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Woodard AM, Peccati F, Navo CD, Jiménez-Osés G, Mitchell DA. Darobactin Substrate Engineering and Computation Show Radical Stability Governs Ether versus C-C Bond Formation. J Am Chem Soc 2024; 146:14328-14340. [PMID: 38728535 PMCID: PMC11225102 DOI: 10.1021/jacs.4c03994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
The Gram-negative selective antibiotic darobactin A has attracted interest owing to its intriguing fused bicyclic structure and unique targeting of the outer membrane protein BamA. Darobactin, a ribosomally synthesized and post-translationally modified peptide (RiPP), is produced by a radical S-adenosyl methionine (rSAM)-dependent enzyme (DarE) and contains one ether and one C-C cross-link. Herein, we analyze the substrate tolerance of DarE and describe an underlying catalytic principle of the enzyme. These efforts produced 51 enzymatically modified darobactin variants, revealing that DarE can install the ether and C-C cross-links independently and in different locations on the substrate. Notable variants with fused bicyclic structures were characterized, including darobactin W3Y, with a non-Trp residue at the twice-modified central position, and darobactin K5F, which displays a fused diether ring pattern. While lacking antibiotic activity, quantum mechanical modeling of darobactins W3Y and K5F aided in the elucidation of the requisite features for high-affinity BamA engagement. We also provide experimental evidence for β-oxo modification, which adds support for a proposed DarE mechanism. Based on these results, ether and C-C cross-link formation was investigated computationally, and it was determined that more stable and longer-lived aromatic Cβ radicals correlated with ether formation. Further, molecular docking and transition state structures based on high-level quantum mechanical calculations support the different indole connectivity observed for ether (Trp-C7) and C-C (Trp-C6) cross-links. Finally, mutational analysis and protein structural predictions identified substrate residues that govern engagement to DarE. Our work informs on darobactin scaffold engineering and further unveils the underlying principles of rSAM catalysis.
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Affiliation(s)
- Austin M Woodard
- Department of Chemistry, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
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Buglak AA. Antioxidant properties of α-amino acids: a density functional theory viewpoint. Free Radic Res 2024; 58:380-387. [PMID: 39101778 DOI: 10.1080/10715762.2024.2385338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/17/2024] [Indexed: 08/06/2024]
Abstract
The antioxidant properties of 21 proteinogenic amino acids (AAs) and 3,4-dioxophenylanine (DOPA) have been studied in implicit water using density functional theory (DFT). All the calculations have been performed according to three oxidation mechanisms: (1) hydrogen-atom transfer (HAT); (2) single electron transfer followed by proton transfer (SET-PT); and (3) sequential proton-loss electron transfer (SPLET). As a result, five AAs with the highest antioxidant capacity have been established: DOPA, selenocysteine (Sec), tyrosine (Tyr), cysteine (Cys), and tryptophan (Trp). Also, global reactivity in terms of hardness/softness has been evaluated, as well as Fukui indices of local reactivity. Trp has been determined as the most reactive molecule, whereas selenium atom of Sec has been established as the most reactive atom. All the findings are in agreement with the recent literature on both experimental and theoretical studies of amino acids antioxidant activity. However, to the best of my knowledge, the calculations for one electron redox reactions of zwitterionic amino acids in implicit water have been performed for the first time.
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Affiliation(s)
- Andrey A Buglak
- Faculty of Physics, St. Petersburg State University, Saint-Petersburg, Russia
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Riedmiller K, Reiser P, Bobkova E, Maltsev K, Gryn'ova G, Friederich P, Gräter F. Substituting density functional theory in reaction barrier calculations for hydrogen atom transfer in proteins. Chem Sci 2024; 15:2518-2527. [PMID: 38362411 PMCID: PMC10866341 DOI: 10.1039/d3sc03922f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024] Open
Abstract
Hydrogen atom transfer (HAT) reactions are important in many biological systems. As these reactions are hard to observe experimentally, it is of high interest to shed light on them using simulations. Here, we present a machine learning model based on graph neural networks for the prediction of energy barriers of HAT reactions in proteins. As input, the model uses exclusively non-optimized structures as obtained from classical simulations. It was trained on more than 17 000 energy barriers calculated using hybrid density functional theory. We built and evaluated the model in the context of HAT in collagen, but we show that the same workflow can easily be applied to HAT reactions in other biological or synthetic polymers. We obtain for relevant reactions (small reaction distances) a model with good predictive power (R2 ∼ 0.9 and mean absolute error of <3 kcal mol-1). As the inference speed is high, this model enables evaluations of dozens of chemical situations within seconds. When combined with molecular dynamics in a kinetic Monte-Carlo scheme, the model paves the way toward reactive simulations.
