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Balaei F, Pouraghajan K, Mohammadi S, Ghobadi S, Khodarahmi R. Enhancing cryo-enzymatic efficiency in cold-adapted lipase from Psychrobacter sp. C18 via site-directed mutagenesis. Arch Biochem Biophys 2025; 768:110388. [PMID: 40090439 DOI: 10.1016/j.abb.2025.110388] [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: 01/03/2025] [Revised: 03/11/2025] [Accepted: 03/12/2025] [Indexed: 03/18/2025]
Abstract
As industrial demands for cold-active enzymes have been increased, psychrophilic lipases present a promising solution with potential for innovation and growth in food, pharmaceutical, and detergent industries. Cold-adapted enzymes achieve high catalytic efficiency at low temperatures through their structural flexibility and conformational adaptability. Therefore, in this study, the lipase gene from Psychrobacter sp. C18 was cloned and subjected to site-directed mutagenesis based on computer aided predictions to enhance the enzyme's cold-adapted properties and flexibility. Mutations were strategically selected in loops of the active site to improve the enzyme's accessibility to the substrate under cold conditions. The P163G, L186G, and Q239W mutations were selected for further analysis. Enzyme activity, along with its stability and structural flexibility, was assessed using techniques including UV-Vis spectroscopy, fluorescence, and circular dichroism (CD) spectroscopy. The obtained data revealed that the optimal temperature for the wild-type lipase was 30 °C, which shifted to lower temperatures in the mutants: 15 °C for P163G and L186G, and 20 °C for Q239W. Additionally, the optimal pH of the mutant lipases shifted to more alkaline conditions compared to the wild-type enzyme. While the thermal and pH stability of the mutant enzymes slightly decreased, these findings can be attributed to their enhanced flexibility. Far-UV CD spectroscopy revealed a reduction in α-helical content of the mutant enzymes. Molecular dynamics simulations corroborated these findings, confirming increased structural flexibility in all three mutants compared to the wild-type enzyme. This research underlines the importance of applying engineered cold-adapted enzymes for industrial application.
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Affiliation(s)
- Fatemeh Balaei
- Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran
| | - Khadijeh Pouraghajan
- Bioinformatics Laboratory, Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran
| | - Soheila Mohammadi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sirous Ghobadi
- Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran.
| | - Reza Khodarahmi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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2
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Ojuromi OT, Giwa AO, Gardberg A, Subramanian S, Myler PJ, Abendroth J, Staker B, Asojo OA. Crystal structures of the putative endoribonuclease L-PSP from Entamoeba histolytica. Acta Crystallogr F Struct Biol Commun 2025; 81:226-234. [PMID: 40314238 PMCID: PMC12121389 DOI: 10.1107/s2053230x25003875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2025] [Accepted: 04/29/2025] [Indexed: 05/03/2025] Open
Abstract
Entamoeba histolytica causes amebiasis, a neglected disease that kills ∼100 000 people globally each year. Due to emerging drug resistance, E. histolytica is one of the target organisms for structure-based drug discovery by the Seattle Structural Genomics Center for Infectious Disease (SSGCID). Purification, crystallization and three structures of the putative drug target endoribonuclease L-PSP from E. histolytica (EhL-PSP) are presented. EhL-PSP has a two-layer α/β-sandwich with structural homology to endoribonuclease L-PSP. All three structures reveal the prototypical YjgF/YER057c/UK114 family trimer topology with accessible allosteric active sites. Citrate molecules from the crystallization solution are bound to the allosteric site in two of the three reported structures. The large allosteric site of EhL-PSP is well conserved with bacterial YjgF/YER057c/UK114 family members and could be targeted for inhibition, drug discovery or repurposing.
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Affiliation(s)
| | | | - Anna Gardberg
- Freelance Structural Biology Consultant, Greater Boston Area, Massachusetts, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, USA
- Center for Global Infectious Disease ResearchSeattle Children’s Research Institute307 Westlake Avenue North, Suite 500SeattleWA98109USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, USA
- Center for Global Infectious Disease ResearchSeattle Children’s Research Institute307 Westlake Avenue North, Suite 500SeattleWA98109USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, USA
- UCB BioSciences, Bainbridge Island, WA98110, USA
| | - Bart Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, USA
- Center for Global Infectious Disease ResearchSeattle Children’s Research Institute307 Westlake Avenue North, Suite 500SeattleWA98109USA
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3
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Palmai Z. Sucrose and Gibberellic Acid Binding Stabilize the Inward-Open Conformation of AtSWEET13: A Molecular Dynamics Study. Proteins 2025; 93:1141-1156. [PMID: 39815685 DOI: 10.1002/prot.26799] [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: 10/04/2024] [Revised: 12/28/2024] [Accepted: 01/06/2025] [Indexed: 01/18/2025]
Abstract
In plants, sugar will eventually be exported transporters (SWEETs) facilitate the translocation of mono- and disaccharides across membranes and play a critical role in modulating responses to gibberellin (GA3), a key growth hormone. However, the dynamic mechanisms underlying sucrose and GA3 binding and transport remain elusive. Here, we employed microsecond-scale molecular dynamics (MD) simulations to investigate the influence of sucrose and GA3 binding on SWEET13 transporter motions. While sucrose exhibits high flexibility within the binding pocket, GA3 remains firmly anchored in the central cavity. Binding of both ligands increases the average channel radius along the transporter's principal axis. In contrast to the apo form, which retains its initial conformation throughout the simulation, ligand-bound complexes undergo a significant conformational transition characterized by further opening of the intracellular gate relative to the inward-open crystal structure (5XPD). This opening is driven by ligand-induced bending of helix V, stabilizing the inward-open state. Sucrose binding notably enhances the flexibility of the intracellular gate and amplifies anticorrelated motions between the N- and C-terminal domains at the intracellular side, suggesting an opening-closing motion of these domains. Principal component analysis revealed that this gating motion is most pronounced in the sucrose complex and minimal in the apo form, highlighting sucrose's ability to induce high-amplitude gating. Our binding free energy calculations indicate that SWEET13 has lower binding affinity for sucrose compared to GA3, consistent with its role in sugar transport. These results provide insight into key residues involved in sucrose and GA3 binding and transport, advancing our understanding of SWEET13 dynamics.
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Affiliation(s)
- Zoltan Palmai
- Institute of Transformative bio-Molecules, Nagoya University, Nagoya, Japan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
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4
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Chen N, Jiang Z, Xie Z, Zhou S, Zeng T, Jiang S, Zheng Y, Yuan Y, Wu R. An Effective Computational Strategy for UGTs Catalytic Function Prediction. ACS Synth Biol 2025. [PMID: 40377913 DOI: 10.1021/acssynbio.4c00886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2025]
Abstract
The GT-B type glycosyltransferases play a crucial post-modification role in synthesizing natural products, such as triterpenoid and steroidal saponins, renowned for their diverse pharmacological activities. Despite phylogenetic analysis aiding in enzyme family classification, distinguishing substrate specificity between triterpenoid and steroidal saponins, with their highly similar cyclic scaffolds, remains a formidable challenge. Our studies unveil the potential transport tunnels for the glycosyl donor and acceptor in PpUGT73CR1, by molecular dynamics simulations. This revelation leads to a plausible substrate transport mechanism, highlighting the regulatory role of the N-terminal domain (NTD) in glycosyl acceptor binding and transport. Inspired by these structural and mechanistic insights, we further analyze the binding pockets of 44 plant-derived UGTs known to glycosylate triterpenes and sterols. Notably, sterol UGTs are found to harbor aromatic and hydrophobic residues with polar residues typically present at the bottom of the active pocket. Drawing inspiration from the substrate binding and product release mechanism revealed through structure-based molecular modeling, we devised a fast sequence-based method for classifying UGTs using the pre-trained ESM2 protein model. This method involved extracting the NTD features of UGTs and performing PCA clustering analysis, enabling accurate identification of enzyme function, and even differentiation of substrate specificity/promiscuity between structurally similar triterpenoid and steroidal substrates, which is further validated by experiments. This work not only deepens our understanding of substrate binding mechanisms but also provides an effective computational protocol for predicting the catalytic function of unknown UGTs.
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Affiliation(s)
- Nianhang Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhennan Jiang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhekai Xie
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Su Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Tao Zeng
- School of Pharmaceutical Sciences, Hainan University, Haikou 570100, China
| | - Siqi Jiang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ying Zheng
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510006, China
| | - Yuan Yuan
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- School of Pharmaceutical Sciences, Hainan University, Haikou 570100, China
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5
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Wu H, Sun L, Huo T, Wensel TG, Horrigan FT, Wang Z. The identification of XPR1 as a voltage- and phosphate-activated phosphate-permeable ion channel. Nat Commun 2025; 16:4519. [PMID: 40374661 PMCID: PMC12081713 DOI: 10.1038/s41467-025-59678-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Accepted: 04/29/2025] [Indexed: 05/17/2025] Open
Abstract
Maintaining a balance of inorganic phosphate (Pi) is vital for cellular functionality. Proper phosphate levels are managed through Pi import and export; and the processes governing Pi export remain the least understood. Xenotropic and Polytropic retrovirus Receptor 1 (XPR1) has been identified as the only known Pi export protein in mammals. In this study, we introduce the cryogenic electron microscopy structure of human XPR1 (hXPR1), unveiling a structural arrangement distinct from that of any known ion transporter. Our structural results suggest that hXPR1 may operate as an ion channel, a hypothesis supported by patch clamp recordings revealing hXPR1's voltage- and Pi-dependent activity and large unitary conductance. Further analyses, including the structure of hXPR1 in presence of Pi, and mutagenesis studies at one of the putative Pi binding sites, lead us to propose a plausible ion permeation pathway. Together, our results provide novel perspectives on the Pi transport mechanism of XPR1.
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Affiliation(s)
- Hongjiang Wu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Liang Sun
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Tong Huo
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Theodore G Wensel
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Frank T Horrigan
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA.
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- CryoEM Core (Advanced Technology Core), Baylor College of Medicine, Houston, TX, USA.
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX, USA.
- Department of Molecular and Cellular Oncology, Division of Basic Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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6
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Kreiman AN, Garner SE, Carroll SC, Sutherland MC. Biochemical mapping reveals a conserved heme transport mechanism via CcmCD in System I bacterial cytochrome c biogenesis. mBio 2025; 16:e0351524. [PMID: 40167305 PMCID: PMC12077264 DOI: 10.1128/mbio.03515-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Accepted: 03/03/2025] [Indexed: 04/02/2025] Open
Abstract
Heme is a redox-active cofactor for essential processes across all domains of life. Heme's redox capabilities are responsible for its biological significance but also make it highly cytotoxic, requiring tight intracellular regulation. Thus, the mechanisms of heme trafficking are still not well understood. To address this, the bacterial cytochrome c biogenesis pathways are being developed into model systems to elucidate mechanisms of heme trafficking. These pathways function to attach heme to apocytochrome c, which requires the transport of heme from inside to outside of the cell. Here, we focus on the System I pathway (CcmABCDEFGH) which is proposed to function in two steps: CcmABCD transports heme across the membrane and attaches it to CcmE. HoloCcmE then transports heme to the holocytochrome c synthase, CcmFH, for attachment to apocytochrome c. To interrogate heme transport across the membrane, we focus on CcmCD, which can form holoCcmE independent of CcmAB, leading to the hypothesis that CcmCD is a heme transporter. A structure-function analysis via cysteine/heme crosslinking identified a heme acceptance domain and heme transport channel in CcmCD. Bioinformatic analysis and structural predictions across prokaryotic organisms determined that the heme acceptance domains are structurally variable, potentially to interact with diverse heme delivery proteins. In contrast, the CcmC transmembrane heme channel is structurally conserved, indicating a common mechanism for transmembrane heme transport. We provide direct biochemical evidence mapping the CcmCD heme channel and providing insights into general mechanisms of heme trafficking by other putative heme transporters. IMPORTANCE Heme is a biologically important cofactor for proteins involved with essential cellular functions, such as oxygen transport and energy production. Heme can also be toxic to cells and thus requires tight regulation and specific trafficking pathways. As a result, much effort has been devoted to understanding how this important, yet cytotoxic, molecule is transported. While several heme transporters/importers/exporters have been identified, the biochemical mechanisms of transport are not well understood, representing a major knowledge gap. Here, the bacterial cytochrome c biogenesis pathway, System I (CcmABCDEFGH), is used to elucidate the transmembrane transport of heme via CcmCD. We utilize a cysteine/heme crosslinking approach, which can trap endogenous heme in specific domains, to biochemically map the heme transport channel in CcmCD, demonstrating that CcmCD is a heme transporter. These results suggest a model for heme trafficking by other heme transporters in both prokaryotes and eukaryotes.
