Tag: Biophysical chemistry

  • Gingras, A. C., Raught, B. & Sonenberg, N. eIF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation. Annu. Rev. Biochem. 68, 913–963 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hinnebusch, A. G. & Lorsch, J. R. The mechanism of eukaryotic translation initiation: new insights and challenges. Cold Spring Harb. Perspect. Biol. 4, a011544 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Merrick, W. C. eIF4F: a retrospective. J. Biol. Chem. 290, 24091–24099 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Abramson, R. D. et al. The ATP-dependent interaction of eukaryotic initiation factors with mRNA. J. Biol. Chem. 262, 3826–3832 (1987).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kaye, N. M., Emmett, K. J., Merrick, W. C. & Jankowsky, E. Intrinsic RNA binding by the eukaryotic initiation factor 4F depends on a minimal RNA length but not on the m7G cap. J. Biol. Chem. 284, 17742–17750 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • von der Haar, T. & McCarthy, J. E. Intracellular translation initiation factor levels in Saccharomyces cerevisiae and their role in cap-complex function. Mol. Microbiol. 46, 531–544 (2002).

    Article 
    PubMed 

    Google Scholar
     

  • Martinez-Salas, E., Francisco-Velilla, R., Fernandez-Chamorro, J. & Embarek, A. M. Insights into structural and mechanistic features of viral IRES elements. Front. Microbiol. 8, 2629 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Jia, Y., Polunovsky, V., Bitterman, P. B. & Wagner, C. R. Cap-dependent translation initiation factor eIF4E: an emerging anticancer drug target. Med. Res. Rev. 32, 786–814 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Otero, L. J., Ashe, M. P. & Sachs, A. B. The yeast poly(A)-binding protein Pab1p stimulates in vitro poly(A)-dependent and cap-dependent translation by distinct mechanisms. EMBO J. 18, 3153–3163 (1999).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • He, H. et al. The yeast eukaryotic initiation factor 4G (eIF4G) HEAT domain interacts with eIF1 and eIF5 and is involved in stringent AUG selection. Mol. Cell. Biol. 23, 5431–5445 (2003).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yourik, P. et al. Yeast eIF4A enhances recruitment of mRNAs regardless of their structural complexity. eLife 6, e31476 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kumar, P., Hellen, C. U. & Pestova, T. V. Toward the mechanism of eIF4F-mediated ribosomal attachment to mammalian capped mRNAs. Genes Dev. 30, 1573–1588 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gruner, S. et al. The structures of eIF4E-eIF4G complexes reveal an extended interface to regulate translation initiation. Mol. Cell 64, 467–479 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Oberer, M., Marintchev, A. & Wagner, G. Structural basis for the enhancement of eIF4A helicase activity by eIF4G. Genes Dev. 19, 2212–2223 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rajagopal, V., Park, E. H., Hinnebusch, A. G. & Lorsch, J. R. Specific domains in yeast translation initiation factor eIF4G strongly bias RNA unwinding activity of the eIF4F complex toward duplexes with 5′-overhangs. J. Biol. Chem. 287, 20301–20312 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cetin, B. & O’Leary, S. E. mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation. Nucleic Acids Res. 50, 8240–8261 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • O’Sullivan, M. H. & Fraser, C. S. Monitoring RNA restructuring in a human cell-free extract reveals eIF4A-dependent and eIF4A-independent unwinding activity. J. Biol. Chem. 299, 104936 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lanker, S. et al. Interactions of the eIF-4F subunits in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 267, 21167–21171 (1992).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Feoktistova, K., Tuvshintogs, E., Do, A. & Fraser, C. S. Human eIF4E promotes mRNA restructuring by stimulating eIF4A helicase activity. Proc. Natl Acad. Sci. USA 110, 13339–13344 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cetin, B., Song, G. J. & O’Leary, S. E. Heterogeneous dynamics of protein-RNA interactions across transcriptome-derived messenger RNA populations. J. Am. Chem. Soc. 142, 21249–21253 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sokabe, M. & Fraser, C. S. A helicase-independent activity of eIF4A in promoting mRNA recruitment to the human ribosome. Proc. Natl Acad. Sci. USA 114, 6304–6309 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sen, N. D., Zhou, F., Ingolia, N. T. & Hinnebusch, A. G. Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A. Genome Res. 25, 1196–1205 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Harms, U., Andreou, A. Z., Gubaev, A. & Klostermeier, D. eIF4B, eIF4G and RNA regulate eIF4A activity in translation initiation by modulating the eIF4A conformational cycle. Nucleic Acids Res. 42, 7911–7922 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Andreou, A. Z. & Klostermeier, D. eIF4B and eIF4G jointly stimulate eIF4A ATPase and unwinding activities by modulation of the eIF4A conformational cycle. J. Mol. Biol. 426, 51–61 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • O’Leary, S. E., Petrov, A., Chen, J. & Puglisi, J. D. Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E. Structure 21, 2197–2207 (2013).

