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Volume 18   Issue 2   Year 2023
References

  1. Watanabe M., Semchonok D.A., Webber-Birungi M.T., Ehira S., Kondo K., Narikawa R., Ohmori M., Boekema E.J., Ikeuchi M. Attachment of phycobilisomes in an antenna–photosystem I supercomplex of cyanobac-teria. Proceedings of the National Academy of Sciences. 2014;111(7):2512–2517. doi: 10.1073/pnas.1320599111
  2. Simpson D.J., Knoetzel J. Light-harvesting Complexes of Plants and Algae: Introduction, Survey and Nomenclature. Oxygenic Photosynthesis: The Light Reactions. Advances in Photosynthesis and Respiration. 1996;4. doi: 10.1007/0-306-48127-8_27
  3. Naschberger A., Mosebach L., Tobiasson V., Kuhlgert S., Scholz M., Perez-Boerema A., Ho T.T.H., Vidal-Meireles A., Takahashi Y., Hippler M., Amunts A. Algal photosystem I dimer and high-resolution model of PSI-plastocyanin complex. Nat. Plants. 2022;8(10):1191–1201. doi: 10.1038/s41477-022-01253-4
  4. Höhner R., Pribil M., Herbstová M., Lopez L.S., Kunz H.-H., Li M., Wood M., Svoboda V., Puthiyaveetil S., Leister D., Kirchhoff H. Plastocyanin is the long-range electron carrier between photo-system II and photosystem I in plants. Proceedings of the National Academy of Sciences. 2020;117(26):15354–15362. doi: 10.1073/pnas.2005832117
  5. Caspy I., Borovikova-Sheinker A., Klaiman D., Shkolnisky Y., Nelson N. The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin. Nat. Plants. 2020;6:1300–1305. doi: 10.1038/s41477-020-00779-9
  6. Caspy I., Fadeeva M., Kuhlgert S., Borovikova-Sheinker A., Klaiman D., Masrati G., Drepper F., Ben-Tal N., Hippler M., Nelson N. Structure of plant photosystem I-plastocyanin complex reveals strong hydrophobic interactions. Biochem J. 2021;478(12):2371–2384. doi: 10.1042/BCJ20210267
  7. Hippler M., Reichert J., Sutter M., Zak E., Altschmied L., Schröer U., Herrmann R.G., Haehnel W. The plastocyanin binding domain of photosystem I. EMBO J. 1996;15(23):6374–84. doi: 10.1002/j.1460-2075.1996.tb01028.x
  8. Hippler M., Drepper F., Haehnel W. The oxidizing site of photosystem I modulates the electron transfer from plastocyanin to P700+. Photosyntthesis: from Light to Biosphere. 1995;2:99–102. doi: 10.1007/978-94-009-0173-5_254
  9. Drepper F., Hippler M., Nitschke W., Haehnel W. Binding dynamics and electron transfer between plastocyanin and photosystem I. Biochemistry. 1996;35:1282–1295. doi: 10.1021/bi951471e
  10. Fedorov V.A., Kovalenko I.B., Khruschev S.S., Ustinin D.M., Antal T.K., Riznichenko G.Yu., Rubin A.B. Comparative analysis of plastocyanin-cytochrome f complex for-mation in higher plants, green algae and cyanobacteria. Physiologia Plantarum. 2019(166):320–335. doi: 10.1111/ppl.12940
  11. Khruschev S.S., Abaturova A.M., Diakonova A.N., Ustinin D.M., Zlenko D.V., Fedorov V.A., Kovalenko I.B., Riznichenko G.Yu., Rubin A.B. Multi-particle brownian dynamics software ProKSim for protein-protein interactions modeling. Computer Research and Modeling. 2013;5(1):47–64. doi: 10.20537/2076-7633-2013-5-1-47-64
  12. Mazor Y., Borovikova A., Caspy I. Nelson N. Structure of the plant photosystem I supercomplex at 2.6 Å resolution. Nature Plants. 2017;3:17014. doi: 10.1038/nplants.2017.14
  13. Webb B., Sali A. Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics. 2016;54(1). doi: 10.1002/cpbi.3
  14. Schrödinger L.L.C. DeLano W. The PyMOL Molecular Graphics System, Version 2.5. https://pymol.org (accessed 20.11.2023).
