The presence of substrate warrants oxygen access tunnels toward the catalytic site of lipoxygenases Article Swipe
Thiliban Manivarma
,
Wiesław Nowak
,
Yulia Y. Tyurina
,
Vladimir A. Tyurin
,
Hülya Bayır
,
Valerian E. Kagan
,
Karolina Mikulska‐Ruminska
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1016/j.redox.2025.103636
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1016/j.redox.2025.103636
Ferroptosis is a regulated form of cell death driven by lipid peroxidation, with 15-lipoxygenase (15LOX) enzyme playing a critical role in catalyzing the oxygenation of polyunsaturated fatty acid-containing phospholipids, such as 1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphoethanolamine (SAPE), to initiate this process. The molecular oxygen required for this catalytic reaction is subject to continuous competition among various oxygen-consuming enzymes, which influences the efficiency of lipid peroxidation. In this study, we utilized structure-based modeling and all-atom molecular dynamics simulations to explore the oxygen diffusion pathways in 15LOX-1 under varying oxygen concentrations and in the presence of key components, including a substrate, binding partner PE-binding protein 1 (PEBP1), and the membrane environment. Extensive computational experiments were performed on various system configurations, examining the role of substrate binding, membrane presence, and PEBP1 association in oxygen acquisition. Our computational results indicate that the substrate binding induces a conformational change in 15LOX-1, facilitating the simultaneous recruitment of one or two O2 molecules, which drive peroxidation, leading predominantly to monohydroperoxide products and, less frequently, to dihydroperoxide products. A similar trend was observed in our redox lipidomics analysis. Moreover, we noticed that the presence of the membrane significantly reduces irrelevant oxygen binding spots, directing oxygen molecules toward a primary tunnel essential for the catalytic activity. We identified two primary oxygen tunnels with sequentially and structurally conserved regions across the lipoxygenase family. These findings provide novel insights into the regulation of oxygen acquisition mechanism for LOX members, shedding light on the molecular basis of ferroptosis signaling.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1016/j.redox.2025.103636
- OA Status
- gold
- Cited By
- 2
- References
- 62
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4409371470
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4409371470Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1016/j.redox.2025.103636Digital Object Identifier
- Title
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The presence of substrate warrants oxygen access tunnels toward the catalytic site of lipoxygenasesWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-04-11Full publication date if available
- Authors
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Thiliban Manivarma, Wiesław Nowak, Yulia Y. Tyurina, Vladimir A. Tyurin, Hülya Bayır, Valerian E. Kagan, Karolina Mikulska‐RuminskaList of authors in order
- Landing page
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https://doi.org/10.1016/j.redox.2025.103636Publisher landing page
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://doi.org/10.1016/j.redox.2025.103636Direct OA link when available
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Substrate (aquarium), Catalysis, Oxygen, Chemistry, Substrate specificity, Enzyme, Biochemistry, Cell biology, Biophysics, Business, Biology, Ecology, Organic chemistryTop concepts (fields/topics) attached by OpenAlex
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2Total citation count in OpenAlex
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2025: 2Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.similar | 167 |
| abstract_inverted_index.subject | 46 |
| abstract_inverted_index.tunnels | 208 |
| abstract_inverted_index.various | 51, 111 |
| abstract_inverted_index.varying | 82 |
| abstract_inverted_index.(PEBP1), | 100 |
| abstract_inverted_index.15LOX-1, | 141 |
| abstract_inverted_index.all-atom | 69 |
| abstract_inverted_index.binding, | 119 |
