БЕСКОНТАКТНАЯ АТОМНО-СИЛОВАЯ МИКРОСКОПИЯ ДЛЯ ИССЛЕДОВАНИЯ БИОМОЛЕКУЛ В ЖИДКОСТИ
- Авторы: Мамедов Т.1, Швирст А.1, Федотова М.В2, Чуев Г.Н1
-
Учреждения:
- Институт теоретической и экспериментальной биофизики РАН
- Институт химии растворов им. Г.А. Крестова РАН
- Выпуск: Том 69, № 4 (2024)
- Страницы: 723-736
- Раздел: Молекулярная биофизика
- URL: https://kazanmedjournal.ru/0006-3029/article/view/675880
- DOI: https://doi.org/10.31857/S0006302924040056
- EDN: https://elibrary.ru/NHSYHJ
- ID: 675880
Цитировать
Аннотация
Бесконтактная атомно-силовая микроскопия, разновидность сканирующей зондовой микроскопии, в последние два десятилетия активно используется для изучения гидратированных биомолекул. В частности, как показывает анализ современной литературы, она является весьма перспективной в исследовании адсорбированных биомакромолекул и биомакромолекулярных комплексов на границе раздела фаз или на поверхности мембран. В настоящем мини-обзоре описываются основы данного метода, его применение для биомолекул, обсуждаются требования к методу и возможности его расширения за счет дополнительной обработки полученных экспериментальных данных с помощью теоретического анализа, молекулярного моделирования или машинного обучения.
Об авторах
Т. Мамедов
Институт теоретической и экспериментальной биофизики РАНПущино, Россия
А. Швирст
Институт теоретической и экспериментальной биофизики РАНПущино, Россия
М. В Федотова
Институт химии растворов им. Г.А. Крестова РАНИваново, Россия
Г. Н Чуев
Институт теоретической и экспериментальной биофизики РАН
Email: genchuev@rambler.ru
Пущино, Россия
Список литературы
- Binnig G. and Rohrer H. Scanning tunneling microscopy. Helvetica Phys. Acta, 55, 726–735 (1982).
- Binnig G., Quate C. F., and Gerber C. Atomic force microscope. Phys. Rev. Lett., 56 (9), 930–933 (1986). doi: 10.1103/PhysRevLett.56.930
- Garcia R., Amplitude modulation atomic force microscopy (Wiley‐VCH Verlag GmbH & Co., 2010). doi: 10.1002/9783527632183
- Morris V. J., Kirby A. R., and Gunning A. P. Atomic force microscopy for biologists (Imperial College Press, 2009).
- Melitz W., Shen J., Kummel A. C., and Lee S. Kelvin probe force microscopy and its application. Surface Sci. Rep., 66 (1), 1–27 (2011). doi: 10.1016/j.surfrep.2010.10.001
- Chen X., Li B., Liao Z., Li J., Li X., Yin J., and Guo W. Principles and applications of liquid-environment atomic force microscopy. Adv. Mater. Interfaces, 9 (35), 2201864 (2022). doi: 10.1002/admi.202201864
- Baro A. M. and Reifenberger R. G. Atomic force microscopy in liquid (Wiley-VCH Verlag GmbH & Co., 2012). doi: 10.1002/9783527649808
- Kominami H., Kobayashi K., and Yamada H. Molecularscale visualization and surface charge density measurement of Z-DNA in aqueous solution. Sci. Rep., 9, 6851 (2019). doi: 10.1038/s41598-019-42394-5
- Kuchuk K. and Sivan U. Hydration structure of a single DNA molecule revealed by frequency-modulation atomic force microscopy. Nano Lett., 18 (4), 2733–2737 (2018). doi: 10.1021/acs.nanolett.8b00854
- Heenan P. R. and Perkins T. T. Imaging DNA Equilibrated onto mica in liquid using biochemically relevant deposition conditions. ACS Nano, 13 (4), 4220–4229 (2019). doi: 10.1021/acsnano.8b09234
- Sotres J. and Baro A. M. AFM imaging and analysis of electrostatic double layer forces on single DNA molecules. Biophys. J., 98 (9), 1995–2004 (2010). doi: 10.1016/j.bpj.2009.12.4330
- Sumikama T., Foster A. S., and Fukuma T. Computed atomic force microscopy images of chromosomes by calculating forces with oscillating probes. J. Phys. Chem. C., 124 (3), 2213–2218 (2020). doi: 10.1021/acs.jpcc.9b10263
- Ido S., Kobayashi K., Oyabu N., Hirata Y., Matsushige K., and Yamada H. Structured water molecules on membrane proteins resolved by atomic force microscopy. Nano Lett., 22 (6), 2391–2397 (2022). doi: 10.1021/acs.nanolett.2c00029
- Philippsen A., Im W., Engel A., Schirmer T., Roux B., and Muller D. J. Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin. Biophys. J., 82 (3), 1667–1676 (2003). doi: 10.1016/S0006-3495(02)75517-3
- MacKerell A. D., Bashford D., Bellott M., Dunbrack R. L., Evanseck J. D., Field M. J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F. T., Mattos C., Michnick S., Ngo T., Nguyen D. T., Prodhom B., Reiher W. E., Roux B., Schlenkrich M., Smith J. C., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Yin D., and Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B., 102 (18), 3586–3616 (1998). doi: 10.1021/jp973084f
- Hernando-Perez M., Cartagena-Rivera A. X., Lošdorfer Božič A., Carrillo P. J., San Martin C., Mateu M. G., Raman A., Podgornik R., and Pablo P. Quantitative nanoscale electrostatics of viruses. J. Nanoscale, 7 (41), 17289–17298 (2015). doi: 10.1039/C5NR04274G
- Heldt C. L., Areo O., Joshi P. U., Mi X., Ivanova Y., and Berrill A. Empty and full AAV capsid charge and hydrophobicity differences measured with single-particle AFM. Langmuir, 39 (16), 5641–5648 (2023). doi: 10.1021/acs.langmuir.2c02643
- Дерягин Б. В., Чураев Н. В., и Муллер В. М. Поверхностные силы (Наука, М., 1985).
