ПРОСТОЙ МЕТОД ПОЛУЧЕНИЯ ШАПЕРОНА С ПЕРЕМЕННЫМ ЧИСЛОМ САЙТОВ СВЯЗЫВАНИЯ НЕНАТИВНЫХ БЕЛКОВ
Ключевые слова:
белковый дизайн, гетеро-олигомер, мультивалентное связывание, Sm-подобные белки, шаперон
Аннотация
Белки являются одним из ключевых элементов клетки. Их правильное сворачивание и предотвращение агрегации в условиях стресса обеспечивают белки-шапероны. Понимание принципов функционирования шаперонов позволяет модифицировать и создавать новые шапероны для решения исследовательских задач и применения в биотехнологии. Мы создали искусственный шаперон на основе апикального домена GroEL. В данной работе мы представляем подход, позволяющий изменять количество сайтов связывания ненативных белков на этом шапероне. Такой подход позволил нам оценить стехиометрию и силу связывания ненативного белка созданным нами шапероном. Показано, что для прочного связывания ненативной αLA необходимо его взаимодействие с несколькими апикальными доменами GroEL. В то же время константа диссоциации такого комплекса существенно не меняется при увеличении числа связывающих доменов в олигомере. С полным гептамерным кольцом апикальных доменов может быть связано до 4 молекул αLA. В будущем предложенный в данной работе метод также можно будет использовать не только для изучения шаперонов, но и для получения белков с комбинацией любых функциональных доменов.
Литература
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5. Martos, V., Castreno, P., Valero, J., Mendoza, J. Binding to protein surfaces by supramolecular multivalent scaffolds, in Current Opinion in Chemical Biology, 2008, vol. 12, pp. 698-706.
6. Scheepers, M.R.W., IJzendoorn, L.J., Prins, M.W.J. Multivalent weak interactions enhance selectivity of interparticle binding, in PNAS, 2020, vol. 117, no. 37, pp. 22690-22697.
7. Csizmar, C.M., Petersburg, J., Perry, T.J., Rozumalski, L., Hackel, B.J., Wagner, C.R. Multivalent Ligand Binding to Cell Membrane Antigens: Defining the Interplay of Affinity, Valency, and Expression Density, in J. Am. Chem. Soc., 2018, vol. 1, pp 1-36.
8. Dernedde, J. Multivalency in Biosystems, in Multivalency: Concepts, Research & Applications, 2018, vol. 4, pp. 103-120.
9. Marchenkov, V., Gorokhovatsky, A., Marchenko, N., Ivashina, T., Semisotnov, G. Back to GroEL-Assisted Protein Folding: GroES Binding-Induced Displacement of Denatured Proteins from GroEL to Bulk Solution, in Biomolecules, 2020, vol. 10, no. 1, pp. 162-174.
10. Errington, W.J., Bruncsics, D., Sarkar, C.A. Mechanisms of noncanonical binding dynamics in multivalent protein-protein interactions, in PNAS, 2019, vol. 116, no. 51, pp. 25659-25667.
11. Tan, Z.C., Meyera, A.S. A general model of multivalent binding with ligands of heterotypic subunits and multiple surface receptors, in Math Biosci., 2021, vol. 342, pp. 108714.
12. Bruncsics, B., Errington, W.J., Sarkar, C.A. MVsim is a toolset for quantifying and designing multivalent interactions, in Nature Communications, 2022, vol. 13, no. 5029, pp. 1-13.
13. Douzi, B. Protein-Protein Interactions: Surface Plasmon Resonance, in Methods. Mol. Biol., 2017, vol. 1615, 257-275.
14. Sultana, A., Lee, J.E. Measuring protein-protein and protein-nucleic Acid interactions by biolayer interferometry, in Curr. Protoc. Protein. Sci., 2015, vol. 19, no. 25, pp. 1-26.
15. Jerabek-Willemsen, M., André, T., Wanner, R., Roth, H.M., Duhr, S., Baaske, P., Breitsprecher, D. MicroScale Thermophoresis: Interaction analysis and beyond, in Journal of Molecular Structure, 2014, vol. 1077, pp. 101-113.
16. Pierce, M.M., Raman, C.S., Nall B.T. Isothermal titration calorimetry of protein-protein interactions, in Methods, 1999, vol. 19, no. 2, pp. 213-221.
