1ll8 Citations

Structure and interactions of PAS kinase N-terminal PAS domain: model for intramolecular kinase regulation.

Structure 10 1349-61 (2002)
Cited: 97 times
EuropePMC logo PMID: 12377121

Abstract

PAS domains are sensory modules in signal-transducing proteins that control responses to various environmental stimuli. To examine how those domains can regulate a eukaryotic kinase, we have studied the structure and binding interactions of the N-terminal PAS domain of human PAS kinase using solution NMR methods. While this domain adopts a characteristic PAS fold, two regions are unusually flexible in solution. One of these serves as a portal that allows small organic compounds to enter into the core of the domain, while the other binds and inhibits the kinase domain within the same protein. Structural and functional analyses of point mutants demonstrate that the compound and ligand binding regions are linked, suggesting that the PAS domain serves as a ligand-regulated switch for this eukaryotic signaling system.

Reviews - 1ll8 mentioned but not cited (1)

  1. Structure and signaling mechanism of Per-ARNT-Sim domains. Möglich A, Ayers RA, Moffat K. Structure 17 1282-1294 (2009)

Articles - 1ll8 mentioned but not cited (7)

  1. Structural basis for PAS domain heterodimerization in the basic helix--loop--helix-PAS transcription factor hypoxia-inducible factor. Erbel PJ, Card PB, Karakuzu O, Bruick RK, Gardner KH. Proc Natl Acad Sci U S A 100 15504-15509 (2003)
  2. Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis. Pandini A, Denison MS, Song Y, Soshilov AA, Bonati L. Biochemistry 46 696-708 (2007)
  3. Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR. Szöllősi D, Erdei Á, Gyimesi G, Magyar C, Hegedűs T. PLoS One 11 e0146066 (2016)
  4. Origin and functional diversification of PAS domain, a ubiquitous intracellular sensor. Xing J, Gumerov VM, Zhulin IB. Sci Adv 9 eadi4517 (2023)
  5. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. F1000Res 2 286 (2013)
  6. research-article Signal-regulated unmasking of the nuclear localization motif in the PAS domain regulates the nuclear translocation of PASK. Xiao M, Dhungel S, Azad R, Favaro DC, Rajesh RP, Gardner KH, Kikani CK. bioRxiv 2023.09.06.556462 (2023)
  7. Two-Component System Sensor Kinases from Asgardian Archaea May Be Witnesses to Eukaryotic Cell Evolution. Padilla-Vaca F, de la Mora J, García-Contreras R, Ramírez-Prado JH, Alva-Murillo N, Fonseca-Yepez S, Serna-Gutiérrez I, Moreno-Galván CL, Montufar-Rodríguez JM, Vicente-Gómez M, Rangel-Serrano Á, Vargas-Maya NI, Franco B. Molecules 28 5042 (2023)


Reviews citing this publication (23)