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Affiliation(s)
- Alicia N. Kreiman
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Sarah E. Garner
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Susan C. Carroll
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Molly C. Sutherland
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
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7
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Sindic CT, Muiño PL, Callis PR. Surveying Enzyme Crystal Structures Reveals the Commonality of Active-Site Solvent Accessibility and Enzymatic Water Networks. ACS OMEGA 2025; 10:18419-18427. [PMID: 40385134 PMCID: PMC12079200 DOI: 10.1021/acsomega.4c10721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 04/07/2025] [Accepted: 04/17/2025] [Indexed: 05/20/2025]
Abstract
Despite the demonstrable dependence of enzyme functionality on solvation, the notion of water being directly chemically required for catalysis inside active sites remains unexplored. Here we report that over 99% of 1013 enzyme crystals obtained by X-ray crystallography with high resolution (<1.5 Å) contain continuous chains of water linking residues within the active site to bulk water. Also reported are the findings which inspired this study-that electric fields experienced by water hydrogen atoms are on average twice as strong in the active sites of both chains of bacterial polynucleotide kinase (PDB 4QM6) structures compared to those in bulk water. These results point to the possibility that water molecules within active sites may be paramount to the immense catalytic power of enzymes, especially for mechanisms requiring hydronium or hydroxide ions.
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Affiliation(s)
- Caleb
M. T. Sindic
- Montana
State University, Chemistry
and Biochemistry Building, PO Box 173400, Bozeman, Montana 59717, United States
| | - Pedro L. Muiño
- Department
of Chemistry, Saint Francis University, PO Box 600, Loretto, Pennsylvania 15940, United States
| | - Patrik R. Callis
- Montana
State University, Chemistry
and Biochemistry Building, PO Box 173400, Bozeman, Montana 59717, United States
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8
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Doherty DZ, De Voss JJ, Bruning JB, Bell SG. Evolutionary insights into the selectivity of sterol oxidising cytochrome P450 enzymes based on ancestral sequence reconstruction. Chem Sci 2025:d5sc01863c. [PMID: 40417289 PMCID: PMC12100521 DOI: 10.1039/d5sc01863c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2025] [Accepted: 05/12/2025] [Indexed: 05/27/2025] Open
Abstract
The cytochrome P450 (CYP) enzyme CYP125A1 is a crucial enzyme for the long-term survival and pathogenicity of Mycobacterium tuberculosis. CYP125 genes are found not only in pathogenic mycobacteria but are also widely dispersed within the Actinobacteria phylum, with many species possessing multiple copies of CYP125 encoding genes. Their primary function is the catalytic hydroxylation of the terminal methyl group of cholesterol and phytosterols. We have previously shown that CYP125 enzymes from distinct mycobacteria have substrate selectivity preferences for animal versus plant steroid oxidation. An evolutionary understanding of this selectivity is not known. Here, we use Ancestral Sequence Reconstruction (ASR), to support the hypothesis that some CYP125 enzymes evolved in a manner reflective of their adaptation to a pathogenic niche. We constructed a maximum-likelihood, most-recent common ancestor of the CYP125 clade (CYP125MRCA). We were then able to produce and characterise this enzyme both functionally and structurally. We found that CYP125MRCA was able to catalyse the terminal hydroxylation of cholesterol, phytosterols, and vitamin D3 (cholecalciferol); the latter was hydroxylated at both C-25 and C-26. This is the first example to date of vitamin D3 oxidation by a CYP125 enzyme, thereby demonstrating an increased substrate range of CYP125MRCA relative to its characterised extant relatives. The X-ray crystal structures of CYP125MRCA bound with sitosterol and vitamin D3 were determined, providing important insight into the changes that enable the expanded substrate range.
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Affiliation(s)
- Daniel Z Doherty
- Department of Chemistry, University of Adelaide Adelaide South Australia 5005 Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland Brisbane Queensland 4072 Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide SA 5005 Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide Adelaide South Australia 5005 Australia
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9
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Yang Z, Wei H, Gan Y, Liu H, Cao Y, An H, Que X, Gao Y, Zhu L, Tan S, Liu X, Sun L. Structural insights into auxin influx mediated by the Arabidopsis AUX1. Cell 2025:S0092-8674(25)00463-5. [PMID: 40378849 DOI: 10.1016/j.cell.2025.04.028] [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: 09/27/2024] [Revised: 02/28/2025] [Accepted: 04/21/2025] [Indexed: 05/19/2025]
Abstract
Auxin is crucial in orchestrating diverse aspects of plant growth and development and modulating responses to environmental signals. The asymmetric spatiotemporal distribution of auxin generates local gradient patterns, which are regulated by both cellular auxin influx and efflux. The AUXIN1/LIKE-AUX1 (AUX1/LAX) family transporters have been identified as major auxin influx carriers. Here, we characterize the auxin uptake mediated by AUX1 from Arabidopsis thaliana. Using cryoelectron microscopy (cryo-EM), we determine its structure in three states: the auxin-unbound, the auxin-bound, and the competitive inhibitor, 3-chloro-4-hydroxyphenylacetic acid (CHPAA)-bound state. All structures adopt an inward-facing conformation. In the auxin-bound structure, indole-3-acetic acid (IAA) is coordinated to AUX1 primarily through hydrogen bonds with its carboxyl group. The functional roles of key residues in IAA binding are validated by in vitro and in planta analyses. CHPAA binds to the same site as IAA. These findings advance our understanding of auxin transport in plants.
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Affiliation(s)
- Zhisen Yang
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Hong Wei
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yulin Gan
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Huihui Liu
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yang Cao
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Huihui An
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xiuzheng Que
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yongxiang Gao
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Lizhe Zhu
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Shutang Tan
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China.
| | - Xin Liu
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China.
| | - Linfeng Sun
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China.
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10
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Li Y, Yu H, Ye L. Protein Engineering for Enhancing Electron Transfer in P450-Mediated Catalysis. Biotechnol Bioeng 2025. [PMID: 40344219 DOI: 10.1002/bit.29023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2025] [Revised: 04/28/2025] [Accepted: 04/29/2025] [Indexed: 05/11/2025]
Abstract
Cytochrome P450 enzymes (P450s) are versatile biocatalysts with applications spanning pharmaceutical development and natural product biosynthesis. A critical bottleneck in P450-mediated reactions is the electron transfer process, which often limits catalytic efficiency and promotes uncoupling events leading to reactive oxygen species (ROS) formation. This review comprehensively examines recent protein engineering strategies aimed at enhancing electron transfer efficiency in P450 systems. We explore the design and application of different fusion constructs, which improve proximity between the P450 enzyme and its redox partners (RPs), as well as scaffold-mediated protein assembly, enabling precise spatial organization of P450s and RPs. Furthermore, we discuss targeted modifications at the P450-RP interaction interface and optimization of electron transfer pathways through site-directed mutagenesis and directed evolution. These strategies enhance catalytic activity, improve coupling efficiency, and reduce ROS formation. Finally, we address the remaining challenges in understanding and engineering P450 electron transfer, and discuss the future directions, emphasizing the need for advanced computational modeling, structural characterization, and integration of synthetic and systems biology approaches.
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Affiliation(s)
- Yuemin Li
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Hongwei Yu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Lidan Ye
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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11
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Marques SM, Borko S, Vavra O, Dvorsky J, Kohout P, Kabourek P, Hejtmanek L, Damborsky J, Bednar D. Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins. Nucleic Acids Res 2025:gkaf399. [PMID: 40337920 DOI: 10.1093/nar/gkaf399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2025] [Revised: 04/17/2025] [Accepted: 04/30/2025] [Indexed: 05/09/2025] Open
Abstract
Enzymes with buried active sites utilize molecular tunnels to exchange substrates, products, and solvent molecules with the surface. These transport mechanisms are crucial for protein function and influence various properties. As proteins are inherently dynamic, their tunnels also vary structurally. Understanding these dynamics is essential for elucidating structure-function relationships, drug discovery, and bioengineering. Caver Web 2.0 is a user-friendly web server that retains all Caver Web 1.0 functionalities while introducing key improvements: (i) generation of dynamic ensembles via automated molecular dynamics with YASARA, (ii) analysis of dynamic tunnels with CAVER 3.0, (iii) prediction of ligand trajectories in multiple snapshots with CaverDock 1.2, and (iv) customizable ligand libraries for virtual screening. Users can assess protein flexibility, identify and characterize tunnels, and predict ligand trajectories and energy profiles in both static and dynamic structures. Additionally, the platform supports virtual screening with FDA/EMA-approved drugs and user-defined datasets. Caver Web 2.0 is a versatile tool for biological research, protein engineering, and drug discovery, aiding the identification of strong inhibitors or new substrates to bind to the active sites or tunnels, and supporting drug repurposing efforts. The server is freely accessible at https://loschmidt.chemi.muni.cz/caverweb.
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Affiliation(s)
- Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, 65691 Brno, Czech Republic
| | - Simeon Borko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, 65691 Brno, Czech Republic
| | - Ondrej Vavra
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, 65691 Brno, Czech Republic
| | - Jan Dvorsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, 65691 Brno, Czech Republic
| | - Petr Kohout
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Petr Kabourek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, 65691 Brno, Czech Republic
| | - Lukas Hejtmanek
- Institute of Computer Science, Masaryk University, 60200 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, 65691 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, 65691 Brno, Czech Republic
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12
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Chatterjee S, Rankin JA, Farrugia MA, J S Rifayee SB, Christov CZ, Hu J, Hausinger RP. Biochemical, Structural, and Conformational Characterization of a Fungal Ethylene-Forming Enzyme. Biochemistry 2025; 64:2054-2067. [PMID: 40052306 PMCID: PMC12060275 DOI: 10.1021/acs.biochem.5c00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2025] [Revised: 02/25/2025] [Accepted: 02/28/2025] [Indexed: 05/07/2025]
Abstract
The ethylene-forming enzyme (EFE) from the fungus Penicillium digitatum strain Pd1 was heterologously produced in Escherichia coli and its properties were compared to the extensively characterized bacterial enzyme from Pseudomonas savastanoi strain PK2. Both enzymes catalyze four reactions: the conversion of 2-oxoglutarate (2OG) to ethylene and CO2, oxidative decarboxylation of 2OG coupled to l-arginine (l-Arg) hydroxylation, uncoupled oxidative decarboxylation of 2OG, and the production of 3-hydroxypropionate (3-HP) from 2OG. The strain Pd1 enzyme exhibited a greater ratio of ethylene production over l-Arg hydroxylation than the PK2 strain EFE. The uncoupled decarboxylation of 2OG and 3-HP production are minor reactions in both cases, but they occur to a greater extent using the fungal enzyme. Additional distinctions of the fungal versus bacterial enzyme are noted in the absorbance maxima and l-Arg dependence of their anaerobic electronic spectra. The structures of the Pd1 EFE apoprotein and the EFE·Mn(II)·2OG complex resembled the corresponding structures of the PK2 enzyme, but notable structural differences were observed in the computationally predicted Pd1 EFE·Fe(II)·2OG·l-Arg complex versus the PK2 EFE·Mn(II)·2OG·l-Arg crystal structure. These studies extend our biochemical understanding and represent the first structural and conformational characterization of a eukaryotic EFE.