    Article 
    PubMed 

    Google Scholar
     

  • Krause, L., Willing, F., Andreou, A. Z. & Klostermeier, D. The domains of yeast eIF4G, eIF4E and the cap fine-tune eIF4A activities through an intricate network of stimulatory and inhibitory effects. Nucleic Acids Res. 50, 6497–6510 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schutz, P. et al. Crystal structure of the yeast eIF4A-eIF4G complex: an RNA-helicase controlled by protein-protein interactions. Proc. Natl Acad. Sci. USA 105, 9564–9569 (2008).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rozen, F. et al. Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F. Mol. Cell. Biol. 10, 1134–1144 (1990).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ray, B. K. et al. ATP-dependent unwinding of messenger RNA structure by eukaryotic initiation factors. J. Biol. Chem. 260, 7651–7658 (1985).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mitchell, S. F. et al. The 5′-7-methylguanosine cap on eukaryotic mRNAs serves both to stimulate canonical translation initiation and to block an alternative pathway. Mol. Cell 39, 950–962 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marcotrigiano, J. et al. A conserved HEAT domain within eIF4G directs assembly of the translation initiation machinery. Mol. Cell 7, 193–203 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hershey, P. E. et al. The Cap-binding protein eIF4E promotes folding of a functional domain of yeast translation initiation factor eIF4G1. J. Biol. Chem. 274, 21297–21304 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rogers, G. W. Jr, Komar, A. A. & Merrick, W. C. eIF4A: the godfather of the DEAD box helicases. Prog. Nucleic Acid Res. Mol. Biol. 72, 307–331 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lindqvist, L., Imataka, H. & Pelletier, J. Cap-dependent eukaryotic initiation factor-mRNA interactions probed by cross-linking. RNA 14, 960–969 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, X., Schuessler, P. J., Sahoo, A. & Walker, S. E. Reconstitution and analyses of RNA interactions with eukaryotic translation initiation factors and ribosomal preinitiation complexes. Methods 162-163, 42–53 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hilbert, M., Kebbel, F., Gubaev, A. & Klostermeier, D. eIF4G stimulates the activity of the DEAD box protein eIF4A by a conformational guidance mechanism. Nucleic Acids Res. 39, 2260–2270 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Andreou, A. Z., Harms, U. & Klostermeier, D. eIF4B stimulates eIF4A ATPase and unwinding activities by direct interaction through its 7-repeats region. RNA Biol. 14, 113–123 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Querido, J. B. et al. The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. Nat. Struct. Mol. Biol. 31, 455–464 (2024).