- van Oss C. J. The extended DLVO theory. Interface Sci. Technol., 16, 31–48 (2008). doi: 10.1016/S1573-4285(08)00203-2
- Sharma P. K. and Hanumantha R. K. Adhesion of paenibacillus polymyxa on chalcopyrite and pyrite: surface thermodynamics and extended DLVO theory. Colloids and Surfaces B: Biointerfaces, 29 (1), 21–38 (2003). doi: 10.1016/S0927-7765(02)00180-7
- Liang Y., Hilal N., Langston P., and Starov V. Interaction forces between colloidal particles in liquid: theory and experiment. J. Adv. Colloid Interface Sci., 134–135, 151–166 (2007). doi: 10.1016/j.cis.2007.04.003
- Klaassen A., Liu F., Mugele F., and Siretanu I. Correlation between electrostatic and hydration forces on silica and gibbsite surfaces: an atomic force microscopy study. Langmuir, 38 (3), 914–926 (2022). doi: 10.1021/acs.langmuir.1c02077
- Li L., Eppell S., and Zypman F. Method to quantify nanoscale surface charge in liquid with atomic force microscopy. Langmuir, 36 (15), 4123–4134 (2020). doi: 10.1021/acs.langmuir.9b03602
- Li L., Steinmetz N., Eppell S., and Zypman F. Charge calibration standard for atomic force microscope tips in liquids. Langmuir, 36 (45), 13621–13632 (2020). doi: 10.1021/acs.langmuir.0c02455
- Blum L. J. Invariant Expansion for two‐body correlations: thermodynamic functions, scattering, and the Ornstein–Zernike equation. J. Chem. Phys., 56, 303–310 (1972). doi: 10.1063/1.1676864
- Ikeguchi M. and Doi J. Direct numerical solution of the Ornstein–Zernike integral equation and spatial distribution of water around hydrophobic molecules. J. Chem. Phys., 103 (12), 5011–5017 (1995). doi: 10.1063/1.470587
- Ishizuka R. and Yoshida N. Extended molecular Ornstein−Zernike integral equation for fully anisotropic solute molecules: formulation in a rectangular coordinate system. J. Chem. Phys., 139 (8), 084119 (2013). doi: 10.1063/1.4819211
- Fedotova M. V. and Kruchinin S. E. Ion-binding of glycine zwitterion with inorganic ions in biologically relevant aqueous electrolyte solutions. Biophys. Chem., 190–191, 25–31 (2014). doi: 10.1016/j.bpc.2014.04.001
- Dmitrieva O. A. and Fedotova M. V. Characterization of selective binding of biologically relevant inorganic ions with the proline zwitterion by 3D-RISM theory. New J. Chem., 39 (11), 8594–8601 (2015). doi: 10.1039/C5NJ01559F
- Fedotova M. V. and Dmitrieva O. A. Proline hydration at low temperatures: its role in the protection of cell from freeze-induced stress. Amino Acids, 48 (7), 1685–1694 (2016). doi: 10.1007/s00726-016-2232-1
- Fedotova M. V., Kruchinin S. E., and Chuev G. N. Hydration structure of osmolyte TMAO: concentration/pressure-induced response. New J. Chem., 41 (3), 1219–1228 (2017). doi: 10.1039/C6NJ03296F
- Fedotova M. V. and Kruchinin S. E. Hydration and ion-binding of glycine betaine: How they may be involved into protection of proteins under abiotic stresses. J. Mol. Liq., 244, 489–498 (2017). doi: 10.1016/j.molliq.2017.08.117
- Fedotova M. V. Compatible osmolytes – bioprotectants: Is there a common link between their hydration and their protective action under abiotic stresses? J. Mol. Liq., 292, 111339 (2019). doi: 10.1016/j.molliq.2019.111339
- Fedotova M. V., Kruchinin S. E., and Chuev G. N. Hydration features of the neurotransmitter acetylcholine. J. Mol. Liq., 304, 112757 (2020). doi: 10.1016/j.molliq.2020.112757