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Affiliation(s)
- Shramana Chatterjee
- Department
of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Joel A. Rankin
- Department
of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Mark A. Farrugia
- Department
of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
| | | | - Christo Z. Christov
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Jian Hu
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Robert P. Hausinger
- Department
of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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13
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Ding Z, Zhao J, Liu R, Ni B, Wang Y, Li W, Li X. Molecular cloning, overexpression, characterization, and mechanism explanation of an esterase RasEst3 for ester synthesis under aqueous phase. Int J Biol Macromol 2025; 307:142190. [PMID: 40101817 DOI: 10.1016/j.ijbiomac.2025.142190] [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: 11/12/2024] [Revised: 02/17/2025] [Accepted: 03/15/2025] [Indexed: 03/20/2025]
Abstract
Fatty acid esters are widely used in fragrance compounds, solvents, lubricants, and biofuels. Enzymatic synthesis of these esters in aqueous phase is an environmentally friendly approach. In this study, an esterase RasEst3 from Rasamsonia emersonii was identified for fatty acid ester synthesis through sequence alignment. The gene encoding RasEst3 was heterologously expressed in Escherichia coli BL21(DE3), and its enzymatic properties were analyzed. The enzyme exhibited optimal activity at pH 3.5 and 30 °C, with a preference for medium-chain substrates. Structurally, RasEst3 contains a lid domain and a catalytic domain, with a catalytic triad composed of Ser146-His227-Asp214. The smaller pocket spatial site resistance and the hydrophobicity of the substrate channel facilitate effective substrate binding to the active center. Site-directed mutagenesis and molecular dynamics simulations revealed that the oxygen anion holes formed by Gly69 and Thr70, along with the π-bond stacking formed by Tyr112 and Tyr145, play crucial roles in catalysis. After removing a loop region from RasEst3, its ethyl octanoate synthesis activity increased by 253.22 % compared to the wild-type enzyme. This study not only clarifies the structure-function relationship of RasEst3 but also provides valuable insights for developing novel biocatalysts in green chemistry.
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Affiliation(s)
- Ze Ding
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Jingrong Zhao
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Ruiqi Liu
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Bingqian Ni
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Yize Wang
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Weiwei Li
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
| | - Xiuting Li
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Beijing 100048, China; China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China; China Bio-Specialty Food Enzyme Technology Research Development and Promotion Center, Beijing 100048, China.
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14
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Biała-Leonhard W, Bigos A, Brezovsky J, Jasiński M. Message hidden in α-helices-toward a better understanding of plant ABCG transporters' multispecificity. PLANT PHYSIOLOGY 2025; 198:kiaf146. [PMID: 40220341 PMCID: PMC12117657 DOI: 10.1093/plphys/kiaf146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2025] [Accepted: 03/10/2025] [Indexed: 04/14/2025]
Affiliation(s)
- Wanda Biała-Leonhard
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Aleksandra Bigos
- Faculty of Biology, Department of Gene Expression, Laboratory of Biomolecular Interactions and Transport, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Jan Brezovsky
- Faculty of Biology, Department of Gene Expression, Laboratory of Biomolecular Interactions and Transport, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Michał Jasiński
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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15
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Hoeser F, Saura P, Harter C, Kaila VRI, Friedrich T. A leigh syndrome mutation perturbs long-range energy coupling in respiratory complex I. Chem Sci 2025; 16:7374-7386. [PMID: 40151474 PMCID: PMC11938283 DOI: 10.1039/d4sc04036h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 03/19/2025] [Indexed: 03/29/2025] Open
Abstract
Respiratory complex I is a central enzyme of cellular energy metabolism that couples electron transfer with proton translocation across a biological membrane. In doing so, it powers oxidative phosphorylation that drives energy consuming processes. Mutations in complex I lead to severe neurodegenerative diseases in humans. However, the biochemical consequences of these mutations remain largely unknown. Here, we use the Escherichia coli complex I as a model to biochemically characterize the F124LMT-ND5 mutation found in patients suffering from Leigh syndrome. We show that the mutation drastically perturbs proton translocation and electron transfer activities to the same extent, despite the remarkable 140 Å distance between the mutated position and the electron transfer domain. Our molecular dynamics simulations suggest that the disease-causing mutation induces conformational changes that hamper the propagation of an electric wave through an ion-paired network essential for proton translocation. Our findings imply that malfunction of the proton translocation domain is entirely transmitted to the electron transfer domain underlining the action-at-a-distance coupling in the proton-coupled electron transfer of respiratory complex I.
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Affiliation(s)
- Franziska Hoeser
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg Germany
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University Sweden
| | - Caroline Harter
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University Sweden
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16
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Kawai S, Karasawa M, Moriwaki Y, Terada T, Katsuyama Y, Ohnishi Y. Structural Basis for the Catalytic Mechanism of ATP-Dependent Diazotase CmaA6. Angew Chem Int Ed Engl 2025:e202505851. [PMID: 40275441 DOI: 10.1002/anie.202505851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2025] [Accepted: 04/24/2025] [Indexed: 04/26/2025]
Abstract
Although several diazotases have been recently reported, the details of the reaction mechanism are not yet understood. In this study, we investigated the mechanism of CmaA6, an ATP-dependent diazotase, which catalyzes the diazotization of 3-aminocoumaric acid using nitrous acid. X-ray crystallography and cryogenic electron microscopy-single particle analysis revealed CmaA6 structures in the substrate-free and AMP-binding states. Kinetic analysis suggested that CmaA6 catalyzes diazotization via a sequential reaction mechanism in which three substrates (nitrous acid, ATP, and 3-aminocoumaric acid) are simultaneously bound in the reaction pocket. The nitrous acid and 3-aminocoumaric acid binding sites were predicted based on the AMP-binding state and confirmed by site-directed mutagenesis. In addition, computational analysis revealed a tunnel for 3-aminocoumaric acid to enter the reaction pocket, which was advantageous for the sequential reaction mechanism. This study provides important insights into the catalytic mechanism of diazotization in natural product biosynthesis.
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Affiliation(s)
- Seiji Kawai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Masayuki Karasawa
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoshitaka Moriwaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
- Division of Computational Drug Discovery and Design, Medical Research Laboratory, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
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17
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Aydin AO, de Lichtenberg C, Liang F, Forsman J, Graça AT, Chernev P, Zhu S, Mateus A, Magnuson A, Cheah MH, Schröder WP, Ho F, Lindblad P, Debus RJ, Mamedov F, Messinger J. Probing substrate water access through the O1 channel of Photosystem II by single site mutations and membrane inlet mass spectrometry. PHOTOSYNTHESIS RESEARCH 2025; 163:28. [PMID: 40263146 PMCID: PMC12014804 DOI: 10.1007/s11120-025-01147-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Accepted: 03/18/2025] [Indexed: 04/24/2025]
Abstract
Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn4CaO5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated from Thermosynechococcus vestitus (T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn4CaO5 cluster during its S2→S3 and S3→S4→S0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacterium Synechocystis sp. PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitus numbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn4CaO5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn4CaO5 cluster that includes the pentameric, near planar 'water wheel' of the O1 channel.
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Affiliation(s)
- A Orkun Aydin
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala, 751 20, Sweden
| | - Casper de Lichtenberg
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala, 751 20, Sweden
| | - Feiyan Liang
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala, 751 20, Sweden
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Jack Forsman
- Department of Chemistry, Chemical Biology Centre, Umeå University, Umeå, 907 36, Sweden
- Department of Plant Physiology, Umeå Plant Science Center (UPSC), Umeå University, Umeå, 901 87, Sweden
| | - André T Graça
- Department of Chemistry, Chemical Biology Centre, Umeå University, Umeå, 907 36, Sweden
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, 38042, France
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala, 751 20, Sweden
| | - Shaochun Zhu
- Department of Chemistry, Chemical Biology Centre, Umeå University, Umeå, 907 36, Sweden
| | - André Mateus
- Department of Chemistry, Chemical Biology Centre, Umeå University, Umeå, 907 36, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, 907 36, Sweden
| | - Ann Magnuson
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala, 751 20, Sweden
| | - Mun Hon Cheah
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala, 751 20, Sweden
| | - Wolfgang P Schröder
- Department of Chemistry, Chemical Biology Centre, Umeå University, Umeå, 907 36, Sweden
- Department of Plant Physiology, Umeå Plant Science Center (UPSC), Umeå University, Umeå, 901 87, Sweden
| | - Felix Ho
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala, 751 20, Sweden
| | - Peter Lindblad
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala, 751 20, Sweden
| | - Richard J Debus
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Fikret Mamedov
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala, 751 20, Sweden
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala, 751 20, Sweden.
- Department of Plant Physiology, Umeå Plant Science Center (UPSC), Umeå University, Umeå, 901 87, Sweden.
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18
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Mwaniki RM, Veldman W, Sanyanga A, Chamboko CR, Tastan Bishop Ö. Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored. J Mol Biol 2025:169160. [PMID: 40252954 DOI: 10.1016/j.jmb.2025.169160] [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: 03/10/2025] [Revised: 04/10/2025] [Accepted: 04/14/2025] [Indexed: 04/21/2025]
Abstract
There is growing research on the allosteric behaviour of proteins, including studies on allosteric mutations that contribute to human diseases and the development of allosteric drugs. Allostery also plays a key role in drug metabolism, an essential factor in drug development. However, population specific variations, particularly in 3D protein structures, remain understudied. This study focuses on CYP3A4, a key enzyme responsible for metabolizing over 50% of FDA-approved drugs and often linked to adverse drug reactions. Given the vast genetic diversity of Africa, we investigated 13 CYP3A4 alleles from African populations using post-molecular dynamics analyses, with 12 being single variations and one containing a double variation. Except for one, all allele variations were located away from the active site, suggesting allosteric effects. Our comparative analyses of reference and variant structures, through hydrogen bond interactions, dynamic residue network analysis and substrate channel dynamics, revealed notable differences at both global and residue levels. The *32-I335T variant showed the largest changes compared to the reference structure, while *3-M445T (near normal metabolizer) exhibited the least change, with other variants falling in between. The *32-I335T variant showed a distorted conformation in the radius of gyration, a distinct kink in the I helix with specific hydrogen bonds and altered channel patterns. The *12-L373F variant, associated with reduced metabolism of midazolam and quinine, showed increased rigidity in its vicinity, potentially interfering with catalytic activity. Our findings align with clinical and wet lab data, suggesting that our approaches could be applied to analyse variants without clinical evidence.
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Affiliation(s)
- Rehema Mukami Mwaniki
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, South Africa
| | - Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, South Africa
| | - Allan Sanyanga
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, South Africa
| | - Chiratidzo R Chamboko
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, South Africa; National Institute for Theoretical and Computational Sciences (NITheCS), South Africa.
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19
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Liu M, Wang K, Zhang Y, Zhou X, Li W, Han W. Mechanistic Study of Protein Interaction with Natto Inhibitory Peptides Targeting Xanthine Oxidase: Insights from Machine Learning and Molecular Dynamics Simulations. J Chem Inf Model 2025; 65:3682-3696. [PMID: 40125929 DOI: 10.1021/acs.jcim.5c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2025]
Abstract
Bioactive peptides from food sources offer a safe and biocompatible approach to enzyme inhibition, with potential applications in managing metabolic disorders such as hyperuricemia and gout, conditions linked to excessive xanthine oxidase activity. Using a machine learning-based screening approach inspired by the bioactivity of natto, two peptides, ECFK and FECK, were identified from the Bacillus subtilis proteome and validated as xanthine oxidase inhibitors with IC50 values of 37.36 and 71.57 mM, respectively. Further experiments confirmed their safety through cytotoxicity assays, and electronic tongue analysis demonstrated their mild sensory properties, supporting their edibility. Molecular dynamics simulations revealed that these peptides stabilize critical enzyme regions, with ECFK showing a higher dissociation energy barrier (52.08 kcal/mol) than FECK (46.39 kcal/mol), indicating strong, stable interactions. This study highlights food-derived peptides as safe and natural inhibitors of xanthine oxidase, offering promising therapeutic potential for metabolic disorder management.