  1. Phototropin blue-light receptors. Christie JM. Annu Rev Plant Biol 58 21-45 (2007)
  2. The mammalian basic helix-loop-helix/PAS family of transcriptional regulators. Kewley RJ, Whitelaw ML, Chapman-Smith A. Int J Biochem Cell Biol 36 189-204 (2004)
  3. Ligand-binding PAS domains in a genomic, cellular, and structural context. Henry JT, Crosson S. Annu Rev Microbiol 65 261-286 (2011)
  4. Glucolipotoxicity of the pancreatic beta cell. Poitout V, Amyot J, Semache M, Zarrouki B, Hagman D, Fontés G. Biochim Biophys Acta 1801 289-298 (2010)
  5. Regulation of glycogen metabolism in yeast and bacteria. Wilson WA, Roach PJ, Montero M, Baroja-Fernández E, Muñoz FJ, Eydallin G, Viale AM, Pozueta-Romero J. FEMS Microbiol Rev 34 952-985 (2010)
  6. Nutrient sensing and metabolic decisions. Lindsley JE, Rutter J. Comp Biochem Physiol B Biochem Mol Biol 139 543-559 (2004)
  7. Nutrient-regulated protein kinases in budding yeast. Wilson WA, Roach PJ. Cell 111 155-158 (2002)
  8. Emerging models for the molecular basis of mammalian circadian timing. Gustafson CL, Partch CL. Biochemistry 54 134-149 (2015)
  9. Coactivator recruitment: a new role for PAS domains in transcriptional regulation by the bHLH-PAS family. Partch CL, Gardner KH. J Cell Physiol 223 553-557 (2010)
  10. Evolutionary connections between bacterial and eukaryotic signaling systems: a genomic perspective. Aravind L, Anantharaman V, Iyer LM. Curr Opin Microbiol 6 490-497 (2003)
  11. Hypoxia Sensing in Plants: On a Quest for Ion Channels as Putative Oxygen Sensors. Wang F, Chen ZH, Shabala S. Plant Cell Physiol 58 1126-1142 (2017)
  12. The hypoxic testis and post-meiotic expression of PAS domain proteins. Wenger RH, Katschinski DM. Semin Cell Dev Biol 16 547-553 (2005)
  13. Genome-wide comparative analyses of domain organisation of repertoires of protein kinases of Arabidopsis thaliana and Oryza sativa. Krupa A, Anamika, Srinivasan N. Gene 380 1-13 (2006)
  14. The role of PAS kinase in regulating energy metabolism. Hao HX, Rutter J. IUBMB Life 60 204-209 (2008)
  15. Per-Arnt-Sim Kinase (PASK): An Emerging Regulator of Mammalian Glucose and Lipid Metabolism. Zhang DD, Zhang JG, Wang YZ, Liu Y, Liu GL, Li XY. Nutrients 7 7437-7450 (2015)
  16. Structural and thermodynamic consequences of b heme binding for monomeric apoglobins and other apoproteins. Landfried DA, Vuletich DA, Pond MP, Lecomte JT. Gene 398 12-28 (2007)
  17. PAS kinase: a nutrient sensing regulator of glucose homeostasis. DeMille D, Grose JH. IUBMB Life 65 921-929 (2013)
  18. The role of PAS kinase in PASsing the glucose signal. Grose JH, Rutter J. Sensors (Basel) 10 5668-5682 (2010)
  19. PAS kinase: integrating nutrient sensing with nutrient partitioning. Cardon CM, Rutter J. Semin Cell Dev Biol 23 626-630 (2012)
  20. Ser/Thr kinases and polyamines in the regulation of non-canonical functions of elongation factor 1A. Migliaccio N, Martucci NM, Ruggiero I, Sanges C, Ohkubo S, Lamberti A, Agostinelli E, Arcari P. Amino Acids 48 2339-2352 (2016)
  21. Preventing Oxidative Stress in the Liver: An Opportunity for GLP-1 and/or PASK. Hurtado-Carneiro V, Dongil P, Pérez-García A, Álvarez E, Sanz C. Antioxidants (Basel) 10 2028 (2021)
  22. Structural biology: a high-tech tool for biomedical research. Machius M. Curr Opin Nephrol Hypertens 12 431-438 (2003)
  23. Metabolic "Sense Relay" in Stem Cells: A Short But Impactful Life of PAS Kinase Balancing Stem Cell Fates. Kikani CK. Cells 12 1751 (2023)

Articles citing this publication (66)