| abstract_inverted_index.critical | 18 |
| abstract_inverted_index.dynamics | 71 |
| abstract_inverted_index.enzymes, | 53 |
| abstract_inverted_index.findings | 220 |
| abstract_inverted_index.indicate | 131 |
| abstract_inverted_index.initiate | 34 |
| abstract_inverted_index.insights | 223 |
| abstract_inverted_index.members, | 233 |
| abstract_inverted_index.membrane | 103, 120, 184 |
| abstract_inverted_index.modeling | 67 |
| abstract_inverted_index.observed | 170 |
| abstract_inverted_index.pathways | 78 |
| abstract_inverted_index.presence | 88, 181 |
| abstract_inverted_index.process. | 36 |
| abstract_inverted_index.products | 159 |
| abstract_inverted_index.reaction | 44 |
| abstract_inverted_index.required | 40 |
| abstract_inverted_index.shedding | 234 |
| abstract_inverted_index.utilized | 65 |
| abstract_inverted_index.Extensive | 105 |
| abstract_inverted_index.Moreover, | 176 |
| abstract_inverted_index.activity. | 202 |
| abstract_inverted_index.analysis. | 175 |
| abstract_inverted_index.catalytic | 43, 201 |
| abstract_inverted_index.conserved | 213 |
| abstract_inverted_index.diffusion | 77 |
| abstract_inverted_index.directing | 191 |
| abstract_inverted_index.essential | 198 |
| abstract_inverted_index.examining | 114 |
| abstract_inverted_index.including | 92 |
| abstract_inverted_index.mechanism | 230 |
| abstract_inverted_index.molecular | 38, 70, 238 |
| abstract_inverted_index.molecules | 193 |
| abstract_inverted_index.performed | 109 |
| abstract_inverted_index.presence, | 121 |
| abstract_inverted_index.products. | 165 |
| abstract_inverted_index.regulated | 3 |
| abstract_inverted_index.substrate | 118, 134 |
| abstract_inverted_index.PE-binding | 97 |
| abstract_inverted_index.catalyzing | 21 |
| abstract_inverted_index.continuous | 48 |
| abstract_inverted_index.efficiency | 57 |
| abstract_inverted_index.identified | 204 |
| abstract_inverted_index.influences | 55 |
| abstract_inverted_index.irrelevant | 187 |
| abstract_inverted_index.lipidomics | 174 |
| abstract_inverted_index.molecules, | 151 |
| abstract_inverted_index.regulation | 226 |
| abstract_inverted_index.signaling. | 242 |
| abstract_inverted_index.substrate, | 94 |
| abstract_inverted_index.Ferroptosis | 0 |
| abstract_inverted_index.acquisition | 229 |
| abstract_inverted_index.association | 124 |
| abstract_inverted_index.competition | 49 |
| abstract_inverted_index.components, | 91 |
| abstract_inverted_index.experiments | 107 |
| abstract_inverted_index.ferroptosis | 241 |
| abstract_inverted_index.frequently, | 162 |
| abstract_inverted_index.oxygenation | 23 |
| abstract_inverted_index.recruitment | 145 |
| abstract_inverted_index.simulations | 72 |
| abstract_inverted_index.acquisition. | 127 |
| abstract_inverted_index.environment. | 104 |
| abstract_inverted_index.facilitating | 142 |
| abstract_inverted_index.lipoxygenase | 217 |
| abstract_inverted_index.sequentially | 210 |
| abstract_inverted_index.simultaneous | 144 |
| abstract_inverted_index.structurally | 212 |
| abstract_inverted_index.O<sub>2</sub> | 150 |
| abstract_inverted_index.computational | 106, 129 |
| abstract_inverted_index.peroxidation, | 11, 154 |
| abstract_inverted_index.peroxidation. | 60 |
| abstract_inverted_index.predominantly | 156 |
| abstract_inverted_index.significantly | 185 |
| abstract_inverted_index.concentrations | 84 |
| abstract_inverted_index.conformational | 138 |
| abstract_inverted_index.phospholipids, | 28 |
| abstract_inverted_index.15-lipoxygenase | 13 |
| abstract_inverted_index.acid-containing | 27 |
| abstract_inverted_index.configurations, | 113 |
| abstract_inverted_index.dihydroperoxide | 164 |
| abstract_inverted_index.polyunsaturated | 25 |
| abstract_inverted_index.structure-based | 66 |
| abstract_inverted_index.oxygen-consuming | 52 |
| abstract_inverted_index.monohydroperoxide | 158 |
| abstract_inverted_index.1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphoethanolamine | 31 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 95 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 7 |
| citation_normalized_percentile.value | 0.89642767 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |