic and Bioprocesses , D-14476 Potsdam-Golm, Germany
| | - Harald Seitz
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytic and Bioprocesses , D-14476 Potsdam-Golm, Germany
| | - Susann Meyer
- Federal Institute for Materials Research and Testing , D-12205 Berlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam , D-14476 Potsdam, Germany
| | - Hans-Jörg Kunte
- Federal Institute for Materials Research and Testing , D-12205 Berlin, Germany
| | - Johannes Zeman
- Institute for Computational Physics, University of Stuttgart , D-70569 Stuttgart, Germany
| | - Frank Uhlig
- Institute for Computational Physics, University of Stuttgart , D-70569 Stuttgart, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart , D-70569 Stuttgart, Germany
| | - Heinz Sturm
- Federal Institute for Materials Research and Testing , D-12205 Berlin, Germany.,Technical University Berlin , D-10587 Berlin, Germany
| |
Collapse
|
12
|
Wang S, Zhang N, Hu T, Dai W, Feng X, Zhang X, Qian F. Viscosity-Lowering Effect of Amino Acids and Salts on Highly Concentrated Solutions of Two IgG1 Monoclonal Antibodies. Mol Pharm 2015; 12:4478-87. [DOI: 10.1021/acs.molpharmaceut.5b00643] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Shujing Wang
- School
of Pharmaceutical Sciences
and Collaborative Innovation Center for Diagnosis and Treatment of
Infectious Diseases, Tsinghua University, Beijing 100084, China
| | - Ning Zhang
- China R&D and Scientific Affair, Shanghai Discovery Center, Janssen Research & Development, Johnson & Johnson, Shanghai 200030, China
| | - Tao Hu
- China R&D and Scientific Affair, Shanghai Discovery Center, Janssen Research & Development, Johnson & Johnson, Shanghai 200030, China
| | - Weiguo Dai
- Janssen Research & Development, Johnson & Johnson, Malvern, Pennsylvania 19355, United States
| | - Xiuying Feng
- China R&D and Scientific Affair, Shanghai Discovery Center, Janssen Research & Development, Johnson & Johnson, Shanghai 200030, China
| | - Xinyi Zhang
- School
of Pharmaceutical Sciences
and Collaborative Innovation Center for Diagnosis and Treatment of
Infectious Diseases, Tsinghua University, Beijing 100084, China
| | - Feng Qian
- School
of Pharmaceutical Sciences
and Collaborative Innovation Center for Diagnosis and Treatment of
Infectious Diseases, Tsinghua University, Beijing 100084, China
| |
Collapse
|
13
|
Menzen T, Friess W. Temperature-Ramped Studies on the Aggregation, Unfolding, and Interaction of a Therapeutic Monoclonal Antibody. J Pharm Sci 2014; 103:445-55. [DOI: 10.1002/jps.23827] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 12/04/2013] [Accepted: 12/04/2013] [Indexed: 12/11/2022]
|
14
|
Molecular dynamics simulations and structure-guided mutagenesis provide insight into the architecture of the catalytic core of the ectoine hydroxylase. J Mol Biol 2013; 426:586-600. [PMID: 24184278 DOI: 10.1016/j.jmb.2013.10.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 09/29/2013] [Accepted: 10/23/2013] [Indexed: 11/21/2022]
Abstract
Many bacteria amass compatible solutes to fend-off the detrimental effects of high osmolarity on cellular physiology and water content. These solutes also function as stabilizers of macromolecules, a property for which they are referred to as chemical chaperones. The tetrahydropyrimidine ectoine is such a compatible solute and is widely synthesized by members of the Bacteria. Many ectoine producers also synthesize the stress protectant 5-hydroxyectoine from the precursor ectoine, a process that is catalyzed by the ectoine hydroxylase (EctD). The EctD enzyme is a member of the non-heme-containing iron(II) and 2-oxoglutarate-dependent dioxygenase superfamily. A crystal structure of the EctD protein from the moderate halophile Virgibacillus salexigens has previously been reported and revealed the coordination of the iron catalyst, but it lacked the substrate ectoine and the co-substrate 2-oxoglutarate. Here we used this crystal structure as a template to assess the likely positioning of the ectoine and 2-oxoglutarate ligands within the active site by structural comparison, molecular dynamics simulations, and site-directed mutagenesis. Collectively, these approaches suggest the positioning of the iron, ectoine, and 2-oxoglutarate ligands in close proximity to each other and with a spatial orientation that will allow the region-selective and stereo-specific hydroxylation of (4S)-ectoine to (4S,5S)-5-hydroxyectoine. Our study thus provides a view into the catalytic core of the ectoine hydroxylase and suggests an intricate network of interactions between the three ligands and evolutionarily highly conserved residues in members of the EctD protein family.
Collapse
|