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Affiliation(s)
- Minghao Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Kaiyu Wang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yan Zhang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xue Zhou
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Wannan Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
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20
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Haloi N, Karlsson E, Delarue M, Howard RJ, Lindahl E. Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT 3A receptor. SCIENCE ADVANCES 2025; 11:eadr0797. [PMID: 40215320 PMCID: PMC11988449 DOI: 10.1126/sciadv.adr0797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 03/07/2025] [Indexed: 04/14/2025]
Abstract
A diverse set of modulators, including stimulants and anesthetics, regulates ion channel function in our nervous system. However, structures of ligand-bound complexes can be difficult to capture by experimental methods, particularly when binding is dynamic. Here, we used computational methods and electrophysiology to identify a possible bound state of a modulatory stimulant derivative in a cryptic vestibular pocket of a mammalian serotonin-3 receptor. We first applied a molecular dynamics simulation-based goal-oriented adaptive sampling method to identify possible open-pocket conformations, followed by Boltzmann docking that combines traditional docking with Markov state modeling. Clustering and analysis of stability and accessibility of docked poses supported a preferred binding site; we further validated this site by mutagenesis and electrophysiology, suggesting a mechanism of potentiation by stabilizing intersubunit contacts. Given the pharmaceutical relevance of serotonin-3 receptors in emesis, psychiatric, and gastrointestinal diseases, characterizing relatively unexplored modulatory sites such as these could open valuable avenues to understanding conformational cycling and designing state-dependent drugs.
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Affiliation(s)
- Nandan Haloi
- SciLifeLab, Department of Applied Physics, KTH Royal Institute of Technology, Tomtebodävagen 23, Solna, 17165 Stockholm, Sweden
| | - Emelia Karlsson
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Tomtebodavägen 23, Solna, 17165 Stockholm, Sweden
| | - Marc Delarue
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, FR-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, FR-75015 Paris, France
| | - Rebecca J. Howard
- SciLifeLab, Department of Applied Physics, KTH Royal Institute of Technology, Tomtebodävagen 23, Solna, 17165 Stockholm, Sweden
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Tomtebodavägen 23, Solna, 17165 Stockholm, Sweden
| | - Erik Lindahl
- SciLifeLab, Department of Applied Physics, KTH Royal Institute of Technology, Tomtebodävagen 23, Solna, 17165 Stockholm, Sweden
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Tomtebodavägen 23, Solna, 17165 Stockholm, Sweden
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21
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Zhang J, Zhang X, Zhang J, Wu J, Yang P, Tang C, Zou F, Ying H, Zhuang W. Polyethylenimine-Assisted Interfacial Modulation Based on Electrostatic Balancing and Hierarchical Channel to the Cytidine 5'-Monophosphate Conversion Performance of Uridine-Cytosine Kinase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:8426-8439. [PMID: 40131736 DOI: 10.1021/acs.jafc.5c00153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2025]
Abstract
Interfacial modulation of protein microenvironments plays a pivotal role in enhancing enzyme immobilization and catalysis. In this study, we proposed a polyethylenimine (PEI)-assisted strategy that combines electrostatic and affinity interactions to improve the performance of Cytidine 5'-Monophosphate (CMP) conversion by uridine-cytidine kinase (UCK). The PEI-modified interface creates an optimal local microenvironment that maintains a balanced charge distribution, stabilizes UCK's conformation, and prevents denaturation. Electrostatic interactions promote product adsorption, enhance diffusion, and reduce substrate accumulation, boosting reaction efficiency. The kinetic assays revealed an increase in the maximum reaction rate from 16.8 to 113.2 μM·min-1 with a remarkable increase in substrate affinity and enzyme activity. The relative enzyme activity at the optimal substrate concentration increased from 70.4 to 106.9%, and by 113.3% under conditions of substrate inhibition. This study provides theoretical and technical support for the efficient production of CMP with promising applications in food, feed, and medical fields.
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Affiliation(s)
- Jihang Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Xiao Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jinming Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jinglan Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Pengpeng Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Chenglun Tang
- Jiangsu Institute of Industrial Biotechnology, JITRI Co., Ltd, 11 Yaogu Avenue, Nanjing 210044, China
| | - Fengxia Zou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
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22
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Ortega FM, Hossain F, Volobouev VV, Meloni G, Torabifard H, Morcos F. Generative Landscapes and Dynamics to Design Multidomain Artificial Transmembrane Transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.28.645293. [PMID: 40236216 PMCID: PMC11996383 DOI: 10.1101/2025.03.28.645293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Protein design is challenging as it requires simultaneous consideration of interconnected factors, such as fold, dynamics, and function. These evolutionary constraints are encoded in protein sequences and can be learned through the latent generative landscape (LGL) framework to predict functional sequences by leveraging evolutionary patterns, enabling exploration of uncharted sequence space. By simulating designed proteins through molecular dynamics (MD), we gain deeper insights into the interdependencies governing structure and dynamics. We present a synergized workflow combining LGL with MD and biochemical characterization, allowing us to explore the sequence space effectively. This approach has been applied to design and characterize two artificial multidomain ATP-driven transmembrane copper transporters, with native-like functionality. This integrative approach proved effective in unraveling the intricate relationships between sequence, structure, and function.
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23
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Deng M, Wang B, Zhou J, Dong J, Ni Y, Han R. Ancestral Sequence Reconstruction and Semirational Engineering of Glycosyltransferase for Efficient Synthesis of Rare Ginsenoside Rh1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:7944-7953. [PMID: 40105367 DOI: 10.1021/acs.jafc.5c00964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2025]
Abstract
Rare ginsenoside Rh1, exhibiting great potential in the food industry, is limited by its natural scarcity. This constraint has driven the development of biocatalytic synthesis approaches, yet robust enzymes capable of efficient production remain elusive. Here, we employed the ancestral sequence reconstruction (ASR) approach to create a thermostable UDP-dependent glycosyltransferase (UGT227) for Rh1 synthesis from 20(S)-protopanaxatriol (PPT). UGT227 exhibited enhanced thermostability (t1/2 = 44.2 h at 60 °C) but initially yielded only 15% Rh1. Semirational engineering generated the I83A/F285 M variant, increasing the yield to 92%. For economic viability, the I83A/F285 M variant was coexpressed with Arabidopsis thaliana sucrose synthase (AtSUS1), enabling the use of cost-effective sucrose for UDP-glucose regeneration. This integration achieved a 99.9% yield at a 1 mM PPT. Molecular dynamics simulations revealed that the enlarged binding pocket entrance of I83A/F285 M contributed to the enhanced Rh1 yield. Our findings offer strategies for efficient biosynthesis of Rh1 and pave the way for economically feasible production.
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Affiliation(s)
- Meijuan Deng
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Binhao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jieyu Zhou
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jinjun Dong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Ye Ni
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Ruizhi Han
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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24
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Muñoz-Vargas MA, López-Jaramillo J, González-Gordo S, Taboada J, Palma JM, Corpas FJ. Peroxisomal H 2O 2-generating sulfite oxidase (SOX) from pepper fruits is negatively modulated by NO and H 2S. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2025; 221:109591. [PMID: 39970565 DOI: 10.1016/j.plaphy.2025.109591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 01/28/2025] [Accepted: 01/30/2025] [Indexed: 02/21/2025]
Abstract
Nitric oxide and hydrogen sulfide are signal molecules that can exert regulatory functions in diverse plant processes including fruit ripening. Sulfite oxidase (SOX) is a peroxisomal enzyme that catalyzes the oxidation of sulfite (SO32-) to sulfate (SO42-) with the concomitant generation of H2O2. SOX requires the molybdenum cofactor (Moco) and it has been proposed that SOX functions as a mechanism of protection against sulfite toxicity. Based on the analysis of the pepper genome and fruit transcriptome (RNA-seq), a single gene encoding for a SOX, was identified in chromosome 2. The CaSOX gene expression analysis during fruit ripening, from green immature (G) to red ripe (R) indicates that its expression increased. In-gel analysis using non-denaturing PAGE of a 50-75% (NH4)2SO4 protein fraction allowed the detection of its SOX activity in green pepper fruits. In vitro assay of the SOX from pepper fruits showed that the SOX activity is differently regulated by NO and H2S. Mass spectrometric analysis of the nitrated recombinant pepper SOX enables us to corroborate that this enzyme undergoes inhibition by nitration in Tyr10. Protein modeling analysis also reveals that Cys70 and Cys163 are susceptible targets for S-nitrosation and persulfidation. These findings suggest that NO and H2S could function upstream of the peroxisomal H2O2-generating SOX, highlighting the intricate network of signaling molecules within this subcellular compartment.
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Affiliation(s)
- María A Muñoz-Vargas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture. Estación Experimental del Zaidín (Spanish National Research Council, CSIC), Granada, Spain
| | | | - Salvador González-Gordo
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture. Estación Experimental del Zaidín (Spanish National Research Council, CSIC), Granada, Spain
| | - Jorge Taboada
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture. Estación Experimental del Zaidín (Spanish National Research Council, CSIC), Granada, Spain
| | - José M Palma
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture. Estación Experimental del Zaidín (Spanish National Research Council, CSIC), Granada, Spain
| | - Francisco J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture. Estación Experimental del Zaidín (Spanish National Research Council, CSIC), Granada, Spain.
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25
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Meng Y, Peplowski L, Wu T, Gong H, Gu R, Han L, Xia Y, Liu Z, Zhou Z, Cheng Z. A Versatile Protein Scaffold Engineered for the Hierarchical Assembly of Robust and Highly Active Enzymes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2500405. [PMID: 39985242 PMCID: PMC12005783 DOI: 10.1002/advs.202500405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Indexed: 02/24/2025]
Abstract
Scaffold proteins play immense roles in bringing enzymes together to enhance their properties. However, the direct fusion of scaffold with bulky guest enzymes may disrupt the assembly process or diminish catalytic efficiency. Most self-assembling protein scaffolds are engineered to form structures beforehand, and then carry guest proteins via different conjugation strategies in vitro. Here, a robust self-assembling scaffold is presented, engineered from Methanococcus jannaschii using disulfide bonds, which efficiently assembles bulky enzymes into higher-order helices without additional chemistry or bio-conjugation in vitro. When fused directly with monomeric Endo-1,4-beta-xylanase A, the catalytic efficiency of the guest enzyme increased by 2.5 times with enhanced thermostability. Additionally, integrating the scaffold with the multimeric metalloenzyme nitrile hydratase overcame the typical stability-activity trade-off of such industrial enzyme, yielding three-fold higher activity and 28-fold higher thermostability. Structural analyses suggest that the artificially made helical twist structures create new interface interactions and provide a concentration of active sites of guest enzymes. Further fusion of fluorescent protein pairs with the scaffold exhibited a 12-fold higher FRET efficiency, suggesting its potential for dual-enzyme cascade applications. Overall, this study showcases a simple yet powerful protein scaffold that organizes guest enzymes into hierarchical structures with enhanced catalytic performance.
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Affiliation(s)
- Yiwei Meng
- Key Laboratory of Industrial Biotechnology (Ministry of Education)School of BiotechnologyJiangnan UniversityWuxiJiangsuChina
| | - Lukasz Peplowski
- Institute of PhysicsFaculty of PhysicsAstronomy and InformaticsNicolaus Copernicus University in TorunGrudziadzka 5Torun87–100Poland
| | - Tong Wu
- Key Laboratory of Industrial Biotechnology (Ministry of Education)School of BiotechnologyJiangnan UniversityWuxiJiangsuChina
| | - Heng Gong
- Key Laboratory of Industrial Biotechnology (Ministry of Education)School of BiotechnologyJiangnan UniversityWuxiJiangsuChina
| | - Ran Gu
- Key Laboratory of Industrial Biotechnology (Ministry of Education)School of BiotechnologyJiangnan UniversityWuxiJiangsuChina
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology (Ministry of Education)School of BiotechnologyJiangnan UniversityWuxiJiangsuChina
| | - Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology (Ministry of Education)School of BiotechnologyJiangnan UniversityWuxiJiangsuChina
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology (Ministry of Education)School of BiotechnologyJiangnan UniversityWuxiJiangsuChina
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (Ministry of Education)School of BiotechnologyJiangnan UniversityWuxiJiangsuChina
- Jiangnan University (Rugao) Food Biotechnology Research InstituteRugaoJiangsuChina
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology (Ministry of Education)School of BiotechnologyJiangnan UniversityWuxiJiangsuChina
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26
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Braza MKE, Dennis EA, Amaro RE. Conformational dynamics and activation of membrane-associated human Group IVA cytosolic phospholipase A 2 (cPLA 2 ). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.22.644760. [PMID: 40196679 PMCID: PMC11974688 DOI: 10.1101/2025.03.22.644760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
Cytosolic phospholipase A 2 (cPLA 2 ) associates with membranes where it hydrolyzes phospholipids containing arachidonic acid to initiate an inflammatory cascade. All-atom molecular dynamics simulations were employed to understand the activation process when cPLA 2 associates with the endoplasmic reticulum (ER) membrane of macrophages where it acts. We found that membrane association causes the lid region of cPLA 2 to undergo a closed-to-open state transition that is accompanied by the sideways movement of loop 495-540, allowing the exposure of a cluster of lysine residues (K488, K541, K543, and K544), which binds the allosteric activator PIP 2 in the membrane. The active site of the open form of cPLA 2 , containing the catalytic dyad residues S228 and D549, exhibited a three-fold larger cavity than the closed form of cPLA 2 in aqueous solution. These findings provide mechanistic insight as to how cPLA 2 ER membrane association promotes major transitions between conformational states critical to allosteric activation and enzymatic phospholipid hydrolysis.