  • Haizel, S. A., Bhardwaj, U., Gonzalez, R. L. Jr, Mitra, S. & Goss, D. J. 5′-UTR recruitment of the translation initiation factor eIF4GI or DAP5 drives cap-independent translation of a subset of human mRNAs. J. Biol. Chem. 295, 11693–11706 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Acker, M. G., Kolitz, S. E., Mitchell, S. F., Nanda, J. S. & Lorsch, J. R. Reconstitution of yeast translation initiation. Methods Enzymol. 430, 111–145 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, J. et al. eIF5B gates the transition from translation initiation to elongation. Nature 573, 605–608 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jarmoskaite, I., AlSadhan, I., Vaidyanathan, P. P. & Herschlag, D. How to measure and evaluate binding affinities. eLife 9, e57264 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Buttner, L., Javadi-Zarnaghi, F. & Hobartner, C. Site-specific labeling of RNA at internal ribose hydroxyl groups: terbium-assisted deoxyribozymes at work. J. Am. Chem. Soc. 136, 8131–8137 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Graham, J. S., Johnson, R. C. & Marko, J. F. Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Res. 39, 2249–2259 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kamar, R. I. et al. Facilitated dissociation of transcription factors from single DNA binding sites. Proc. Natl Acad. Sci. USA 114, E3251–E3257 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kosar, Z., Attar, A. G. & Erbas, A. Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement. Biophys. J. 121, 1119–1133 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Luo, Y., North, J. A., Rose, S. D. & Poirier, M. G. Nucleosomes accelerate transcription factor dissociation. Nucleic Acids Res. 42, 3017–3027 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • MacDougall, D. D. & Gonzalez, R. L. Jr Translation initiation factor 3 regulates switching between different modes of ribosomal subunit joining. J. Mol. Biol. 427, 1801–1818 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, J. et al. Rapid 40S scanning and its regulation by mRNA structure during eukaryotic translation initiation. Cell 185, 4474–4487 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rajyaguru, P., She, M. & Parker, R. Scd6 targets eIF4G to repress translation: RGG motif proteins as a class of eIF4G-binding proteins. Mol. Cell 45, 244–254 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gupta, N., Lorsch, J. R. & Hinnebusch, A. G. Yeast Ded1 promotes 48S translation pre-initiation complex assembly in an mRNA-specific and eIF4F-dependent manner. eLife 7, e38892 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Linder, P. & Jankowsky, E. From unwinding to clamping—the DEAD box RNA helicase family. Nat. Rev. Mol. Cell Biol. 12, 505–516 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sen, N. D. et al. Functional interplay between DEAD-box RNA helicases Ded1 and Dbp1 in preinitiation complex attachment and scanning on structured mRNAs in vivo. Nucleic Acids Res. 47, 8785–8806 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sharma, D. & Jankowsky, E. The Ded1/DDX3 subfamily of DEAD-box RNA helicases. Crit. Rev. Biochem. Mol. Biol. 49, 343–360 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Brito Querido, J. et al. The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. Nat. Struct. Mol. Biol. 31, 455–464 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bohlen, J., Fenzl, K., Kramer, G., Bukau, B. & Teleman, A. A. Selective 40S footprinting reveals cap-tethered ribosome scanning in human cells. Mol. Cell 79, 561–574 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pause, A., Methot, N., Svitkin, Y., Merrick, W. C. & Sonenberg, N. Dominant negative mutants of mammalian translation initiation factor eIF-4A define a critical role for eIF-4F in cap-dependent and cap-independent initiation of translation. EMBO J. 13, 1205–1215 (1994).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Livingston, N. M. et al. Bursting translation on single mRNAs in live cells. Mol. Cell 83, 2276–2289 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zinshteyn, B., Rojas-Duran, M. F. & Gilbert, W. V. Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs. RNA 23, 1365–1375 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tamarkin-Ben-Harush, A., Vasseur, J. J., Debart, F., Ulitsky, I. & Dikstein, R. Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress. eLife 6, e21907 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lakowicz, J. R. Principles of Fluorescence Spectroscopy 3rd edn (Springer, 2006).

  • Blanchard, S. C., Kim, H. D., Gonzalez, R. L. Jr, Puglisi, J. D. & Chu, S. tRNA dynamics on the ribosome during translation. Proc. Natl Acad. Sci. USA 101, 12893–12898 (2004).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Blanchard, S. C., Gonzalez, R. L., Kim, H. D., Chu, S. & Puglisi, J. D. tRNA selection and kinetic proofreading in translation. Nat. Struct. Mol. Biol. 11, 1008–1014 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Edelstein, A., Amodaj, N., Hoover, K., Vale, R. & Stuurman, N. Computer control of microscopes using microManager. Curr. Protoc. Mol. Biol. https://doi.org/10.1002/0471142727.mb1420s92 (2010).

  • Ray, K. K. et al. Entropic control of the free-energy landscape of an archetypal biomolecular machine. Proc. Natl Acad. Sci. USA 120, e2220591120 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Verma, A. R. et al. Increasing the accuracy of single-molecule data analysis using tMAVEN. Biophys J. 123, 2765–2780 (2024).

  • Bronson, J. E., Fei, J., Hofman, J. M., Gonzalez, R. L. Jr & Wiggins, C. H. Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data. Biophys. J. 97, 3196–3205 (2009).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

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  • Seader, J. D., Henley, E. J. & Roper, D. K. Separation Process Principles (Wiley, 2011).