17. Linke, P., Amaning, K., Maschberger, M., Vallee, F., Steier, V., Baaske, P., Duhr, S., Breitsprecher, D., Rak, A. An Automated Microscale Thermophoresis Screening Approach for Fragment-Based Lead Discovery, in J Biomol Screen, 2016, vol. 21, no. 4, pp. 414-21.
18. Mikhaylina A.O., Lekontseva N.V., Marchenkov V.V., Kolesnikova V.V., Khairetdinova A.R., Nikonov O.S., Balobanov V.A. The New Functional Hybrid Chaperone Protein ADGroEL-SacSm, in Molecules, 2023, vol. 28, pp. 6196.
19. Lekontseva, N.V., Stolboushkina, E.A., Nikulin, A.D. Diversity of LSM Family Proteins: Similarities and Differences, in Biochemistry (Moscow), 2021, vol. 86, pp. S38-S49.
20. Mura, C., Randolph, P.S., Patterson, J., Cozen, A.E. Archaeal and eukaryotic homologs of Hfq, in RNA Biology, 2013, vol. 10, no. 4, pp. 636-651.
21. Murina, V.N., Melnik, B.S., Filimonov, V.V., Ühlein, M., Weiss, M.S., Müller, U., Nikulin, A.D. Effect of Conserved Intersubunit Amino Acid Substitutions on Hfq Protein Structure and Stability, in Biochemistry (Moscow), 2014, vol. 79, no. 5, pp. 469-477.
22. Horovitz, A., Reingewertz, Y.H., Cuéllar, J., Valpuesta, J.M. Chaperonin Mechanisms: Multiple and (Mis)Understood? in Annu. Rev. Biophys., 2022, vol. 51, pp. 115-33.
23. Marchenkov, V., Lekontseva, N., Marchenko, N., Kashparov, I., Murina, V., Nikulin, A., Filimonov, V., Semisotnov, G. The Denaturant- and Mutation-Induced Disassembly of Pseudomonas aeruginosa Hexameric Hfq Y55W Mutant, in Molecules, 2022, vol. 27, no. 12, pp. 3821.
24. Zahn, R., Buckle, A.M., Perrett, S., Johnson, C.M, Corrales, F.J., Golbik, R., Fersht, A.R. Chaperone activity and structure of monomeric polypeptide binding domains of GroEL, in Proc. Natl. Acad. Sci. USA, 1996, vol. 93, no. 26, pp. 15024-15029.
2. Merminod, S., Edisonb, J.R., Fanga, H., Hagana, M.F., Rogers, W.B. Avidity and surface mobility in multivalent ligand-receptor binding, in Nanoscale, 2021, vol. 13, no. 29, pp. 12602-12612.
3. Xia, X., Zhang, G., Ciamarra, M.P., Jiao, Y., Ni, R. The Role of Receptor Uniformity in Multivalent Binding, in JACS Au, 2023, vol. 3, pp. 1385-1391.
4. Curk, T., Dobnikar, J., Frenkel, D. Design Principles for Super Selectivity using Multivalent Interactions, in Multivalency: Concepts, Research & Applications, 2018, vol. 3, pp. 75-101.
5. Martos, V., Castreno, P., Valero, J., Mendoza, J. Binding to protein surfaces by supramolecular multivalent scaffolds, in Current Opinion in Chemical Biology, 2008, vol. 12, pp. 698-706.
6. Scheepers, M.R.W., IJzendoorn, L.J., Prins, M.W.J. Multivalent weak interactions enhance selectivity of interparticle binding, in PNAS, 2020, vol. 117, no. 37, pp. 22690-22697.
7. Csizmar, C.M., Petersburg, J., Perry, T.J., Rozumalski, L., Hackel, B.J., Wagner, C.R. Multivalent Ligand Binding to Cell Membrane Antigens: Defining the Interplay of Affinity, Valency, and Expression Density, in J. Am. Chem. Soc., 2018, vol. 1, pp 1-36.
8. Dernedde, J. Multivalency in Biosystems, in Multivalency: Concepts, Research & Applications, 2018, vol. 4, pp. 103-120.