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27
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Yu W, Weber DJ, MacKerell AD. Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation. J Chem Inf Model 2025; 65:3022-3034. [PMID: 39729368 PMCID: PMC11932794 DOI: 10.1021/acs.jcim.4c01814] [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: 12/29/2024]
Abstract
Drug efficacy often correlates better with dissociation kinetics than binding affinity alone. To study binding kinetics computationally, it is necessary to identify all of the possible ligand dissociation pathways. The site identification by ligand competitive saturation (SILCS) method involves the precomputation of a set of maps (FragMaps), which describe the free energy landscapes of typical chemical functionalities in and around a target protein or RNA. In the current work, we present and implement a method to use SILCS to identify ligand dissociation pathways, termed "SILCS-Pathway." The A* pathfinding algorithm is utilized to enumerate ligand dissociation pathways between the ligand binding site and the surrounding bulk solvent environment defined on evenly spaced points around the protein based on a Fibonacci lattice. The cost function for the A* algorithm is calculated using the SILCS exclusion maps and the SILCS grid free energy scores, thereby identifying paths that account for local protein flexibility and potential favorable interactions with the ligand. By traversing all evenly distributed bulk solvent points around the protein, we located all possible dissociation pathways and clustered them to identify general ligand unbinding pathways. The procedure is verified by using proteins studied previously with enhanced sampling molecular dynamics (MD) techniques and is shown to be capable of capturing important ligand dissociation routes in a highly computationally efficient manner. The identified pathways will act as the foundation for determining ligand dissociation kinetics using SILCS free energy profiles, which will be described in a subsequent article.
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Affiliation(s)
- Wenbo Yu
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland 20850, United States
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - David J. Weber
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland 20850, United States
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland 20850, United States
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
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28
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Justen SF, Fenwick MK, Axt KK, Cherry JA, Ealick SE, Philmus B. Crystal Structure, Modeling, and Identification of Key Residues Provide Insights into the Mechanism of the Key Toxoflavin Biosynthesis Protein ToxD. Biochemistry 2025; 64:1199-1211. [PMID: 40047534 PMCID: PMC11989309 DOI: 10.1021/acs.biochem.4c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
Toxoflavin, a toxic secondary metabolite produced by a variety of bacteria, has been implicated as a causative agent in food poisoning and a virulence factor in phytopathogenic bacteria. This toxin is produced by genes encoded in the tox operon in Burkholderia glumae, in which the encoded protein, ToxD, was previously characterized as essential for toxoflavin production. To better understand the function of ToxD in toxoflavin biosynthesis and provide a basis for future work to develop inhibitors of ToxD, we undertook the identification of structurally and catalytically important amino acid residues through a combination of X-ray crystallography and site directed mutagenesis. We solved the structure of BgToxD, which crystallized as a dimer, to 1.8 Å resolution. We identified a citrate molecule in the putative active site. To investigate the role of individual residues, we used Pseudomonas protegens Pf-5, a BL1 plant protective bacterium known to produce toxoflavin, and created mutants in the ToxD-homologue PFL1035. Using a multiple sequence alignment and the BgToxD structure, we identified and explored the functional importance of 12 conserved residues in the putative active site. Eight variants of PFL1035 resulted in no observable production of toxoflavin. In contrast, four ToxD variants resulted in reduced but detectable toxoflavin production suggesting a nonessential role. The crystal structure and structural models of the substrate and intermediate bound enzyme provide a molecular interpretation for the mutagenesis data.
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Affiliation(s)
- Savannah F. Justen
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Michael K. Fenwick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kyle K. Axt
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - James A. Cherry
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA
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29
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Spanke VA, Egger-Hoerschinger VJ, Ruzsanyi V, Liedl KR. From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4. J Comput Aided Mol Des 2025; 39:12. [PMID: 40095179 PMCID: PMC11913904 DOI: 10.1007/s10822-025-00589-1] [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: 09/18/2024] [Accepted: 03/01/2025] [Indexed: 03/19/2025]
Abstract
Cytochrome P450 3A4 (CYP3A4) is a membrane bound monooxygenase. It metabolizes the largest proportion of all orally ingested drugs. Ligands can enter and exit the enzyme through flexible tunnels, which co-determine CYP3A4's ligand promiscuity. The flexibility can be represented by distinct conformational states of the enzyme. However, previous state definitions relied solely on crystal structures. We employed conventional molecular dynamics (cMD) simulations to sample the conformational space of CYP3A4. Five conformationally different crystal structures embedded in a membrane were simulated for 1 µs each. A Markov state model (MSM) coupled with spectral clustering (Robust Perron Cluster Analysis PCCA +) resulted in three distinct states: Two open conformations and an intermediate conformation. The tunnels inside CYP3A4 were calculated with CAVER3.0. Notably, we observed variations in bottleneck radii compared to those derived from crystallographic data. We want to point out the importance of simulations to characterize the dynamic behaviour. Moreover, we identified a mechanism, in which the membrane supports the opening of a tunnel. Therefore, CYP3A4 must be investigated in its membrane-bound state.
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Affiliation(s)
- Vera A Spanke
- Department of Theoretical Chemistry, Universität Innsbruck, Innsbruck, Austria
| | | | - Veronika Ruzsanyi
- Department of Breath Research, Universität Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Department of Theoretical Chemistry, Universität Innsbruck, Innsbruck, Austria.
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30
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Funke FJ, Schlee S, Bento I, Bourenkov G, Sterner R, Wilmanns M. Activity Regulation of a Glutamine Amidotransferase Bienzyme Complex by Substrate-Induced Subunit Interface Expansion. ACS Catal 2025; 15:4359-4373. [PMID: 40365074 PMCID: PMC7617670 DOI: 10.1021/acscatal.4c07438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2025]
Abstract
Glutamine amidotransferases are multienzyme machineries in which reactive ammonia is generated by a glutaminase and then transferred through a sequestered protein tunnel to a synthase active site for incorporation into diverse metabolites. To avoid wasteful metabolite consumption, there is a requirement for synchronized catalysis, but any generally applicable mechanistic insight is still lacking. As synthase activity depends on glutamine turnover, we investigated possible mechanisms controlling glutaminase catalysis using aminodeoxychorismate synthase involved in folate biosynthesis as a model. By analyzing this system in distinct states of catalysis, we found that incubation with glutamine leads to a subunit interface expansion by one-third of its original area. These changes completely enclose the glutaminase active site for sequestered catalysis and the subsequent transport of volatile ammonia to the synthase active site. In view of similar rearrangements in other glutamine amidotransferases, our observations may provide a general mechanism for the catalysis synchronization of this multienzyme family.
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Affiliation(s)
- Franziska Jasmin Funke
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg 93040, Germany
| | - Sandra Schlee
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg 93040, Germany
| | - Isabel Bento
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg 93040, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany; University Hamburg Clinical Center Hamburg-Eppendorf, Hamburg 20251, Germany
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31
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Wang J, Ouyang X, Meng S, Zhao B, Liu L, Li C, Li H, Zheng H, Liu Y, Shi T, Zhao YL, Ni J. Rational multienzyme architecture design with iMARS. Cell 2025; 188:1349-1362.e17. [PMID: 39855196 DOI: 10.1016/j.cell.2024.12.029] [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: 01/31/2024] [Revised: 11/20/2024] [Accepted: 12/19/2024] [Indexed: 01/27/2025]
Abstract
Biocatalytic cascades with spatial proximity can orchestrate multistep pathways to form metabolic highways, which enhance the overall catalytic efficiency. However, the effect of spatial organization on catalytic activity is poorly understood, and multienzyme architectural engineering with predictable performance remains unrealized. Here, we developed a standardized framework, called iMARS, to rapidly design the optimal multienzyme architecture by integrating high-throughput activity tests and structural analysis. The approach showed potential for industrial-scale applications, with artificial fusion enzymes designed by iMARS significantly improving the production of resveratrol by 45.1-fold and raspberry ketone by 11.3-fold in vivo, as well as enhancing ergothioneine synthesis in fed-batch fermentation. In addition, iMARS greatly enhanced the in vitro catalytic efficiency of the multienzyme complexes for PET plastic depolymerization and vanillin biosynthesis. As a generalizable and flexible strategy at molecular level, iMARS could greatly facilitate green chemistry, synthetic biology, and biomanufacturing.
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Affiliation(s)
- Jiawei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xingyu Ouyang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiyu Meng
- Research Center for Proteins & Bits, Lumy Biotechnology, Changzhou, Jiangsu 213200, China
| | - Bowen Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liangxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chaofeng Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hengrun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haotian Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yihan Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China; Research Center for Proteins & Bits, Lumy Biotechnology, Changzhou, Jiangsu 213200, China.
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Martinez Grundman JE, Schultz TD, Schlessman JL, Johnson EA, Gillilan RE, Lecomte JTJ. Extremophilic hemoglobins: The structure of Shewanella benthica truncated hemoglobin N. J Biol Chem 2025; 301:108223. [PMID: 39864624 PMCID: PMC11904497 DOI: 10.1016/j.jbc.2025.108223] [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: 10/11/2024] [Revised: 01/16/2025] [Accepted: 01/19/2025] [Indexed: 01/28/2025] Open
Abstract
Truncated hemoglobins (TrHbs) have an ancient origin and are widely distributed in microorganisms where they often serve roles other than dioxygen transport and storage. In extremophiles, these small heme proteins must have features that secure function under challenging conditions: at minimum, they must be folded, retain the heme group, allow substrates to access the heme cavity, and maintain their quaternary structure if present and essential. The genome of the obligate psychropiezophile Shewanella benthica strain KT99 harbors a gene for a TrHb belonging to a little-studied clade of globins (subgroup 2 of group N). In the present work, we characterized the structure of this protein (SbHbN) with electronic absorption spectroscopy and X-ray crystallography and inspected its structural integrity under hydrostatic pressure with NMR spectroscopy and small-angle X-ray scattering. We found that SbHbN self-associates weakly in solution and contains an extensive network of hydrophobic tunnels connecting the active site to the surface. Amino acid replacements at the dimeric interface formed by helices G and H in the crystal confirmed this region to be the site of intermolecular interactions. High hydrostatic pressure dissociated the assemblies while the porous subunits resisted unfolding and heme loss. Preservation of structural integrity under pressure is also observed in nonpiezophilic TrHbs, which suggests that this ancient property is derived from functional requirements. Added to the inability of SbHbN to combine reversibly with dioxygen and a propensity to form heme d, the study broadens our perception of the TrHb lineage and the resistance of globins to extreme environmental conditions.
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Affiliation(s)
| | - Thomas D Schultz
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Eric A Johnson
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.