  1. Allosteric inhibition of hypoxia inducible factor-2 with small molecules. Scheuermann TH, Li Q, Ma HW, Key J, Zhang L, Chen R, Garcia JA, Naidoo J, Longgood J, Frantz DE, Tambar UK, Gardner KH, Bruick RK. Nat Chem Biol 9 271-276 (2013)
  2. Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor. Scheuermann TH, Tomchick DR, Machius M, Guo Y, Bruick RK, Gardner KH. Proc Natl Acad Sci U S A 106 450-455 (2009)
  3. Identification of small-molecule antagonists that inhibit an activator: coactivator interaction. Best JL, Amezcua CA, Mayr B, Flechner L, Murawsky CM, Emerson B, Zor T, Gardner KH, Montminy M. Proc Natl Acad Sci U S A 101 17622-17627 (2004)
  4. Regulation of LuxPQ receptor activity by the quorum-sensing signal autoinducer-2. Neiditch MB, Federle MJ, Miller ST, Bassler BL, Hughson FM. Mol Cell 18 507-518 (2005)
  5. Syntenin-1 is a new component of tetraspanin-enriched microdomains: mechanisms and consequences of the interaction of syntenin-1 with CD63. Latysheva N, Muratov G, Rajesh S, Padgett M, Hotchin NA, Overduin M, Berditchevski F. Mol Cell Biol 26 7707-7718 (2006)
  6. Rim15 and the crossroads of nutrient signalling pathways in Saccharomyces cerevisiae. Swinnen E, Wanke V, Roosen J, Smets B, Dubouloz F, Pedruzzi I, Cameroni E, De Virgilio C, Winderickx J. Cell Div 1 3 (2006)
  7. The PAS fold. A redefinition of the PAS domain based upon structural prediction. Hefti MH, Françoijs KJ, de Vries SC, Dixon R, Vervoort J. Eur J Biochem 271 1198-1208 (2004)
  8. The structure of the periplasmic ligand-binding domain of the sensor kinase CitA reveals the first extracellular PAS domain. Reinelt S, Hofmann E, Gerharz T, Bott M, Madden DR. J Biol Chem 278 39189-39196 (2003)
  9. Coordinate regulation of sugar flux and translation by PAS kinase. Rutter J, Probst BL, McKnight SL. Cell 111 17-28 (2002)
  10. Crystal structure and interactions of the PAS repeat region of the Drosophila clock protein PERIOD. Yildiz O, Doi M, Yujnovsky I, Cardone L, Berndt A, Hennig S, Schulze S, Urbanke C, Sassone-Corsi P, Wolf E. Mol Cell 17 69-82 (2005)
  11. PAS-mediated dimerization of soluble guanylyl cyclase revealed by signal transduction histidine kinase domain crystal structure. Ma X, Sayed N, Baskaran P, Beuve A, van den Akker F. J Biol Chem 283 1167-1178 (2008)
  12. Principles of ligand binding within a completely buried cavity in HIF2alpha PAS-B. Key J, Scheuermann TH, Anderson PC, Daggett V, Gardner KH. J Am Chem Soc 131 17647-17654 (2009)
  13. Contribution of the Per/Arnt/Sim (PAS) domains to DNA binding by the basic helix-loop-helix PAS transcriptional regulators. Chapman-Smith A, Lutwyche JK, Whitelaw ML. J Biol Chem 279 5353-5362 (2004)
  14. PAS kinase is required for normal cellular energy balance. Hao HX, Cardon CM, Swiatek W, Cooksey RC, Smith TL, Wilde J, Boudina S, Abel ED, McClain DA, Rutter J. Proc Natl Acad Sci U S A 104 15466-15471 (2007)
  15. Structure of the NCoA-1/SRC-1 PAS-B domain bound to the LXXLL motif of the STAT6 transactivation domain. Razeto A, Ramakrishnan V, Litterst CM, Giller K, Griesinger C, Carlomagno T, Lakomek N, Heimburg T, Lodrini M, Pfitzner E, Becker S. J Mol Biol 336 319-329 (2004)
  16. Structure-function relationships in the HAMP and proximal signaling domains of the aerotaxis receptor Aer. Watts KJ, Johnson MS, Taylor BL. J Bacteriol 190 2118-2127 (2008)
  17. Involvement of Per-Arnt-Sim Kinase and extracellular-regulated kinases-1/2 in palmitate inhibition of insulin gene expression in pancreatic beta-cells. Fontés G, Semache M, Hagman DK, Tremblay C, Shah R, Rhodes CJ, Rutter J, Poitout V. Diabetes 58 2048-2058 (2009)