  15. Huang J., Rauscher S., Nawrocki G., Ran T., Feig M., Groot B., Grubmüller H. MacKerell A.D.Jr. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nature Methods. 2017;14(1):71–73. doi: 10.1038/nmeth.4067
  16. Vanommeslaeghe K., Hatcher E., Acharya C., Kundu S., Zhong S., Shim J., Darian E., Guvench O., Lopes P., Vorobyov I., Mackerell A. D. Jr. CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields. Journal of Computational Chemistry. 2010;31(4):671–690. doi: 10.1002/jcc.21367
  17. Adam S., Knapp‐Mohammady M., Yi.J., Bondar A.N. Revised CHARMM force field parameters for iron‐containing cofactors of photosystem II. Journal of Computational Chemistry. 2018;39(1):7–20. doi: 10.1002/jcc.24918
  18. Huang J., MacKerell Jr A.D. CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry. 2013;34(25):2135–2145. doi: 10.1002/jcc.23354
  19. Vanommeslaeghe K., MacKerell Jr A.D. Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. Journal of Chemical Information and Modeling. 2012;52(12):3144–3154. doi: 10.1021/ci300363c
  20. Vanommeslaeghe K., Raman E.P., MacKerell Jr A.D. Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. Journal of Chemical Information and Modeling. 2012;52(12):3155–3168. doi: 10.1021/ci3003649
  21. Grudzinski W., Nierzwicki L., Welc R., Reszczynska E., Luchowski R., Czub J., Gruszecki W.I. Localization and orientation of xanthophylls in a lipid bilayer. Scientific Reports. 2017;7(1):1–10. doi: 10.1038/s41598-017-10183-7
  22. Teixeira M.H., Arantes G.M. Effects of lipid composition on membrane distribution and permeability of natural quinones. RSC Advances. 2019;9(29):16892–16899. doi: 10.1039/C9RA01681C
  23. Jo S., Kim T., Iyer V.G., Im W. CHARMM‐GUI: a web‐based graphical user interface for CHARMM. Journal of Computational Chemistry. 2008;29(11):1859–1865. doi: 10.1002/jcc.20945
  24. Lee J., Patel D.S., Ståhle J., Park S.-J., Kern N.R., Kim S., Lee J., Cheng X., Valvano M.A., Holst O., Knirel Y.A., Qi Y., Jo S., Klauda J.B., Widmalm G., Im W. CHARMM-GUI membrane builder for complex biological membrane simulations with glycolipids and lipoglycans. Journal of Chemical Theory and Computation. 2018;15(1):775–786. doi: 10.1021/acs.jctc.8b01066
  25. Chang C.H., Kim K. Density functional theory calculation of bonding and charge parameters for molecular dynamics studies on [FeFe] hydrogenases. Journal of Chemical Theory and Computation. 2009;5(4):1137–1145. doi: 10.1021/ct800342w
  26. Abraham M.J., Murtola T., Schulz R., Páll S., Smith J. C., Hess B., Lindahl E. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1:19–25. doi: 10.1016/j.softx.2015.06.001
  27. Gross E.L., Pearson Jr. D.C., Pearson D.C. Brownian dynamics simulations of the interaction of Chlamydomonas cytochrome f with plastocyanin and cytochrome c6. Biophys. J. 2003;85(3):2055–2068. doi: 10.1016/S0006-3495(03)74633-5
  28. Langevin P. On the theory of Brownian motion. C. R. Acad. Sci. 1908;146:530–533.
  29. Fogolari F., Brigo A., Molinari H. The Poisson-Boltzmann Equation for Biomolecular Electrostatics: A Tool for Structural Biology. J. Mol. Recognit. 2002;15:377–392. doi: 10.1002/jmr.577
  30. Ankerst M., Breunig M.M., Kriegel H.P., Sander J. OPTICS: Ordering Points to Identify the Clustering Structure. Proc. ACM SIGMOD. 1999:49–60. doi: 10.1145/304181.304187
  31. Elke A., Böhm C., Kröger P. DeLiClu: boosting robustness, completeness, usability, and efficiency of hierarchical clustering by a closest pair ranking. In: Proc. 10th Pacific-Asian Conf. Adv. Knowl. Discov. Data Min. 2006. P. 119–128. doi: 10.1007/11731139_16
  32. Sander J., Qin X., Lu Z., Niu N., Kovarsky A. Automatic extraction of clusters from hierarchical clustering representations. In: Proc. 7th Pacific-Asia Conf. Knowl. Discov. DataMining. 2003. P. 75–87. doi: 10.1007/3-540-36175-8_8
  33. Fedorov V.A., Khruschev S.S., Kovalenko I.B. Analysis of Brownian and molecular dynamics trajectories of to reveal the mechanisms of protein-protein interactions. Computer Research and Modeling. 2023;15(3):723–738. doi: 10.20537/2076-7633-2023-15-3-723-738
  34. Young S., Sigfridsson K., Olesen K., Hansson Ö. The involvement of the two acidic patches of spinach plastocyanin in the reaction with photosystem I. Biochimica et Biophysica Acta (BBA)-Bioenergetics. 1997;1322(2–3):106–114. doi: 10.1016/S0005-2728(97)00064-9
Table of Contents
Original Article
Fedorov V.A., Volkhin I.A., Khrushchev S.S., Antal T.K., Kovalenko I.B. Role of Charged Amino Acid Residues of Plastocyanin in Interaction with Cytochrome B6f Complex and Photosystem I of Higher Plants: A Study Using the Brownian Dynamics Method. Ìàthematical biology and bioinformatics. 2023;18(2):434-445. doi: 10.17537/2023.18.434
(published in Russian)

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