  • Baker, R. W. Membrane Technology and Applications (Wiley, 2023).

  • Davies, H. et al. Mutations of the BRAF gene in human cancer. Nature 417, 949–954 (2002).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Welton, T. & Reichardt, C. Solvents and Solvent Effects in Organic Chemistry (Wiley, 2011).

  • Grover, P. K. & Ryall, R. L. Critical appraisal of salting-out and its implications for chemical and biological sciences. Chem. Rev. 105, 1–10 (2005).

    CAS 
    PubMed 

    Google Scholar
     

  • Boeynaems, S. et al. Protein phase separation: a new phase in cell biology. Trends Cell Biol. 28, 420–435 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Arakawa, T. & Timasheff, S. N. Mechanism of protein salting in and salting out by divalent cation salts: balance between hydration and salt binding. Biochemistry 23, 5912–5923 (1984).

    CAS 
    PubMed 

    Google Scholar
     

  • Langmuir, I. The role of attractive and repulsive forces in the formation of tactoids, thixotropic gels, protein crystals and coacervates. J. Chem. Phys. 6, 873–896 (1938).

    ADS 
    CAS 

    Google Scholar
     

  • Zhang, F. et al. Reentrant condensation, liquid–liquid phase separation and crystallization in protein solutions induced by multivalent metal ions. Pure Appl. Chem. 86, 191–202 (2014).

    CAS 

    Google Scholar
     

  • Luisi, P. The Emergence of Life (Cambridge Univ. Press, 2006).

  • Banani, S. F., Lee, H. O., Hyman, A. A. & Rosen, M. K. Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18, 285–298 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gouveia, B. et al. Capillary forces generated by biomolecular condensates. Nature 609, 255–264 (2022).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Zarzar, L. D. et al. Dynamically reconfigurable complex emulsions via tunable interfacial tensions. Nature 518, 520–524 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nagelberg, S. et al. Reconfigurable and responsive droplet-based compound micro-lenses. Nat. Commun. 8, 14673 (2017).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goodling, A. E. et al. Colouration by total internal reflection and interference at microscale concave interfaces. Nature 566, 523–527 (2019).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Concellón, A., Fong, D. & Swager, T. M. Complex liquid crystal emulsions for biosensing. J. Am. Chem. Soc. 143, 9177–9182 (2021).

    PubMed 

    Google Scholar
     

  • Cacace, M. G., Landau, E. M. & Ramsden, J. J. The Hofmeister series: salt and solvent effects on interfacial phenomena. Q. Rev. Biophys. 30, 241–277 (1997).

    CAS 
    PubMed 

    Google Scholar
     

  • Duong-Ly, K. C. & Gabelli, S. B. Salting out of proteins using ammonium sulfate precipitation. Methods Enzymol. 541, 85–94 (2014).

    CAS 
    PubMed 

    Google Scholar
     

  • Bailey, F. E. Jr. & Callard, R. W. Some properties of poly(ethylene oxide)1 in aqueous solution. J. Appl. Polym. Sci. 1, 56–62 (1959).

    CAS 

    Google Scholar
     

  • Kim, C. W. & Rha, C. Phase separation of polyethylene glycol/salt aqueous two-phase systems. Phys. Chem. Liquids 38, 181–191 (2000).

    CAS 

    Google Scholar
     

  • Chao, Y. & Shum, H. C. Emerging aqueous two-phase systems: from fundamentals of interfaces to biomedical applications. Chem. Soc. Rev. 49, 114–142 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Watanabe, C. et al. Cell-sized confinement initiates phase separation of polymer blends and promotes fractionation upon competitive membrane wetting. ACS Mater. Lett. 4, 1742–1748 (2022).

    CAS 

    Google Scholar
     

  • Mangiarotti, A., Chen, N., Zhao, Z., Lipowsky, R. & Dimova, R. Wetting and complex remodeling of membranes by biomolecular condensates. Nat. Commun. 14, 2809 (2023).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mori, S. & Barth, H. G. Size Exclusion Chromatography (Springer, 2011).

  • Snyder, L. R., Kirkland, J. J. & Dolan, J. W. Introduction to Modern Liquid Chromatography (Wiley, 2010).

  • Deegan, R. D. et al. Capillary flow as the cause of ring stains from dried liquid drops. Nature 389, 827–829 (1997).