  18. New aryl hydrocarbon receptor homology model targeted to improve docking reliability. Motto I, Bordogna A, Soshilov AA, Denison MS, Bonati L. J Chem Inf Model 51 2868-2881 (2011)
  19. Molecular model of a soluble guanylyl cyclase fragment determined by small-angle X-ray scattering and chemical cross-linking. Fritz BG, Roberts SA, Ahmed A, Breci L, Li W, Weichsel A, Brailey JL, Wysocki VH, Tama F, Montfort WR. Biochemistry 52 1568-1582 (2013)
  20. Targeted disruption of the mouse PAS domain serine/threonine kinase PASKIN. Katschinski DM, Marti HH, Wagner KF, Shibata J, Eckhardt K, Martin F, Depping R, Paasch U, Gassmann M, Ledermann B, Desbaillets I, Wenger RH. Mol Cell Biol 23 6780-6789 (2003)
  21. PAS kinase is activated by direct SNF1-dependent phosphorylation and mediates inhibition of TORC1 through the phosphorylation and activation of Pbp1. DeMille D, Badal BD, Evans JB, Mathis AD, Anderson JF, Grose JH. Mol Biol Cell 26 569-582 (2015)
  22. Structures and solution properties of two novel periplasmic sensor domains with c-type heme from chemotaxis proteins of Geobacter sulfurreducens: implications for signal transduction. Pokkuluri PR, Pessanha M, Londer YY, Wood SJ, Duke NE, Wilton R, Catarino T, Salgueiro CA, Schiffer M. J Mol Biol 377 1498-1517 (2008)
  23. The Drosophila juvenile hormone receptor candidates methoprene-tolerant (MET) and germ cell-expressed (GCE) utilize a conserved LIXXL motif to bind the FTZ-F1 nuclear receptor. Bernardo TJ, Dubrovsky EB. J Biol Chem 287 7821-7833 (2012)
  24. Identification of residues in the N-terminal PAS domains important for dimerization of Arnt and AhR. Hao N, Whitelaw ML, Shearwin KE, Dodd IB, Chapman-Smith A. Nucleic Acids Res 39 3695-3709 (2011)
  25. CED-9 and mitochondrial homeostasis in C. elegans muscle. Tan FJ, Husain M, Manlandro CM, Koppenol M, Fire AZ, Hill RB. J Cell Sci 121 3373-3382 (2008)
  26. Crystal structure of the Alpha subunit PAS domain from soluble guanylyl cyclase. Purohit R, Weichsel A, Montfort WR. Protein Sci 22 1439-1444 (2013)
  27. Regulating the ARNT/TACC3 axis: multiple approaches to manipulating protein/protein interactions with small molecules. Guo Y, Partch CL, Key J, Card PB, Pashkov V, Patel A, Bruick RK, Wurdak H, Gardner KH. ACS Chem Biol 8 626-635 (2013)
  28. Calbindin D28K interacts with Ran-binding protein M: identification of interacting domains by NMR spectroscopy. Lutz W, Frank EM, Craig TA, Thompson R, Venters RA, Kojetin D, Cavanagh J, Kumar R. Biochem Biophys Res Commun 303 1186-1192 (2003)
  29. Blue light regulated two-component systems: enzymatic and functional analyses of light-oxygen-voltage (LOV)-histidine kinases and downstream response regulators. Correa F, Ko WH, Ocasio V, Bogomolni RA, Gardner KH. Biochemistry 52 4656-4666 (2013)
  30. AlphaFold2 models indicate that protein sequence determines both structure and dynamics. Guo HB, Perminov A, Bekele S, Kedziora G, Farajollahi S, Varaljay V, Hinkle K, Molinero V, Meister K, Hung C, Dennis P, Kelley-Loughnane N, Berry R. Sci Rep 12 10696 (2022)
  31. Bypass suppression analysis maps the signalling pathway within a multidomain protein: the RsbP energy stress phosphatase 2C from Bacillus subtilis. Brody MS, Stewart V, Price CW. Mol Microbiol 72 1221-1234 (2009)
  32. CP-HISQC: a better version of HSQC experiment for intrinsically disordered proteins under physiological conditions. Yuwen T, Skrynnikov NR. J Biomol NMR 58 175-192 (2014)