- Kumawat N., Tucs A., Bera S., Chuev G. N., Valiev M., Fedotova M. V., Kruchinin S. E., Tsuda K., Sljoka A., and Chakraborty A. Site density functional theory and structural bioinformatics analysis of the SARS-CoV spike protein and hACE2 complex. Molecules, 27 (3), 799 (2022). doi: 10.3390/molecules27030799
- Kruchinin S. E., Kislinskaya E. E., Chuev G. N., and Fedotova M. V. Protein 3D hydration: a case of bovine pancreatic trypsin inhibitor. Int. J. Mol. Sci., 23 (23), 14785 (2022). doi: 10.3390/ijms232314785
- Kruchinin S. E., Chuev G. N., and Fedotova M. V. Molecular insight on hydration of protein tyrosine phosphatase 1B and its complexes with ligands. J. Mol. Liq., 384, 122281 (2023). doi: 10.1016/j.molliq.2023.122281
- Кручинин С. Е., Федотова М. В., Кислинская Е. Е. и Чуев Г. Н. In silico исследование сольватационных эффектов в растворах биомолекул: возможности подхода, основанного на 3D-распределении атомной плотности растворителя. Биофизика, 68 (5), 837–849 (2023). doi: 10.31857/S0006302923050010
- Chandler D. and Andersen H. C. Optimized cluster expansions for classical fluids. II. Theory of molecular liquids. J. Chem. Phys., 57 (5), 1930 (1972). doi: 10.1063/1.1678513
- Hirata F., Rossky P. J., and Pettitt B. M. The interionic potential of mean force in a molecular polar solvent from an extended RISM equation. J. Chem. Phys., 78 (6), 4133–4144 (1983). doi: 10.1063/1.445090
- Perkyns J. and Pettitt B. M. A site–site theory for finite concentration saline solutions. J. Chem. Phys., 97 (10), 7656–7666 (1992). doi: 10.1063/1.463485
- Harada M. and Tsukada M. Tip-sample interaction force mediated by water molecules for AFM in water: Three-dimensional reference interaction site model theory. J. Physical Review B., 82 (3), 035414 (2010). doi: 10.1103/PhysRevB.82.035414
- Watkins M. and Reischl B. A simple approximation for forces exerted on an AFM tip in liquid. J. Chem. Phys., 138 (15), 154703 (2013). doi: 10.1063/1.4800770
- Miyazawa K., Kobayashi N., Watkins M., Shluger A., Amano K., and Fukuma T. A relationship between three-dimensional surface hydration structures and force distribution measured by atomic force microscopy. J. Nanoscale, 8, 7334–7342 (2016). doi: 10.1039/C5NR08092D
- Trabuco L. G., Villa E., Mitra K., Frank J., and Schulten K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. J. Structure, 16 (5), 673–683 (2008). doi: 10.1016/j.str.2008.03.005
- Fuchigami S. and Takada S. Inferring conformational state of myosin motor in an atomic force microscopy image via flexible fitting molecular simulations. J. Frontiers in Molecular Biosciences, 9, 882989 (2022). doi: 10.3389/fmolb.2022.882989
- LeCun Y., Boser B., Denker J. S., Henderson D., Howard R. E., Hubbard W., and Jackel L. D. Backpropagation applied to handwritten zip code recognition. J. Neural Computation, 1 (4), 541–551 (1989). doi: 10.1162/neco.1989.1.4.541
- Oinonen N., Xu C., Alldritt B., Canova F. F., Urtev F., Cai S., Krejci O., Kannala J., Liljeroth P., and Foster A. S. Correction to electrostatic discovery atomic force microscopy. J. ACS Nano, 16, 89 (2022). doi: 10.1021/acsnano.2c08130
- Fukuma T., Ueda Y., Yoshioka Sh., and Asakawa H. Atomic-scale distribution of water molecules at the micawater interface visualized by three-dimensional scanning force microscopy. Phys. Rev. Lett., 104 (1), 016101 (2010). doi: 10.1103/PhysRevLett.104.016101
Дополнительные файлы