    ADS 
    CAS 

    Google Scholar
     

  • Yunker, P. J., Still, T., Lohr, M. A. & Yodh, A. G. Suppression of the coffee-ring effect by shape-dependent capillary interactions. Nature 476, 308–311 (2011).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Wong, T.-S., Chen, T.-H., Shen, X. & Ho, C.-M. Nanochromatography driven by the coffee ring effect. Anal. Chem. 83, 1871–1873 (2011).

    CAS 
    PubMed 

    Google Scholar
     

  • Tanner, L. H. The spreading of silicone oil drops on horizontal surfaces. J. Phys. D Appl. Phys. 12, 1473–1484 (1979).

    ADS 
    CAS 

    Google Scholar
     

  • Bonn, D., Eggers, J., Indekeu, J., Meunier, J. & Rolley, E. Wetting and spreading. Rev. Mod. Phys. 81, 739–805 (2009).

    ADS 
    CAS 

    Google Scholar
     

  • Hayes, R., Warr, G. G. & Atkin, R. Structure and nanostructure in ionic liquids. Chem. Rev. 115, 6357–6426 (2015).

    CAS 
    PubMed 

    Google Scholar
     

  • Mezger, M. et al. Molecular layering of fluorinated ionic liquids at a charged sapphire (0001) surface. Science 322, 424–428 (2008).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Sauerbrey, G. The use of quartz oscillators for weighing thin layers and for microweighing. Z. Fur. Phys. 155, 206–222 (1959).

    ADS 
    CAS 

    Google Scholar
     

  • Pappu, R. V., Cohen, S. R., Dar, F., Farag, M. & Kar, M. Phase transitions of associative biomacromolecules. Chem. Rev. 123, 8945–8987 (2023).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Qian, D. et al. Tie-line analysis reveals interactions driving heteromolecular condensate formation. Phys. Rev. 12, 041038 (2022).

    CAS 

    Google Scholar
     

  • Zhang, W. et al. Liquid–liquid equilibrium of aqueous two-phase systems containing poly(ethylene glycol) of different molecular weights and several ammonium salts at 298.15 K. Thermochim. Acta 560, 47–54 (2013).

    CAS 

    Google Scholar
     

  • Wysoczanska, K. & Macedo, E. A. Influence of the molecular weight of PEG on the polymer/salt phase diagrams of aqueous two-phase systems. J. Chem. Eng. Data 61, 4229–4235 (2016).

    CAS 

    Google Scholar
     

  • Zhao, X. et al. Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell 186, 5517–5535 (2023).

    CAS 
    PubMed 

    Google Scholar
     

  • Entelis, S. G., Evreinov, V. V. & Gorshkov, A. V. Functionality and molecular weight distribution of telechelic polymers. Adv. Polym. Sci. 76, 129–175 (1987).


    Google Scholar
     

  • Gorbunov, A. & Trathnigg, B. Theory of liquid chromatography of mono- and difunctional macromolecules: I. Studies in the critical interaction mode. J. Chromatogr. A 955, 9–17 (2002).

    CAS 
    PubMed 

    Google Scholar
     

  • Le Ouay, B. et al. Selective sorting of polymers with different terminal groups using metal-organic frameworks. Nat. Commun. 9, 3635 (2018).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Peng, S. et al. Efficient separation of nucleic acids with different secondary structures by metal–organic frameworks. J. Am. Chem. Soc. 142, 5049–5059 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Schneider, C., Rasband, W. & Eliceiri, K. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hau, W. L. W., Trau, D. W., Sucher, N. J., Wong, M. & Zohar, Y. Surface-chemistry technology for microfluidics. J. Micromech. Microeng. 13, 272–278 (2003).

    ADS 
    CAS 

    Google Scholar
     

  • Chakraborty, A. & Sen, K. Impact of pH and temperature on phase diagrams of different aqueous biphasic systems. J. Chromatogr. A 1433, 41–55 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Miller, W. L. & McPherson, R. H. The behavior of colloidal suspensions with immiscible solvents. J. Phys. Chem. 12, 706–716 (1908).


    Google Scholar
     

  • Williamson, J. C. Liquid–liquid demonstrations: phase equilibria and the lever rule. J. Chem. Educ. 98, 2356–2363 (2021).