9. Marchenkov, V., Gorokhovatsky, A., Marchenko, N., Ivashina, T., Semisotnov, G. Back to GroEL-Assisted Protein Folding: GroES Binding-Induced Displacement of Denatured Proteins from GroEL to Bulk Solution, in Biomolecules, 2020, vol. 10, no. 1, pp. 162-174.
10. Errington, W.J., Bruncsics, D., Sarkar, C.A. Mechanisms of noncanonical binding dynamics in multivalent protein-protein interactions, in PNAS, 2019, vol. 116, no. 51, pp. 25659-25667.
11. Tan, Z.C., Meyera, A.S. A general model of multivalent binding with ligands of heterotypic subunits and multiple surface receptors, in Math Biosci., 2021, vol. 342, pp. 108714.
12. Bruncsics, B., Errington, W.J., Sarkar, C.A. MVsim is a toolset for quantifying and designing multivalent interactions, in Nature Communications, 2022, vol. 13, no. 5029, pp. 1-13.
13. Douzi, B. Protein-Protein Interactions: Surface Plasmon Resonance, in Methods. Mol. Biol., 2017, vol. 1615, 257-275.
14. Sultana, A., Lee, J.E. Measuring protein-protein and protein-nucleic Acid interactions by biolayer interferometry, in Curr. Protoc. Protein. Sci., 2015, vol. 19, no. 25, pp. 1-26.
15. Jerabek-Willemsen, M., André, T., Wanner, R., Roth, H.M., Duhr, S., Baaske, P., Breitsprecher, D. MicroScale Thermophoresis: Interaction analysis and beyond, in Journal of Molecular Structure, 2014, vol. 1077, pp. 101-113.
16. Pierce, M.M., Raman, C.S., Nall B.T. Isothermal titration calorimetry of protein-protein interactions, in Methods, 1999, vol. 19, no. 2, pp. 213-221.
17. Linke, P., Amaning, K., Maschberger, M., Vallee, F., Steier, V., Baaske, P., Duhr, S., Breitsprecher, D., Rak, A. An Automated Microscale Thermophoresis Screening Approach for Fragment-Based Lead Discovery, in J Biomol Screen, 2016, vol. 21, no. 4, pp. 414-21.
18. Mikhaylina A.O., Lekontseva N.V., Marchenkov V.V., Kolesnikova V.V., Khairetdinova A.R., Nikonov O.S., Balobanov V.A. The New Functional Hybrid Chaperone Protein ADGroEL-SacSm, in Molecules, 2023, vol. 28, pp. 6196.
19. Lekontseva, N.V., Stolboushkina, E.A., Nikulin, A.D. Diversity of LSM Family Proteins: Similarities and Differences, in Biochemistry (Moscow), 2021, vol. 86, pp. S38-S49.
20. Mura, C., Randolph, P.S., Patterson, J., Cozen, A.E. Archaeal and eukaryotic homologs of Hfq, in RNA Biology, 2013, vol. 10, no. 4, pp. 636-651.
21. Murina, V.N., Melnik, B.S., Filimonov, V.V., Ühlein, M., Weiss, M.S., Müller, U., Nikulin, A.D. Effect of Conserved Intersubunit Amino Acid Substitutions on Hfq Protein Structure and Stability, in Biochemistry (Moscow), 2014, vol. 79, no. 5, pp. 469-477.
22. Horovitz, A., Reingewertz, Y.H., Cuéllar, J., Valpuesta, J.M. Chaperonin Mechanisms: Multiple and (Mis)Understood? in Annu. Rev. Biophys., 2022, vol. 51, pp. 115-33.
23. Marchenkov, V., Lekontseva, N., Marchenko, N., Kashparov, I., Murina, V., Nikulin, A., Filimonov, V., Semisotnov, G. The Denaturant- and Mutation-Induced Disassembly of Pseudomonas aeruginosa Hexameric Hfq Y55W Mutant, in Molecules, 2022, vol. 27, no. 12, pp. 3821.
24. Zahn, R., Buckle, A.M., Perrett, S., Johnson, C.M, Corrales, F.J., Golbik, R., Fersht, A.R. Chaperone activity and structure of monomeric polypeptide binding domains of GroEL, in Proc. Natl. Acad. Sci. USA, 1996, vol. 93, no. 26, pp. 15024-15029.
Поступила в редакцию
2023-12-04
Опубликована 2023-12-29
Опубликована 2023-12-29