  33. Structural bases of PAS domain-regulated kinase (PASK) activation in the absence of activation loop phosphorylation. Kikani CK, Antonysamy SA, Bonanno JB, Romero R, Zhang FF, Russell M, Gheyi T, Iizuka M, Emtage S, Sauder JM, Turk BE, Burley SK, Rutter J. J Biol Chem 285 41034-41043 (2010)
  34. Conservation and specialization in PAS domain dynamics. Pandini A, Bonati L. Protein Eng Des Sel 18 127-137 (2005)
  35. Crystal structure of a photoactive yellow protein from a sensor histidine kinase: conformational variability and signal transduction. Rajagopal S, Moffat K. Proc Natl Acad Sci U S A 100 1649-1654 (2003)
  36. Activation of PASK by mTORC1 is required for the onset of the terminal differentiation program. Kikani CK, Wu X, Fogarty S, Kang SAW, Dephoure N, Gygi SP, Sabatini DM, Rutter J. Proc Natl Acad Sci U S A 116 10382-10391 (2019)
  37. Spectroscopic and DNA-binding characterization of the isolated heme-bound basic helix-loop-helix-PAS-A domain of neuronal PAS protein 2 (NPAS2), a transcription activator protein associated with circadian rhythms. Mukaiyama Y, Uchida T, Sato E, Sasaki A, Sato Y, Igarashi J, Kurokawa H, Sagami I, Kitagawa T, Shimizu T. FEBS J 273 2528-2539 (2006)
  38. Human mutation within Per-Arnt-Sim (PAS) domain-containing protein kinase (PASK) causes basal insulin hypersecretion. Semplici F, Vaxillaire M, Fogarty S, Semache M, Bonnefond A, Fontés G, Philippe J, Meur G, Diraison F, Sessions RB, Rutter J, Poitout V, Froguel P, Rutter GA. J Biol Chem 286 44005-44014 (2011)
  39. Solution structure of the PAS domain of a thermophilic YybT protein homolog reveals a potential ligand-binding site. Tan E, Rao F, Pasunooti S, Pham TH, Soehano I, Turner MS, Liew CW, Lescar J, Pervushin K, Liang ZX. J Biol Chem 288 11949-11959 (2013)
  40. Avidity-driven polarity establishment via multivalent lipid-GTPase module interactions. Meca J, Massoni-Laporte A, Martinez D, Sartorel E, Loquet A, Habenstein B, McCusker D. EMBO J 38 e99652 (2019)
  41. Crosstalk between hydroxytyrosol, a major olive oil phenol, and HIF-1 in MCF-7 breast cancer cells. Calahorra J, Martínez-Lara E, Granadino-Roldán JM, Martí JM, Cañuelo A, Blanco S, Oliver FJ, Siles E. Sci Rep 10 6361 (2020)
  42. Glucose-stimulated insulin production in mice deficient for the PAS kinase PASKIN. Borter E, Niessen M, Zuellig R, Spinas GA, Spielmann P, Camenisch G, Wenger RH. Diabetes 56 113-117 (2007)
  43. Spectroscopic characterization of the isolated heme-bound PAS-B domain of neuronal PAS domain protein 2 associated with circadian rhythms. Koudo R, Kurokawa H, Sato E, Igarashi J, Uchida T, Sagami I, Kitagawa T, Shimizu T. FEBS J 272 4153-4162 (2005)
  44. Per-Arnt-Sim kinase regulates pancreatic duodenal homeobox-1 protein stability via phosphorylation of glycogen synthase kinase 3β in pancreatic β-cells. Semache M, Zarrouki B, Fontés G, Fogarty S, Kikani C, Chawki MB, Rutter J, Poitout V. J Biol Chem 288 24825-24833 (2013)
  45. Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms. Bonati L, Corrada D, Tagliabue SG, Motta S. Curr Opin Toxicol 2 42-49 (2017)
  46. UV filters induce transcriptional changes of different hormonal receptors in Chironomus riparius embryos and larvae. Ozáez I, Aquilino M, Morcillo G, Martínez-Guitarte JL. Environ Pollut 214 239-247 (2016)
  47. Responses of wheat seedlings to cadmium, mercury and trichlorobenzene stresses. Ge C, Ding Y, Wang Z, Wan D, Wang Y, Shang Q, Luo S. J Environ Sci (China) 21 806-813 (2009)
  48. Structure and activity of the peptidyl-prolyl isomerase domain from the histone chaperone Fpr4 toward histone H3 proline isomerization. Monneau YR, Soufari H, Nelson CJ, Mackereth CD. J Biol Chem 288 25826-25837 (2013)
