Stabilization and structure determination of integral membrane proteins by termini restraining

Shixuan Liu, Shuang Li, Andrzej M. Krezel, Weikai Li

Published: 2022-01-16 DOI: 10.1038/s41596-021-00656-5

integral membrane proteins

stabilization

structure determination

termini restraining

protein coupler

AI 解读

Supplementary information

Supplementary Information

Supplementary Methods, Supplementary Table 1 and Supplementary Fig. 1.

Supplementary Data 1

DNA sequence of sfGFP in pPICZ-derivatized vector

Supplementary Data 2

DNA sequence of sfGFP restrained human VKOR in pPICZ-derivatized vector

Supplementary Data 3

DNA sequence of sfGFP restrained DsbB in PET28b vector

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References

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Uhlen, M. et al. Proteomics. Tissue-based map of the human proteome. Science 347, 1260419 (2015).
Overington, J. P., Al-Lazikani, B. & Hopkins, A. L. How many drug targets are there? Nat. Rev. Drug Discov. 5, 993–996 (2006).
Fagerberg, L., Jonasson, K., von Heijne, G., Uhlen, M. & Berglund, L. Prediction of the human membrane proteome. Proteomics 10, 1141–1149 (2010).
Yildirim, M. A., Goh, K. I., Cusick, M. E., Barabasi, A. L. & Vidal, M. Drug–target network. Nat. Biotechnol. 25, 1119–1126 (2007).
Bill, R. M. et al. Overcoming barriers to membrane protein structure determination. Nat. Biotechnol. 29, 335–340 (2011).
Carpenter, E. P., Beis, K., Cameron, A. D. & Iwata, S. Overcoming the challenges of membrane protein crystallography. Curr. Opin. Struct. Biol. 18, 581–586 (2008).
Miller, J. L. & Tate, C. G. Engineering an ultra-thermostable β(1)-adrenoceptor. J. Mol. Biol. 413, 628–638 (2011).
Serrano-Vega, M. J., Magnani, F., Shibata, Y. & Tate, C. G. Conformational thermostabilization of the β1-adrenergic receptor in a detergent-resistant form. Proc. Natl Acad. Sci. USA 105, 877–882 (2008).
Tate, C. G. A crystal clear solution for determining G-protein-coupled receptor structures. Trends Biochem. Sci. 37, 343–352 (2012).
Magnani, F. et al. A mutagenesis and screening strategy to generate optimally thermostabilized membrane proteins for structural studies. Nat. Protoc. 11, 1554–1571 (2016).
De Zorzi, R., Mi, W., Liao, M. & Walz, T. Single-particle electron microscopy in the study of membrane protein structure. Microscopy 65, 81–96 (2016).
Gauto, D. F. et al. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nat. Commun. 10, 2697 (2019).
Liu, S., Li, S., Yang, Y. & Li, W. Termini restraining of small membrane proteins enables structure determination at near-atomic resolution. Sci. Adv. https://doi.org/10.1126/sciadv.abe3717 (2020).
Liu, S. et al. Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation. Science https://doi.org/10.1126/science.abc5667 (2021).
Yang, Y. et al. Open conformation of tetraspanins shapes interaction partner networks on cell membranes. EMBO J. 39, e105246 (2020).
Li, S., Liu, S., Liu, X. R., Zhang, M. M. & Li, W. Competitive tight-binding inhibition of VKORC1 underlies warfarin dosage variation and antidotal efficacy. Blood Adv. 4, 2202–2212 (2020).
Li, S., Liu, S., Yang, Y. & Li, W. Characterization of warfarin inhibition kinetics requires stabilization of intramembrane vitamin K epoxide reductases. J. Mol. Biol. 432, 5197–5208 (2020).
Daley, D. O. et al. Global topology analysis of the Escherichia coli inner membrane proteome. Science 308, 1321–1323 (2005).
Kim, H., Melen, K., Osterberg, M. & von Heijne, G. A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc. Natl Acad. Sci. USA 103, 11142–11147 (2006).
Li, W. & Li, F. Cross-crystal averaging with search models to improve molecular replacement phases. Structure 19, 155–161 (2011).
Zhou, Y., Morais-Cabral, J. H., Kaufman, A. & MacKinnon, R. Chemistry of ion coordination and hydration revealed by a K+ channel–Fab complex at 2.0 A resolution. Nature 414, 43–48 (2001).
Kim, J. M. et al. Subnanometre-resolution electron cryomicroscopy structure of a heterodimeric ABC exporter. Nature 517, 396–400 (2015).
Rosenbaum, D. M. et al. GPCR engineering yields high-resolution structural insights into β2-adrenergic receptor function. Science 318, 1266–1273 (2007).
Chun, E. et al. Fusion partner toolchest for the stabilization and crystallization of G protein-coupled receptors. Structure 20, 967–976 (2012).
Baird, G. S., Zacharias, D. A. & Tsien, R. Y. Circular permutation and receptor insertion within green fluorescent proteins. Proc. Natl Acad. Sci. USA 96, 11241–11246 (1999).
Cabantous, S., Terwilliger, T. C. & Waldo, G. S. Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein. Nat. Biotechnol. 23, 102–107 (2005).
Pierre, B., Xiong, T., Hayles, L., Guntaka, V. R. & Kim, J. R. Stability of a guest protein depends on stability of a host protein in insertional fusion. Biotechnol. Bioeng. 108, 1011–1020 (2011).
Palanisamy, N. et al. Split intein-mediated selection of cells containing two plasmids using a single antibiotic. Nat. Commun. 10, 4967 (2019).
Foit, L. et al. Optimizing protein stability in vivo. Mol. Cell 36, 861–871 (2009).
Zhang, R. et al. A CRISPR screen defines a signal peptide processing pathway required by flaviviruses. Nature 535, 164–168 (2016).