    CAS 

    Google Scholar
     

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  • Propofol rescues voltage-dependent gating of HCN1 channel epilepsy mutants

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  • Kaupp, U. B. & Seifert, R. Molecular diversity of pacemaker ion channels. Annu. Rev. Physiol. 63, 235–257 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • DiFrancesco, D. Pacemaker mechanisms in cardiac tissue. Annu. Rev. Physiol. 55, 455–472 (1993).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Biel, M., Wahl-Schott, C., Michalakis, S. & Zong, X. Hyperpolarization-activated cation channels: from genes to function. Physiol. Rev. 89, 847–885 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tibbs, G. R. et al. An anchor-tether ‘hindered’ HCN1 inhibitor is antihyperalgesic in a rat spared nerve injury neuropathic pain model. Br. J. Anaesth. 131, 745–763 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bleakley, L. E. et al. Cation leak underlies neuronal excitability in an HCN1 developmental and epileptic encephalopathy. Brain 144, 2060–2073 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lyashchenko, A. K., Redd, K. J., Yang, J. & Tibbs, G. R. Propofol inhibits HCN1 pacemaker channels by selective association with the closed states of the membrane embedded channel core. J. Physiol. 583, 37–56 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Poduri, A. HCN1 gain-of-function mutations—a new cause of epileptic encephalopathy. Epilepsy Curr. 14, 348–349 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marini, C. et al. HCN1 mutation spectrum: from neonatal epileptic encephalopathy to benign generalized epilepsy and beyond. Brain 141, 3160–3178 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • Lee, C. H. & MacKinnon, R. Structures of the human HCN1 hyperpolarization-activated channel. Cell 168, 111–120 e111 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lee, C. H. & MacKinnon, R. Voltage sensor movements during hyperpolarization in the HCN channel. Cell 179, 1582–1589 e1587 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mannikko, R., Elinder, F. & Larsson, H. P. Voltage-sensing mechanism is conserved among ion channels gated by opposite voltages. Nature 419, 837–841 (2002).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Vemana, S., Pandey, S. & Larsson, H. P. S4 movement in a mammalian HCN channel. J. Gen. Physiol. 123, 21–32 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, X., Cunningham, K. P., Ramentol, R., Perez, M. E. & Larsson, H. P. Similar voltage-sensor movement in spHCN channels can cause closing, opening, or inactivation. J. Gen. Physiol. 155, e202213170 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mandala, V. S. & MacKinnon, R. Voltage-sensor movements in the Eag Kv channel under an applied electric field. Proc. Natl Acad. Sci. USA 119, e2214151119 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Whicher, J. R. & MacKinnon, R. Structure of the voltage-gated K+ channel Eag1 reveals an alternative voltage sensing mechanism. Science 353, 664–669 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, D. M. & Nimigean, C. M. Voltage-gated potassium channels: a structural examination of selectivity and gating. Cold Spring Harb. Perspect. Biol. 8, a029231 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dai, G., Aman, T. K., DiMaio, F. & Zagotta, W. N. The HCN channel voltage sensor undergoes a large downward motion during hyperpolarization. Nat. Struct. Mol. Biol. 26, 686–694 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, X., Ramentol, R., Perez, M. E., Noskov, S. Y. & Larsson, H. P. A second S4 movement opens hyperpolarization-activated HCN channels. Proc. Natl Acad. Sci. USA 118, e2102036118 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lu, Z., Klem, A. M. & Ramu, Y. Coupling between voltage sensors and activation gate in voltage-gated K+ channels. J. Gen. Physiol. 120, 663–676 (2002).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Long, S. B., Campbell, E. B. & Mackinnon, R. Voltage sensor of Kv1.2: structural basis of electromechanical coupling. Science 309, 903–908 (2005).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Lorinczi, E. et al. Voltage-dependent gating of KCNH potassium channels lacking a covalent link between voltage-sensing and pore domains. Nat. Commun. 6, 6672 (2015).