  49. Acid destabilization of the solution conformation of Bcl-xL does not drive its pH-dependent insertion into membranes. Thuduppathy GR, Hill RB. Protein Sci 15 248-257 (2006)
  50. Regulation and function of yeast PAS kinase: a role in the maintenance of cellular integrity. Grose JH, Sundwall E, Rutter J. Cell Cycle 8 1824-1832 (2009)
  51. Substrate preference and phosphatidylinositol monophosphate inhibition of the catalytic domain of the Per-Arnt-Sim domain kinase PASKIN. Schläfli P, Tröger J, Eckhardt K, Borter E, Spielmann P, Wenger RH. FEBS J 278 1757-1768 (2011)
  52. Light-induced global structural changes in phytochrome A regulating photomorphogenesis in plants. Nakasako M, Iwata T, Inoue K, Tokutomi S. FEBS J 272 603-612 (2005)
  53. Evolution of PAS domains and PAS-containing genes in eukaryotes. Mei Q, Dvornyk V. Chromosoma 123 385-405 (2014)
  54. Primary processes during the light-signal transduction of phototropin. Matsuoka D, Iwata T, Zikihara K, Kandori H, Tokutomi S. Photochem Photobiol 83 122-130 (2007)
  55. Solution structure of the low-molecular-weight protein tyrosine phosphatase from Tritrichomonas foetus reveals a flexible phosphate binding loop. Gustafson CL, Stauffacher CV, Hallenga K, Van Etten RL. Protein Sci 14 2515-2525 (2005)
  56. Structure of a LOV protein in apo-state and implications for construction of LOV-based optical tools. Arinkin V, Granzin J, Röllen K, Krauss U, Jaeger KE, Willbold D, Batra-Safferling R. Sci Rep 7 42971 (2017)
  57. Exploring the multiscale signaling behavior of phototropin1 from Chlamydomonas reinhardtii using a full-residue space kinetic Monte Carlo molecular dynamics technique. Peter E, Dick B, Stambolic I, Baeurle SA. Proteins 82 2018-2040 (2014)
  58. Increased mobility in the membrane targeting PX domain induced by phosphatidylinositol 3-phosphate. Cheever ML, Kutateladze TG, Overduin M. Protein Sci 15 1873-1882 (2006)
  59. Validation of PAS Kinase, a Regulator of Hepatic Fatty Acid and Triglyceride Synthesis, as a Therapeutic Target for Nonalcoholic Steatohepatitis. Swiatek W, Parnell KM, Nickols GA, Scharschmidt BF, Rutter J. Hepatol Commun 4 696-707 (2020)
  60. Critical roles of Asp40 at the haem proximal side of haem-regulated phosphodiesterase from Escherichia coli in redox potential, auto-oxidation and catalytic control. Watanabe M, Kurokawa H, Yoshimura-Suzuki T, Sagami I, Shimizu T. Eur J Biochem 271 3937-3942 (2004)
  61. Screening for Non-Pore-Binding Modulators of EAG K+ Channels. Fernandes AS, Morais-Cabral JH, Harley CA. J Biomol Screen 21 758-765 (2016)
  62. Functional characterization of a StyS sensor kinase reveals distinct domains associated with intracellular and extracellular sensing of styrene in P. putida CA-3. O'Leary ND, Mooney A, O'Mahony M, Dobson AD. Bioengineered 5 114-122 (2014)
  63. Fragile protein folds: Sequence and environmental factors affecting the equilibrium of two interconverting, stably folded protein conformations. Xu X, Dikiy I, Evans MR, Marcelino LP, Gardner KH. Magn Reson (Gott) 2 63-76 (2021)
  64. PASsing a signal: low carbs, less protein. Getzoff ED. Chem Biol 9 1165-1166 (2002)
  65. A Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in Bioproduction. Swift CL, Malinov NG, Mondo SJ, Salamov A, Grigoriev IV, O'Malley MA. Front Fungal Biol 2 708358 (2021)
  66. Signal-regulated Unmasking of Nuclear Localization Motif in the PAS Domain Regulates the Nuclear Translocation of PASK. Xiao M, Dhungel S, Azad R, Favaro DC, Rajesh RP, Gardner KH, Kikani CK. J Mol Biol 436 168433 (2024)