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Affiliation(s)
- Kai Riedmiller
- Heidelberg Institute for Theoretical Studies Heidelberg Germany
| | - Patrick Reiser
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology Engler-Bunte-Ring 8 Karlsruhe 76131 Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology Hermann-von-Helmholtz-Platz 1: 76344 Eggenstein-Leopoldshafen Germany
| | | | - Kiril Maltsev
- Heidelberg Institute for Theoretical Studies Heidelberg Germany
| | - Ganna Gryn'ova
- Heidelberg Institute for Theoretical Studies Heidelberg Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University Heidelberg Germany
| | - Pascal Friederich
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology Engler-Bunte-Ring 8 Karlsruhe 76131 Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology Hermann-von-Helmholtz-Platz 1: 76344 Eggenstein-Leopoldshafen Germany
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies Heidelberg Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University Heidelberg Germany
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Woodard AM, Peccati F, Navo CD, Jiménez-Osés G, Mitchell DA. Benzylic Radical Stabilization Permits Ether Formation During Darobactin Biosynthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569256. [PMID: 38076856 PMCID: PMC10705402 DOI: 10.1101/2023.11.29.569256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The Gram-negative selective antibiotic darobactin A has attracted interest owing to its intriguing fused bicyclic structure and unique mode of action. Biosynthetic studies have revealed that darobactin is a ribosomally synthesized and post-translationally modified peptide (RiPP). During maturation, the darobactin precursor peptide (DarA) is modified by a radical S-adenosyl methionine (rSAM)-dependent enzyme (DarE) to contain ether and C-C crosslinks. In this work, we describe the enzymatic tolerance of DarE using a panel of DarA variants, revealing that DarE can install the ether and C-C crosslinks independently and in different locations on DarA. These efforts produced 57 darobactin variants, 50 of which were enzymatically modified. Several new variants with fused bicyclic structures were characterized, including darobactin W3Y, which replaces tryptophan with tyrosine at the twice-modified central position, and darobactin K5F, which displays a fused diether ring pattern. Three additional darobactin variants contained fused diether macrocycles, leading us to investigate the origin of ether versus C-C crosslink formation. Computational analyses found that more stable and long-lived Cβ radicals found on aromatic amino acids correlated with ether formation. Further, molecular docking and calculated transition state structures provide support for the different indole connectivity observed for ether (Trp-C7) and C-C (Trp-C6) crosslink formation. We also provide experimental evidence for a β-oxotryptophan modification, a proposed intermediate during ether crosslink formation. Finally, mutational analysis of the DarA leader region and protein structural predictions identified which residues were dispensable for processing and others that govern substrate engagement by DarE. Our work informs on darobactin scaffold engineering and sheds additional light on the underlying principles of rSAM catalysis.
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Affiliation(s)
- Austin M. Woodard
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Claudio D. Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Rennekamp B, Karfusehr C, Kurth M, Ünal A, Monego D, Riedmiller K, Gryn'ova G, Hudson DM, Gräter F. Collagen breaks at weak sacrificial bonds taming its mechanoradicals. Nat Commun 2023; 14:2075. [PMID: 37045839 PMCID: PMC10097693 DOI: 10.1038/s41467-023-37726-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/29/2023] [Indexed: 04/14/2023] Open
Abstract
Collagen is a force-bearing, hierarchical structural protein important to all connective tissue. In tendon collagen, high load even below macroscopic failure level creates mechanoradicals by homolytic bond scission, similar to polymers. The location and type of initial rupture sites critically decide on both the mechanical and chemical impact of these micro-ruptures on the tissue, but are yet to be explored. We here use scale-bridging simulations supported by gel electrophoresis and mass spectrometry to determine breakage points in collagen. We find collagen crosslinks, as opposed to the backbone, to harbor the weakest bonds, with one particular bond in trivalent crosslinks as the most dominant rupture site. We identify this bond as sacrificial, rupturing prior to other bonds while maintaining the material's integrity. Also, collagen's weak bonds funnel ruptures such that the potentially harmful mechanoradicals are readily stabilized. Our results suggest this unique failure mode of collagen to be tailored towards combatting an early onset of macroscopic failure and material ageing.
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Affiliation(s)
- Benedikt Rennekamp
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Christoph Karfusehr
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstrasse 29, 69120, Heidelberg, Germany
- Physics Department and ZNN, Technical University Munich, Coulombwall 4a, 85748, Garching, Germany
| | - Markus Kurth
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany
| | - Aysecan Ünal
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Debora Monego
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Kai Riedmiller
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Ganna Gryn'ova
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany
| | - David M Hudson
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany.
- Max Planck School Matter to Life, Jahnstrasse 29, 69120, Heidelberg, Germany.
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