    Article 
    ADS 
    MathSciNet 
    PubMed 

    Google Scholar
     

  • Fernandez-Marino, A. I., Harpole, T. J., Oelstrom, K., Delemotte, L. & Chanda, B. Gating interaction maps reveal a noncanonical electromechanical coupling mode in the Shaker K+ channel. Nat. Struct. Mol. Biol. 25, 320–326 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • de la Pena, P., Dominguez, P. & Barros, F. Gating mechanism of Kv11.1 (hERG) K+ channels without covalent connection between voltage sensor and pore domains. Pflugers Arch. 470, 517–536 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • Flynn, G. E. & Zagotta, W. N. Insights into the molecular mechanism for hyperpolarization-dependent activation of HCN channels. Proc. Natl Acad. Sci. USA 115, E8086–E8095 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cowgill, J. & Chanda, B. Mapping electromechanical coupling pathways in voltage-gated ion channels: challenges and the way forward. J. Mol. Biol. 433, 167104 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rivolta, I., Binda, A., Masi, A. & DiFrancesco, J. C. Cardiac and neuronal HCN channelopathies. Pflugers Arch. 472, 931–951 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Butler, K. M., da Silva, C., Alexander, J. J., Hegde, M. & Escayg, A. Diagnostic yield from 339 epilepsy patients screened on a clinical gene panel. Pediatr. Neurol. 77, 61–66 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bleakley, L. E. & Reid, C. A. HCN1 epilepsy: from genetics and mechanisms to precision therapies. J. Neurochem. https://doi.org/10.1111/jnc.15928 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Thollon, C. et al. Use-dependent inhibition of hHCN4 by ivabradine and relationship with reduction in pacemaker activity. Br. J. Pharmacol. 150, 37–46 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lu, X., Smaill, J. B. & Ding, K. New promise and opportunities for allosteric kinase inhibitors. Angew. Chem. Int. Ed. Engl. 59, 13764–13776 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kim, E. D. et al. Allosteric drug discrimination is coupled to mechanochemical changes in the kinesin-5 motor core. J. Biol. Chem. 285, 18650–18661 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhu, S. et al. Structural and dynamic mechanisms of GABAA receptor modulators with opposing activities. Nat. Commun. 13, 4582 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ramirez, D., Zuniga, R., Concha, G. & Zuniga, L. HCN channels: new therapeutic targets for pain treatment. Molecules 23, 2094 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cacheaux, L. P. et al. Impairment of hyperpolarization-activated, cyclic nucleotide-gated channel function by the intravenous general anesthetic propofol. J. Pharmacol. Exp. Ther. 315, 517–525 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Saponaro, A. et al. Gating movements and ion permeation in HCN4 pacemaker channels. Mol. Cell 81, 2929–2943 e2926 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tanguay, J., Callahan, K. M. & D’Avanzo, N. Characterization of drug binding within the HCN1 channel pore. Sci. Rep. 9, 465 (2019).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Faulkner, C., Santos-Carballal, D., Plant, D. F. & de Leeuw, N. H. Atomistic molecular dynamics simulations of propofol and fentanyl in phosphatidylcholine lipid bilayers. ACS Omega 5, 14340–14353 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Joyce, R. L. et al. Alkylphenol inverse agonists of HCN1 gating: H-bond propensity, ring saturation and adduct geometry differentially determine efficacy and potency. Biochem. Pharmacol. 163, 493–508 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shintre, C. et al. Human hyperpolarization activated cyclic nucleotide gated ion channel 4. Zenodo https://doi.org/10.5281/zenodo.1434068 (2018).