Fu, Q., Piai, A., Chen, W., Xia, K. & Chou, J. J. Structure determination protocol for transmembrane domain oligomers. Nat. Protoc. 14, 2483–2520 (2019).
Hagn, F., Nasr, M. L. & Wagner, G. Assembly of phospholipid nanodiscs of controlled size for structural studies of membrane proteins by NMR. Nat. Protoc. 13, 79–98 (2018).
Watzka, M. et al. Thirteen novel VKORC1 mutations associated with oral anticoagulant resistance: insights into improved patient diagnosis and treatment. J. Thromb. Haemost. 9, 109–118 (2011).
Fasco, M. J., Principe, L. M., Walsh, W. A. & Friedman, P. A. Warfarin inhibition of vitamin K 2,3-epoxide reductase in rat liver microsomes. Biochemistry 22, 5655–5660 (1983).
Hodroge, A., Longin-Sauvageon, C., Fourel, I., Benoit, E. & Lattard, V. Biochemical characterization of spontaneous mutants of rat VKORC1 involved in the resistance to antivitamin K anticoagulants. Arch. Biochem. Biophys. 515, 14–20 (2011).
Bevans, C. G. et al. Determination of the warfarin inhibition constant Ki for vitamin K 2,3-epoxide reductase complex subunit-1 (VKORC1) using an in vitro DTT-driven assay. Biochim. Biophys. Acta 1830, 4202–4210 (2013).
Schwarzer, D. & Cole, P. A. Protein semisynthesis and expressed protein ligation: chasing a protein’s tail. Curr. Opin. Chem. Biol. 9, 561–569 (2005).
Li, C. et al. FastCloning: a highly simplified, purification-free, sequence- and ligation-independent PCR cloning method. BMC Biotechnol. 11, 92–92 (2011).
Kawate, T. & Gouaux, E. Fluorescence-detection size-exclusion chromatography for precrystallization screening of integral membrane proteins. Structure 14, 673–681 (2006).
Lee, H. & Kim, H. Membrane topology of transmembrane proteins: determinants and experimental tools. Biochem. Biophys. Res. Commun. 453, 268–276 (2014).
Alexandrov, A. I., Mileni, M., Chien, E. Y., Hanson, M. A. & Stevens, R. C. Microscale fluorescent thermal stability assay for membrane proteins. Structure 16, 351–359 (2008).
Thomas, J. A. & Tate, C. G. Quality control in eukaryotic membrane protein overproduction. J. Mol. Biol. 426, 4139–4154 (2014).
Goehring, A. et al. Screening and large-scale expression of membrane proteins in mammalian cells for structural studies. Nat. Protoc. 9, 2574–2585 (2014).
Miroux, B. & Walker, J. E. Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels. J. Mol. Biol. 260, 289–298 (1996).
Wagner, S. et al. Tuning Escherichia coli for membrane protein overexpression. Proc. Natl Acad. Sci. USA 105, 14371–14376 (2008).
Caffrey, M. & Cherezov, V. Crystallizing membrane proteins using lipidic mesophases. Nat. Protoc. 4, 706–731 (2009).
Tusnády, G. E., Kalmár, L. & Simon, I. TOPDB: Topology Data Bank of Transmembrane Proteins. Nucleic Acids Res. 36, https://doi.org/10.1093/nar/gkm751 (2008).
Jones, D. T. Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23, 538–544 (2007).
Nugent, T. & Jones, D. T. Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics 10, 159 (2009).
Käll, L., Krogh, A. & Sonnhammer, E. L. L. Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server. Nucleic Acids Res. 35, https://doi.org/10.1093/nar/gkm256 (2007).
Krogh, a, Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580 (2001).
Reddy, A. et al. Reliability of nine programs of topological predictions and their application to integral membrane channel and carrier proteins. J. Mol. Microbiol. Biotechnol. 24, 161–190 (2014).
Kulzer, S., Petersen, W., Baser, A., Mandel, K. & Przyborski, J. M. Use of self-assembling GFP to determine protein topology and compartmentalisation in the Plasmodium falciparum-infected erythrocyte. Mol. Biochem. Parasitol. 187, 87–90 (2013).
Toddo, S. et al. Application of split-green fluorescent protein for topology mapping membrane proteins in Escherichia coli. Protein Sci. 21, 1571–1576 (2012).
Doi, N. & Yanagawa, H. Design of generic biosensors based on green fluorescent proteins with allosteric sites by directed evolution. FEBS Lett. 453, 305–307 (1999).
Ghosh, I., Hamilton, A. D. & Regan, L. Antiparallel leucine zipper-directed protein reassembly: application to the green fluorescent protein. J. Am. Chem. Soc. 122, 5658–5659 (2000).
Romei, M. G. & Boxer, S. G. Split green fluorescent proteins: scope, limitations, and outlook. Annu. Rev. Biophys. 48, 19–44 (2019).
Jones, D. T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195–202 (1999).
Oates, M. E. et al. D(2)P(2): database of disordered protein predictions. Nucleic Acids Res. 41, D508–D516 (2013).
Chen, X., Zaro, J. L. & Shen, W. C. Fusion protein linkers: property, design and functionality. Adv. Drug Deliv. Rev. 65, 1357–1369 (2013).
Zheng, L., Baumann, U. & Reymond, J. L. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res. 32, e115 (2004).
Cowtan, K. D. Recent developments in classical density modification. Acta Crystallogr. D. Biol. Crystallogr. 66, 470–478 (2010).
Cowtan, K. D. ‘dm’: an automated procedure for phase improvement by density modification. Jt. CCP4 ESF-EACBM Newsl. Protein Crystallogr. 31, 34–38 (1994).

Stabilization and structure determination of integral membrane proteins by termini restraining

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