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Scocozza MF, Zitare UA, Cancian P, Castro MA, Martins LO, Murgida DH. Molecular basis of H 2O 2/O 2.-/ .OH discrimination during electrochemical activation of DyP peroxidases: The critical role of the distal residues. J Inorg Biochem 2025; 264:112816. [PMID: 39729891 DOI: 10.1016/j.jinorgbio.2024.112816] [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: 08/16/2024] [Revised: 12/03/2024] [Accepted: 12/19/2024] [Indexed: 12/29/2024]
Abstract
Here, we show that the replacement of the distal residues Asp and/or Arg of the DyP peroxidases from Bacillus subtilis and Pseudomonas putida results in functional enzymes, albeit with spectroscopically perturbed active sites. All the enzymes can be activated either by the addition of exogenous H2O2 or by in situ electrochemical generation of the reactive oxygen species (ROS) •OH, O2•- and H2O2. The latter method leads to broader and upshifted pH-activity profiles. Both WT enzymes exhibit a differential predominance of ROS involved in their electrochemical activation, which follows the order •OH > O2•- > H2O2 for BsDyP and O2•- > H2O2 > •OH for PpDyP. This ROS selectivity is preserved in mutants with unperturbed sites but is blurred out for distorted sites. The underlying molecular basis of the selectivity mechanisms is analysed through molecular dynamics simulations, which reveal distorted hydrogen bonding networks and higher throughput of the access tunnels in the variants exhibiting no selectivity. The electrochemical activation method provides superior performance for protein variants with a high prevalence of the alternative •OH and O2•- species. These results constitute a promising advance towards engineering DyPs for electrocatalytic applications.
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Affiliation(s)
- Magalí F Scocozza
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Ulises A Zitare
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Pablo Cancian
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - María A Castro
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Daniel H Murgida
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.
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Zarifi N, Asthana P, Doustmohammadi H, Klaus C, Sanchez J, Hunt SE, Rakotoharisoa RV, Osuna S, Fraser JS, Chica RA. Distal mutations enhance catalysis in designed enzymes by facilitating substrate binding and product release. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.21.639315. [PMID: 40060566 PMCID: PMC11888230 DOI: 10.1101/2025.02.21.639315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/18/2025]
Abstract
The role of amino-acid residues distant from an enzyme's active site in facilitating the complete catalytic cycle-including substrate binding, chemical transformation, and product release-remains poorly understood. Here, we investigate how distal mutations promote the catalytic cycle by engineering mutants of three de novo Kemp eliminases containing either active-site or distal mutations identified through directed evolution. Kinetic analyses, X-ray crystallography, and molecular dynamics simulations reveal that while active-site mutations create preorganized catalytic sites for efficient chemical transformation, distal mutations enhance catalysis by facilitating substrate binding and product release through tuning structural dynamics to widen the active-site entrance and reorganize surface loops. These distinct contributions work synergistically to improve overall activity, demonstrating that a well-organized active site, though necessary, is not sufficient for optimal catalysis. Our findings reveal critical roles that distal residues play in shaping the catalytic cycle to enhance efficiency, yielding valuable insights for enzyme design.
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Affiliation(s)
- Niayesh Zarifi
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
| | - Pooja Asthana
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, California 94158, United States
| | - Hiva Doustmohammadi
- CompBioLab Group, Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Girona, Spain
- ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Cindy Klaus
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
| | - Janet Sanchez
- CompBioLab Group, Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Girona, Spain
- ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Serena E Hunt
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
| | - Rojo V Rakotoharisoa
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Girona, Spain
- ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - James S Fraser
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, California 94158, United States
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
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Khanra NK, Wang C, Delgado BD, Long SB. Structure of the human TWIK-2 potassium channel and its inhibition by pimozide. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.24.639991. [PMID: 40060494 PMCID: PMC11888252 DOI: 10.1101/2025.02.24.639991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2025]
Abstract
The potassium channel TWIK-2 is crucial for ATP-induced activation of the NLRP3 inflammasome in macrophages. The channel is a member of the two-pore domain potassium (K2P) channel superfamily and an emerging therapeutic target to mitigate severe inflammatory injury involving NLRP3 activation. We report the cryo-EM structure of human TWIK-2. In comparison to other K2P channels, the structure reveals a unique 'up' conformation of Tyr111 in the selectivity filter and a SF1-P1 pocket behind the filter that could serve as a binding site for channel modulators. Density for acyl chains is present in fenestrations within the transmembrane region that connect the central cavity of the pore to the lipid membrane. Limited pharmacological tools are available for TWIK-2 despite its importance as a drug target. We show that the small molecule pimozide inhibits TWIK-2 and determine a structure of the channel with pimozide. Pimozide displaces the acyl chains and binds below the selectivity filter to block ion conduction. The drug may access its binding site via the membrane, suggesting that other hydrophobic small molecules could have utility for inhibiting TWIK-2. The work defines the structure of TWIK-2 and provides a structural foundation for development of specific inhibitors with potential utility as anti-inflammatory drugs. Significance Statement The TWIK-2 potassium channel is a member of the two-pore domain potassium (K2P) channel superfamily and a potential therapeutic target to control severe inflammatory injury involving the NLRP3 inflammasome. We report the cryo-EM structure of the human TWIK-2 channel at 2.85 Å resolution, revealing differences in comparison to other K2P channels. We identify that pimozide, an FDA-approved drug for Tourette syndrome, inhibits TWIK-2. A cryo-EM structure of TWIK-2 in complex with pimozide identifies its binding location and mechanism of inhibition. The work provides a structural foundation for development of specific TWIK-2 inhibitors that have potential therapeutic utility for inflammatory diseases involving NLRP3 activation.
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36
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Wang F, Singh S, Permaul K. Improving the hydrophilic microenvironment surrounding the catalytic site of fructosyltransferase enhances its catalytic ability. Biotechnol Lett 2025; 47:30. [PMID: 40011254 PMCID: PMC11865173 DOI: 10.1007/s10529-025-03566-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 12/26/2024] [Accepted: 01/10/2025] [Indexed: 02/28/2025]
Abstract
The hydrophilic microenvironment surrounding an enzyme's active site can influence its catalytic activity. This study examines the effect of enhancing this environment in the Aspergillus niger fructosyltransferase, SucC. Bioinformatics analysis identified a cysteine residue (C66) near the catalytic triad (D64, D194, E271) as vital for maintaining the active site's structure and facilitating substrate transport. Simulated mutagenesis suggested that mutating cysteine to serine (C66S) could increase hydrophilicity without altering the structure significantly. This mutation was predicted to enhance substrate affinity, with binding energy changing from -3.65 to -4.14 kcal mol-1. The C66S mutant, expressed in Pichia pastoris GS115, showed a 61.3% increase in specific activity, a 13.5% decrease in Km (82.20/71.14 mM), and a 21.6% increase in kcat (112.23/136.48 min-1), resulting in a 40.1% increase in catalytic efficiency (1.37/1.92 min-1 mM-1). For fructooligosaccharides (FOS) production, C66S demonstrated enhanced transfructosylation, particularly in the initial stages of the reaction, achieving higher overall FOS yields. These findings highlight that modifying the active site hydrophilicity, without causing major structural changes, is a promising strategy for improving an enzyme's catalytic efficiency.
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Affiliation(s)
- Fanzhi Wang
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, 4001, South Africa
| | - Suren Singh
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, 4001, South Africa
| | - Kugen Permaul
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, 4001, South Africa.
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37
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Chen N, Rao G, Tao L, Britt RD, Wang LP. HydE Catalytic Mechanism Is Powered by a Radical Relay with Redox-Active Fe(I)-Containing Intermediates. J Am Chem Soc 2025; 147:4800-4809. [PMID: 39884680 PMCID: PMC11826987 DOI: 10.1021/jacs.4c12668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 01/17/2025] [Accepted: 01/17/2025] [Indexed: 02/01/2025]
Abstract
[FeFe]-hydrogenases are enzymes that catalyze the redox interconversion of H+ and H2 using a six-iron active site, known as the H-cluster, which consists of a structurally unique [2Fe]H subcluster linked to a [4Fe-4S]H subcluster. A set of enzymes, HydG, HydE, and HydF, are responsible for the biosynthesis of the [2Fe]H subcluster. Among them, it is well established that HydG cleaves tyrosine into CO and CN- and forms a mononuclear [Fe(II)(Cys)(CO)2(CN)] complex. Recent work using EPR spectroscopy and X-ray crystallography show that HydE uses this organometallic Fe complex as its native substrate. The low spin Fe(II) center is reduced into an adenosylated Fe(I) species, which is proposed to form an Fe(I)Fe(I) dimer within HydE. The highly unusual transformation catalyzed by HydE draws interest in both biochemistry and organometallic chemistry. Due to the instability of the substrate, the intermediates, and the proposed product, experimental characterization of the detailed HydE mechanism and its final product is challenging. Herein, the catalytic mechanism of HydE is studied using hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. A radical relay mechanism was found for the cleavage of the cysteine S-Cβ bond that is energetically favored with respect to a closed-shell mechanism involving unconventional proton transfer. In addition, we propose a pathway for the dimerization of two Fe(I) complexes within the HydE hydrophobic cavity, which is consistent with the recent experimental result that HydF can perform [FeFe]-hydrogenase maturation with a synthetic dimer complex as the substrate. These simulation results take us further down the path to a more complete understanding of these enzymes that synthesize one of Nature's most efficient energy conversion catalysts.
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Affiliation(s)
| | - Guodong Rao
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | | | - R. David Britt
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
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38
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Kennedy L, Sandhu JK, Harper ME, Cuperlovic-Culf M. A hybrid machine learning framework for functional annotation of mitochondrial glutathione transport and metabolism proteins in cancers. BMC Bioinformatics 2025; 26:48. [PMID: 39934670 PMCID: PMC11817629 DOI: 10.1186/s12859-025-06051-1] [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: 03/18/2024] [Accepted: 01/15/2025] [Indexed: 02/13/2025] Open
Abstract
BACKGROUND Alterations of metabolism, including changes in mitochondrial metabolism as well as glutathione (GSH) metabolism are a well appreciated hallmark of many cancers. Mitochondrial GSH (mGSH) transport is a poorly characterized aspect of GSH metabolism, which we investigate in the context of cancer. Existing functional annotation approaches from machine (ML) or deep learning (DL) models based only on protein sequences, were unable to annotate functions in biological contexts. RESULTS We develop a flexible ML framework for functional annotation from diverse feature data. This hybrid ML framework leverages cancer cell line multi-omics data and other biological knowledge data as features, to uncover potential genes involved in mGSH metabolism and membrane transport in cancers. This framework achieves strong performance across functional annotation tasks and several cell line and primary tumor cancer samples. For our application, classification models predict the known mGSH transporter SLC25A39 but not SLC25A40 as being highly probably related to mGSH metabolism in cancers. SLC25A10, SLC25A50, and orphan SLC25A24, SLC25A43 are predicted to be associated with mGSH metabolism in multiple biological contexts and structural analysis of these proteins reveal similarities in potential substrate binding regions to the binding residues of SLC25A39. CONCLUSION These findings have implications for a better understanding of cancer cell metabolism and novel therapeutic targets with respect to GSH metabolism through potential novel functional annotations of genes. The hybrid ML framework proposed here can be applied to other biological function classifications or multi-omics datasets to generate hypotheses in various biological contexts. Code and a tutorial for generating models and predictions in this framework are available at: https://github.com/lkenn012/mGSH_cancerClassifiers .
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Affiliation(s)
- Luke Kennedy
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Jagdeep K Sandhu
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Bldg M54, Ottawa, ON, K1A 0R6, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada.
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada.
| | - Miroslava Cuperlovic-Culf
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada.
- Digital Technologies Research Centre, National Research Council Canada, 1200 Montreal Road, Bldg M50, Ottawa, ON, K1A 0R6, Canada.
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Yoneda K, Kobayashi C, Araie H, Morita R, Harada R, Shigeta Y, Endo H, Maeda Y, Suzuki I. Characterization of Delta-7 Alkenone Desaturase in Haptophyte Gephyrocapsa huxleyi Through Heterologous Expression in Tisochrysis lutea. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2025; 27:44. [PMID: 39921736 PMCID: PMC11807052 DOI: 10.1007/s10126-025-10427-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 01/30/2025] [Indexed: 02/10/2025]
Abstract
The marine haptophyte Gephyrocapsa huxleyi is an ecologically and geochemically important phytoplankton due to its contribution to the global carbon cycle and its ability to biosynthesize certain alkenones. These alkenones are long-chain alkyl ketones with two to four trans-type double bonds. The genes encoding alkenone desaturase in G. huxleyi have not been experimentally characterized so far, partly due to the difficulty of inducing genetic transformation in G. huxleyi. Therefore, we introduced the putative alkenone delta-7 desaturase of G. huxleyi (designated "DesT") to the transformable and alkenone-producing haptophyte Tisochrysis lutea. We found two types of coding sequences for DesT, which are probably derived from the expression products of different alleles, and designated them "DesT-1" and "DesT-2." The ratio of C37:3 to C37:2 methyl alkenone in the DesT-1 transformant was significantly higher than that in the mock strain that expressed only the hygromycin resistance gene, suggesting that DesT-1 was an alkenone delta-7 desaturase in G. huxleyi. In the protein structure, a tunnel where a substrate alkenone penetrates was predicted to be located around the histidine box of DesT, and hydrophilic and hydrophobic amino acids were respectively located at the proximal (near side to the histidine box) and distal ends of the tunnel. This is the first study to conduct experimental characterization of the alkenone metabolism-related gene in G. huxleyi. The heterologous expression system using T. lutea paves the way for further characterization of the alkenone metabolism-related genes in less transformable haptophytes.
