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For: Chovancova E, Pavelka A, Benes P, Strnad O, Brezovsky J, Kozlikova B, Gora A, Sustr V, Klvana M, Medek P, Biedermannova L, Sochor J, Damborsky J. CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comput Biol 2012;8:e1002708. [PMID: 23093919 DOI: 10.1371/journal.pcbi.1002708] [Citation(s) in RCA: 938] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 08/01/2012] [Indexed: 11/19/2022]  Open
Number Cited by Other Article(s)
1
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]
2
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
3
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]
4
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]
5
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
6
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
7
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]
8
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
9
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]
10
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]
11
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
12
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]
13
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]
14
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]
15
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
16
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]
17
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]
18
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]
19
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]
20
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-HT3A 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]
21
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]
22
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]
23
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]
24
Muñoz-Vargas MA, López-Jaramillo J, González-Gordo S, Taboada J, Palma JM, Corpas FJ. Peroxisomal H2O2-generating sulfite oxidase (SOX) from pepper fruits is negatively modulated by NO and H2S. 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]
25
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]
26
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]
27
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]
28
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]
29
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]
30
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]
31
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]
32
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
33
Scocozza MF, Zitare UA, Cancian P, Castro MA, Martins LO, Murgida DH. Molecular basis of H2O2/O2.-/.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]
34
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]
35
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]
36
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]
37
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]
38
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
39
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]
40
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]
41
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]
42
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]
43
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
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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]
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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]
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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
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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
48
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]
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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
50
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]
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