  • Schmidpeter, P. A. M. et al. Anionic lipids unlock the gates of select ion channels in the pacemaker family. Nat. Struct. Mol. Biol. 29, 1092–1100 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hung, A. et al. Biophysical analysis of an HCN1 epilepsy variant suggests a critical role for S5 helix Met-305 in voltage sensor to pore domain coupling. Prog. Biophys. Mol. Biol. 166, 156–172 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ludwig, A., Zong, X., Jeglitsch, M., Hofmann, F. & Biel, M. A family of hyperpolarization-activated mammalian cation channels. Nature 393, 587–591 (1998).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Decher, N., Chen, J. & Sanguinetti, M. C. Voltage-dependent gating of hyperpolarization-activated, cyclic nucleotide-gated pacemaker channels: molecular coupling between the S4-S5 and C-linkers. J. Biol. Chem. 279, 13859–13865 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Flynn, G. E. & Zagotta, W. N. Molecular mechanism underlying phosphatidylinositol 4,5-bisphosphate-induced inhibition of SpIH channels. J. Biol. Chem. 286, 15535–15542 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bruening-Wright, A., Elinder, F. & Larsson, H. P. Kinetic relationship between the voltage sensor and the activation gate in spHCN channels. J. Gen. Physiol. 130, 71–81 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ramentol, R., Perez, M. E. & Larsson, H. P. Gating mechanism of hyperpolarization-activated HCN pacemaker channels. Nat. Commun. 11, 1419 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Valley, C. C. et al. The methionine-aromatic motif plays a unique role in stabilizing protein structure. J. Biol. Chem. 287, 34979–34991 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ryu, S. & Yellen, G. Charge movement in gating-locked HCN channels reveals weak coupling of voltage sensors and gate. J. Gen. Physiol. 140, 469–479 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Porro, A. et al. Do the functional properties of HCN1 mutants correlate with the clinical features in epileptic patients? Prog. Biophys. Mol. Biol. 166, 147–155 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Boonsimma, P. et al. Exome sequencing as first-tier genetic testing in infantile-onset pharmacoresistant epilepsy: diagnostic yield and treatment impact. Eur. J. Hum. Genet. 31, 179–187 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kim, J. J. et al. Shared structural mechanisms of general anaesthetics and benzodiazepines. Nature 585, 303–308 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zivanov, J., Nakane, T. & Scheres, S. H. W. Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1. IUCrJ 7, 253–267 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kimanius, D., Dong, L., Sharov, G., Nakane, T. & Scheres, S. H. W. New tools for automated cryo-EM single-particle analysis in RELION-4.0. Biochem. J. 478, 4169–4185 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D Struct. Biol. 75, 861–877 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Casanal, A., Lohkamp, B. & Emsley, P. Current developments in Coot for macromolecular model building of electron cryo-microscopy and crystallographic data. Protein Sci. 29, 1069–1078 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D Struct. Biol. 74, 519–530 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Smart, O. S., Neduvelil, J. G., Wang, X., Wallace, B. A. & Sansom, M. S. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. 14, 354–360 (1996).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Liu, Y. et al. CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Res. 50, W159–W164 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, S., Xie, J., Pei, J. & Lai, L. CavityPlus 2022 update: an integrated platform for comprehensive protein cavity detection and property analyses with user-friendly tools and cavity databases. J. Mol. Biol. 435, 168141 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Maglic, J. B. & Lavendomme, R. MoloVol: an easy-to-use program for analyzing cavities, volumes and surface areas of chemical structures. J. Appl. Crystallogr. 55, 1033–1044 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Laskowski, R. A. & Swindells, M. B. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model. 51, 2778–2786 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jubb, H. C. et al. Arpeggio: a web server for calculating and visualising interatomic interactions in protein structures. J. Mol. Biol. 429, 365–371 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Procter, J. B. et al. Alignment of biological sequences with Jalview. Methods Mol. Biol. 2231, 203–224 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Webb, B. & Sali, A. Comparative protein structure modeling using MODELLER. Curr. Protoc. Bioinformatics 54, 5.6.1–5.6.37 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wu, E. L. et al. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J. Comput. Chem. 35, 1997–2004 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kasimova, M. A. et al. Helix breaking transition in the S4 of HCN channel is critical for hyperpolarization-dependent gating. eLife 8, e53400 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Elbahnsi, A. et al. Interplay between VSD, pore, and membrane lipids in electromechanical coupling in HCN channels. eLife 12, e80303 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Best, R. B. et al. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone ɸ, ψ and side-chain χ1 and χ2 dihedral angles. J. Chem. Theory Comput. 8, 3257–3273 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Arcario, M. J., Mayne, C. G. & Tajkhorshid, E. Atomistic models of general anesthetics for use in in silico biological studies. J. Phys. Chem. B 118, 12075–12086 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Olsson, M. H., Sondergaard, C. R., Rostkowski, M. & Jensen, J. H. PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J. Chem. Theory Comput. 7, 525–537 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Abraham, M. J. et al. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1-2, 19–25 (2015).

    Article 
    ADS 

    Google Scholar
     

  • Tribello, G. A., Bonomi, M., Branduardi, D., Camilloni, C. & Bussi, G. PLUMED 2: new feathers for an old bird. Comput. Phys. Commun. 185, 604–613 (2014).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Darden, T. A., York, D. M. & Pedersen, L. G. Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. G. E. M. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463–1472 (1997).

  • Kim, E. D. et al. Propofol rescues voltage-dependent gating of HCN1 channel epilepsy mutants. Zenodo https://doi.org/10.5281/zenodo.11528212 (2024).

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