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Affiliation(s)
- Kohei Yoneda
- Institute of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Chinatsu Kobayashi
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroya Araie
- Department of Biosciences, College of Science and Technology, Kanto Gakuin University, Mutsuura-Higashi, Kanazawa-Ku, Yokohama, Kanagawa, 236-8501, Japan
| | - Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Hirotoshi Endo
- National Institute of Technology, Tsuruoka College, 104 Sawada, Inooka, Tsuruoka, Yamagata, 997-8511, Japan
| | - Yoshiaki Maeda
- Institute of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Iwane Suzuki
- Institute of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
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40
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Cai Y, Horn PJ. Packaging "vegetable oils": Insights into plant lipid droplet proteins. PLANT PHYSIOLOGY 2025; 197:kiae533. [PMID: 39566075 DOI: 10.1093/plphys/kiae533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 09/06/2024] [Indexed: 11/22/2024]
Abstract
Plant neutral lipids, also known as "vegetable oils", are synthesized within the endoplasmic reticulum (ER) membrane and packaged into subcellular compartments called lipid droplets (LDs) for stable storage in the cytoplasm. The biogenesis, modulation, and degradation of cytoplasmic LDs in plant cells are orchestrated by a variety of proteins localized to the ER, LDs, and peroxisomes. Recent studies of these LD-related proteins have greatly advanced our understanding of LDs not only as steady oil depots in seeds but also as dynamic cell organelles involved in numerous physiological processes in different tissues and developmental stages of plants. In the past 2 decades, technology advances in proteomics, transcriptomics, genome sequencing, cellular imaging and protein structural modeling have markedly expanded the inventory of LD-related proteins, provided unprecedented structural and functional insights into the protein machinery modulating LDs in plant cells, and shed new light on the functions of LDs in nonseed plant tissues as well as in unicellular algae. Here, we review critical advances in revealing new LD proteins in various plant tissues, point out structural and mechanistic insights into key proteins in LD biogenesis and dynamic modulation, and discuss future perspectives on bridging our knowledge gaps in plant LD biology.
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Affiliation(s)
- Yingqi Cai
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Patrick J Horn
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
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41
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Cheng L, Bo Z, Krohn-Hansen B, Yang Y. Directed Evolution and Unusual Protonation Mechanism of Pyridoxal Radical C-C Coupling Enzymes for the Enantiodivergent Photobiocatalytic Synthesis of Noncanonical Amino Acids. J Am Chem Soc 2025; 147:4602-4612. [PMID: 39849356 DOI: 10.1021/jacs.4c16716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2025]
Abstract
Visible light-driven pyridoxal radical biocatalysis has emerged as a new strategy for the stereoselective synthesis of valuable noncanonical amino acids in a protecting-group-free fashion. In our previously developed dehydroxylative C-C coupling using engineered PLP-dependent tryptophan synthases, an enzyme-controlled unusual α-stereochemistry reversal and pH-controlled enantiopreference were observed. Herein, through high-throughput photobiocatalysis, we evolved a set of stereochemically complementary PLP radical enzymes, allowing the synthesis of both l- and d-amino acids with enhanced enantiocontrol across a broad pH window. These newly engineered l- and d-amino acid synthases permitted the use of a broad range of organoboron substrates, including boronates, trifluoroborates, and boronic acids, with excellent efficiency. Mechanistic studies unveiled unexpected PLP racemase activity with our earlier PLP enzyme variants. This promiscuous racemase activity was abolished in our evolved amino acid synthases, shedding light on the origin of enhanced enantiocontrol. Further mechanistic investigations suggest a switch of proton donor to account for the stereoinvertive formation of d-amino acids, highlighting an unusual stereoinversion mechanism that is rare in conventional two-electron PLP enzymology.
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Affiliation(s)
- Lei Cheng
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Zhiyu Bo
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Benjamin Krohn-Hansen
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, California 93106, United States
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42
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Buarque FS, Ribeiro BD, Freire MG, Coelho MAZ, Pereira MM. Assessing the role of deep eutectic solvents in Yarrowia lipolytica inhibition. J Biotechnol 2025; 398:1-10. [PMID: 39615790 DOI: 10.1016/j.jbiotec.2024.11.016] [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: 07/26/2024] [Revised: 11/14/2024] [Accepted: 11/25/2024] [Indexed: 01/27/2025]
Abstract
Yarrowia lipolytica has gained recognition as a microorganism with biological relevance and extensive biotechnological applications. Some of its features include a high enzyme secretion capacity and a high cell-density fermentation mode. Hexokinase (YlHxk) is a vital enzyme in Y. lipolytica growth since it catalyzes glucose metabolism through phosphorylation in the glycolytic pathway. Given the potential application of deep eutectic solvents (DES) as novel solvents in biotechnological processes, this study evaluated the influence of eighteen DES on the growth of Y. lipolytica. Furthermore, this work examined the effects of individual ions on the YlHxk enzyme by analyzing its enzymatic tunnel structure, molecule transport, and molecular docking. The results revealed a significant reduction in yeast growth in the presence of most DES compared to the control (medium without DES), with the exception of the [N8881]Cl: hexanoic acid (1:1) DES. The growth varied between 11.95 ± 0.60 and 0.68 ± 0.17 g dry cell weight L-1. According to the enzymatic tunnel analysis, DES components associated with the lowest microbial growth values were transported through tunnel 1. On the other hand, DES components had their pathway facilitated through tunnel 2 ([N8881]+ and hexanoic acid) and showed growth values close to the control. Molecular docking analysis identified a similarity between all the ligands in this tunnel (including substrate and product), presenting binding interactions with the ASN273 amino acid of the YlHxk active site. Combining experimental results with computational tools provided promising insights at the molecular level, while also potentially reducing analysis costs and time, paving the way for similar approaches in broad biocatalytic reactions.
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Affiliation(s)
- Filipe S Buarque
- Biochemical Engineering Department, School of Chemistry, Federal University of Rio de Janeiro, Brazil; CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Portugal.
| | - Bernardo D Ribeiro
- Biochemical Engineering Department, School of Chemistry, Federal University of Rio de Janeiro, Brazil
| | - Mara G Freire
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Portugal
| | - Maria A Z Coelho
- Biochemical Engineering Department, School of Chemistry, Federal University of Rio de Janeiro, Brazil
| | - Matheus M Pereira
- University of Coimbra, CERES, Department of Chemical Engineering, Rua Sílvio Lima, Pólo II - Pinhal de Marrocos, Coimbra 3030-790, Portugal.
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Horstmeier HJ, Bork S, Nagel MF, Keller W, Sproß J, Diepold N, Ruppel M, Kottke T, Niemann HH. The NADH-dependent flavin reductase ThdF follows an ordered sequential mechanism though crystal structures reveal two FAD molecules in the active site. J Biol Chem 2025; 301:108128. [PMID: 39725031 PMCID: PMC11795597 DOI: 10.1016/j.jbc.2024.108128] [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: 07/27/2024] [Revised: 12/12/2024] [Accepted: 12/18/2024] [Indexed: 12/28/2024] Open
Abstract
Two-component flavin-dependent monooxygenases are of great interest as biocatalysts for the production of pharmaceuticals and other relevant molecules, as they catalyze chemically important reactions such as hydroxylation, epoxidation, and halogenation. The monooxygenase components require a separate flavin reductase which provides the necessary reduced flavin cofactor. The tryptophan halogenase Thal from Streptomyces albogriseolus is a well-characterized two-component flavin-dependent halogenase. Thal exhibits some limitations in terms of halogenation efficiency, also caused by unproductive enzyme-substrate complexes with reduced flavin adenine dinucleotide (FAD). Since the reductase components have an important regulatory function for the activity and efficiency of the monooxygenase by controlling the supply of reduced flavin, here, we studied the so far uncharacterized flavin reductase ThdF from the same gene cluster in S. albogriseolus, which potentially cooperates with Thal. A crystal structure of ThdF in complex with both substrates, FAD and NADH, revealed their orientation for hydride transfer. We obtained two further ThdF structures with two FAD molecules bound to the active site, suggesting a ping-pong bi-bi mechanism. In contrast, steady-state enzyme kinetics clearly showed that ThdF catalyzes flavin reduction via an ordered sequential mechanism, with FAD being bound first and FADH2 released last. Compared to related flavin reductases, ThdF has a low kcat and low KM value. The inhibition of ThdF by NAD+ might limit Thal's halogenation activity when the cellular NADH level is low. These results provide first insights into how the efficiency of Thal could be controlled by flavin reduction at the reductase ThdF.
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Affiliation(s)
- Hendrik J Horstmeier
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Simon Bork
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Marius F Nagel
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Willy Keller
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Jens Sproß
- Industrial Organic Chemistry and Biotechnology - Mass Spectrometry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Niklas Diepold
- Biophysical Chemistry and Diagnostics, Department of Chemistry, Bielefeld University, Bielefeld, Germany; Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Marie Ruppel
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Biophysical Chemistry and Diagnostics, Department of Chemistry, Bielefeld University, Bielefeld, Germany; Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Hartmut H Niemann
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany.
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Sohraby F, Guo JY, Nunes-Alves A. PathInHydro, a Set of Machine Learning Models to Identify Unbinding Pathways of Gas Molecules in [NiFe] Hydrogenases. J Chem Inf Model 2025; 65:589-602. [PMID: 39764769 PMCID: PMC11776054 DOI: 10.1021/acs.jcim.4c01656] [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] [Received: 09/11/2024] [Revised: 12/13/2024] [Accepted: 12/20/2024] [Indexed: 01/28/2025]
Abstract
Machine learning (ML) is a powerful tool for the automated data analysis of molecular dynamics (MD) simulations. Recent studies showed that ML models can be used to identify protein-ligand unbinding pathways and understand the underlying mechanism. To expedite the examination of MD simulations, we constructed PathInHydro, a set of supervised ML models capable of automatically assigning unbinding pathways for the dissociation of gas molecules from [NiFe] hydrogenases, using the unbinding trajectories of CO and H2 fromDesulfovibrio fructosovorans [NiFe] hydrogenase as a training set. [NiFe] hydrogenases are receiving increasing attention in biotechnology due to their high efficiency in the generation of H2, which is considered by many to be the fuel of the future. However, some of these enzymes are sensitive to O2 and CO. Many efforts have been made to rectify this problem and generate air-stable enzymes by introducing mutations that selectively regulate the access of specific gas molecules to the catalytic site. Herein, we showcase the performance of PathInHydro for the identification of unbinding paths in different test sets, including another gas molecule and a different [NiFe] hydrogenase, which demonstrates its feasibility for the trajectory analysis of a diversity of gas molecules along enzymes with mutations and sequence differences. PathInHydro allows the user to skip time-consuming manual analysis and visual inspection, facilitating data analysis for MD simulations of ligand unbinding from [NiFe] hydrogenases. The codes and data sets are available online: https://github.com/FarzinSohraby/PathInHydro.
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Affiliation(s)
- Farzin Sohraby
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, Berlin 10623, Germany
| | - Jing-Yao Guo
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, Berlin 10623, Germany
| | - Ariane Nunes-Alves
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, Berlin 10623, Germany
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45
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De Sciscio ML, Centola F, Saporiti S, D'Abramo M. Dissecting Methionine Oxidation by Hydrogen Peroxide in Proteins: Thermodynamics, Kinetics, and Susceptibility Descriptors. J Chem Inf Model 2025; 65:749-761. [PMID: 39763136 DOI: 10.1021/acs.jcim.4c01617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
The oxidation of Met residues in proteins is a complex process, where protein-specific structural and dynamical features play a relevant role in determining the reaction kinetics. Aiming to a full-side perspective, we report here a comprehensive characterization of Met oxidation kinetics by hydrogen peroxide in a leptin protein case study. To do that, we estimated the reaction-free energy profile of the Met oxidation via a QM/MM approach, while the kinetics of the formation of the reactive species were calculated using classical molecular dynamics (MD) simulations. Our data, validated against the available experimental data on the Met oxidation in this protein, indicated that the protein's local and global motion represent the primary discriminating factor among residues' oxidation rates. Moreover, assuming that the free energy profile is independent of the specific protein system, the different reactivities of Met residues within five proteins (hGCSF, IL-1ra, leptin, somatotropin, and RNase) were qualitatively analyzed in terms of well-known structural/dynamic features, which can affect the kinetics of the whole process. The comprehensive analysis of the reaction thermodynamics and kinetics fingerprint enabled the identification of additional descriptors, helpful in assessing the susceptibility of protein-bound Met residues to oxidation.
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Affiliation(s)
- Maria Laura De Sciscio
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Fabio Centola
- Analytical Excellence and Program Management, Merck Serono S.p.A., 00012 Rome, Italy
| | - Simona Saporiti
- Analytical Excellence and Program Management, Merck Serono S.p.A., 00012 Rome, Italy
| | - Marco D'Abramo
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
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46
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Wang J, Ouyang X, Meng S, Li J, Liu L, Li C, Li H, Zheng H, Liao C, Zhao YL, Ni J. Semi-rational design of an aromatic dioxygenase by substrate tunnel redirection. iScience 2025; 28:111570. [PMID: 39811656 PMCID: PMC11731282 DOI: 10.1016/j.isci.2024.111570] [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: 10/09/2024] [Revised: 11/08/2024] [Accepted: 12/06/2024] [Indexed: 01/16/2025] Open
Abstract
Lignin valorization is crucial for achieving economic and sustainable biorefinery processes. However, the enzyme substrate preferences involved in lignin degradation remain poorly understood, and low activity toward specific substrates presents a significant challenge to the efficient utilization of lignin. In this study, we investigated the substrate promiscuity of ThAdo, a key enzyme involved in lignin valorization. Pre-reaction state analysis revealed that a hydrogen bond network is critical in determining substrate selectivity. By performing targeted saturation mutagenesis on residues surrounding the substrate tunnels, we identified the Y205W and Y205Q mutants, which demonstrated 0.73-fold and 0.72-fold enhancements in activity, respectively. Structural analysis indicated that the redirection of the original substrate tunnel may be responsible for the improved activity. Our study provides essential insights into the substrate preference mechanisms of lignin degrading enzymes and suggests that this tunnel-redirection strategy can be extended to other promiscuous enzymes.
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Affiliation(s)
- Jiawei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xingyu Ouyang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiyu Meng
- Innovation Center for Synthetic Biotechnology, Lumy Biotechnology, Changzhou 213200, Jiangsu, China
| | - Jiayi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liangxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chaofeng Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hengrun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haotian Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao Liao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- Innovation Center for Synthetic Biotechnology, Lumy Biotechnology, Changzhou 213200, Jiangsu, China
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He Q, Zhang R, Tury S, Courgnaud V, Liu F, Battini JL, Li B, Chen Q. Structural basis of phosphate export by human XPR1. Nat Commun 2025; 16:683. [PMID: 39814721 PMCID: PMC11736019 DOI: 10.1038/s41467-025-55995-8] [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: 08/01/2024] [Accepted: 01/07/2025] [Indexed: 01/18/2025] Open
Abstract
Phosphorus in crucial for all living organisms. In vertebrate, cellular phosphate homeostasis is partly controlled by XPR1, a poorly characterized inositol pyrophosphate-dependent phosphate exporter. Here, we report the cryo-EM structure of human XPR1, which forms a loose dimer with 10 transmembrane helices (TM) in each protomer. The structure consists of a scaffold domain (TM1, TM3-4) and a core domain (TM2, TM5-10) structurally related to ion-translocating rhodopsins. Bound phosphate is observed in a tunnel within the core domain at a narrow point that separates the tunnel into intracellular and extracellular vestibules. This site contains a cluster of basic residues that coordinate phosphate and a conserved W573 essential for export function. Loss of inositol pyrophosphate binding is accompanied by structural movements in TM9 and the W573 sidechain, closing the extracellular vestibule and blocking phosphate export. These findings provide insight into XPR1 mechanism and pave the way for further in-depth XPR1 studies.
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Affiliation(s)
- Qixian He
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Ran Zhang
- Department of Anesthesiology, Zhongshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Sandrine Tury
- Institut de Recherche en Infectiologie de Montpellier IRIM - CNRS UMR 9004, Université Montpellier, Montpellier, France
| | - Valérie Courgnaud
- Institut de Génétique Moléculaire de Montpellier IGMM - CNRS UMR 5535, Université Montpellier, Montpellier, France
| | - Fenglian Liu
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Jean-Luc Battini
- Institut de Recherche en Infectiologie de Montpellier IRIM - CNRS UMR 9004, Université Montpellier, Montpellier, France.
| | - Baobin Li
- Department of Anesthesiology, Zhongshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
| | - Qingfeng Chen
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China.
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48
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Thirunavukarasu A, Szleper K, Tanriver G, Marchlewski I, Mitusinska K, Gora A, Brezovsky J. Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model. J Chem Inf Model 2025; 65:326-337. [PMID: 39680044 PMCID: PMC11733929 DOI: 10.1021/acs.jcim.4c01177] [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] [Received: 07/04/2024] [Revised: 10/31/2024] [Accepted: 11/26/2024] [Indexed: 12/17/2024]
Abstract
The utilization of tunnels and water transport within enzymes is crucial for their catalytic function as water molecules can stabilize bound substrates and help with unbinding processes of products and inhibitors. Since the choice of water models for molecular dynamics simulations was shown to determine the accuracy of various calculated properties of the bulk solvent and solvated proteins, we have investigated if and to what extent water transport through the enzyme tunnels depends on the selection of the water model. Here, we focused on simulating enzymes with various well-defined tunnel geometries. In a systematic investigation using haloalkane dehalogenase as a model system, we focused on the well-established TIP3P, OPC, and TIP4P-Ew water models to explore their impact on the use of tunnels for water molecule transport. The TIP3P water model showed significantly faster migration, resulting in the transport of approximately 2.5 times more water molecules compared to that of the OPC and 1.7 times greater than that of the TIP4P-Ew. Finally, the transport was 1.4-fold more pronounced in TIP4P-Ew than in OPC. The increase in migration of TIP3P water molecules was mainly due to faster transit times through dehalogenase tunnels. We observed similar behavior in two different enzymes with buried active sites and different tunnel network topologies, i.e., alditol oxidase and cytochrome P450, indicating that our findings are likely not restricted to a particular enzyme family. Overall, this study showcases the critical importance of water models in comprehending the use of enzyme tunnels for small molecule transport. Given the significant role of water availability in various stages of the catalytic cycle and the solvation of substrates, products, and drugs, choosing an appropriate water model may be crucial for accurate simulations of complex enzymatic reactions, rational enzyme design, and predicting drug residence times.
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Affiliation(s)
- Aravind
Selvaram Thirunavukarasu
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
- International
Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Katarzyna Szleper
- Tunneling
Group, Biotechnology Centre, Silesian University
of Technology, 44-100 Gliwice, Poland
| | - Gamze Tanriver
- Tunneling
Group, Biotechnology Centre, Silesian University
of Technology, 44-100 Gliwice, Poland
| | - Igor Marchlewski
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Karolina Mitusinska
- Tunneling
Group, Biotechnology Centre, Silesian University
of Technology, 44-100 Gliwice, Poland
| | - Artur Gora
- Tunneling
Group, Biotechnology Centre, Silesian University
of Technology, 44-100 Gliwice, Poland
| | - Jan Brezovsky
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
- International
Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
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49
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Yoshimura M, Arai M. Product release and substrate entry of aldehyde deformylating oxygenase revealed by molecular dynamics simulations. Biophys Physicobiol 2025; 22:e220003. [PMID: 40046558 PMCID: PMC11876802 DOI: 10.2142/biophysico.bppb-v22.0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Accepted: 12/27/2024] [Indexed: 04/29/2025] Open
Abstract
Cyanobacteria can produce alkanes equivalent to diesel fuels through a two-step enzymatic process involving acyl-(acyl carrier protein) reductase (AAR) and aldehyde deformylating oxygenase (ADO), providing a potential renewable biofuel source. AAR binds to ADO for efficient delivery of an aldehyde substrate and they have been proposed to dissociate when the alkane product is released from the same site as the substrate entrance of ADO. However, the dynamics of the substrate and product in ADO during substrate entry and product release are poorly understood. Here, we performed molecular dynamics (MD) simulations of ADO in the presence of substrate or product. We found that while the aldehyde substrate remains close to the active center of ADO before catalysis, the alkane product can dynamically rotate within the hydrophobic tunnel inside ADO toward the product exit after catalysis. Furthermore, the parallel cascade selection (PaCS)-MD simulations of ADO and the AAR/ADO complex identified the locations of the substrate entrance and the multiple exits for product release on ADO. Strikingly, the PaCS-MD simulations revealed that the alkane product can be released from the exit different from the substrate entrance without dissociation of AAR. Based on these results, we propose a reaction model for efficient alkane production by the AAR/ADO complex in which aldehydes and alkanes are synthesized simultaneously while AAR and ADO remain bound, and the aldehyde substrate can be delivered to ADO immediately after alkane release. Our study will be useful in improving the efficiency of bioalkane production using AAR and ADO.
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Affiliation(s)
- Masataka Yoshimura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo 153-8902, Japan
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50
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Liu X, Gao S, Cheng A, Lou H. Characterization and functional analysis of type III polyketide synthases in Selaginella moellendorffii. PLANTA 2025; 261:28. [PMID: 39786623 DOI: 10.1007/s00425-024-04602-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 12/26/2024] [Indexed: 01/30/2025]
Abstract
MAIN CONCLUSION The evolutionary conservation of type III polyketide synthases (PKS) in Selaginella has been elucidated, and the critical amino acid residues of the anther-specific chalcone synthase-like enzyme (SmASCL) have been identified. Selaginella species are the oldest known vascular plants and a valuable resource for the study of metabolic evolution in land plants. Polyketides, especially flavonoids and sporopollenin precursors, are essential prerequisites for plant land colonization. Although type III polyketide synthases (PKS) are widely studied in seed plants, the related enzymes in Selaginella remain poorly characterized. Here, eight type III PKSs were identified in the Selaginella moellendorffii genome and classified into three clusters. Two PKSs were selected for further research based on their phylogenetic relationships and protein sequence similarity. Functional studies revealed that they were chalcone synthase (SmCHS) and anther-specific CHS-like enzyme (SmASCL). These enzymes are involved in the biosynthesis of flavonoids and sporopollenin, respectively. Their sequence information and enzymatic activity are similar to the orthologs in other plants. Phylogenetic analysis revealed that the ASCL and CHS enzymes were separated into two clades from the Bryophyta. These results suggest that CHS and ASCL emerged in the first land plants and then remained conserved during plant evolution. To study the structural basis of the enzymatic function of SmASCL, a series of mutants were constructed. The number of condensation reactions catalyzed by the P210L/Y211D and I200V/G201T double mutants exceeds that of the wild-type enzyme. Our study provides insight into the characteristics and functions of type III PKSs in S. moellendorffii. It also offers clues for a deeper understanding of the relationship between active sites and the enzymatic function of ASCLs.
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Affiliation(s)
- Xinyan Liu
- Department of Pharmacy, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, Shandong, China
| | - Shuai Gao
- Department of Pharmacy, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, Shandong, China
| | - Aixia Cheng
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, Shandong, China.
| | - Hongxiang Lou
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Jinan, 250012, Shandong, China.
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