Brownian-dynamics simulations of protein–protein interactions in the photosynthetic electron transport chain

Khruschev, S. S.; Abaturova, A. M.; Diakonova, A. N.; Fedorov, Vladimir A.; Ustinin, D. M.; Kovalenko, I. B.; Riznichenko, G. Yu.; Rubin, A. B.

doi:10.1134/s0006350915020086

Cited by 11 publications

(5 citation statements)

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“…Probabilities of contacts between the tail of a-tubulin and its body were calculated as the average fraction of contacts over the whole simulation time, based on two simulations with one tubulin dimer and three simulations with the longitudinally assembled tubulin dimers (only the minus-end proximal a-tubulins were considered for tetramers) (Figure S3A). The distribution of electrostatic potential on the tubulin surface was mapped in Pymol based on Poisson-Boltzmann calculations performed using the ProKSim software (Khruschev, et al, 2015).…”

Section: Declaration Of Interestsmentioning

confidence: 99%

α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics

et al. 2021

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Section: Declaration Of Interestsmentioning

confidence: 99%

α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics

et al. 2021

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“…The role of electrostatic interactions in the formation of the oxidation-reduction complex of two proteins was studied in the interaction model of the well-studied pair of photosynthetic electron transfer proteins, Pc and Cyt f. This pair of proteins is a classic object of experimental research (reviewed by Cruz-Gallardo et al [25], and Khruschev et al [12]) and Brownian dynamics studies [13,18,23,24,[26][27][28][29]. The physiological function of the protein Pc consists of the shuttle electron transfer between the subunit f of cytochrome complex b6-f and the photosystem I in all higher plants and some algae.…”

Section: Productive and Non-productive Encounter Complexesmentioning

confidence: 99%

“…To simulate the interactions of mobile electron carriers with multi-enzyme complexes in photosynthetic membrane the method of 'direct multi-particle modeling' was developed at the Lomonosov Moscow State University by the Department of Biophysics of the Biological Faculty together with the Department of Computer Methods in Physics of the Physics Faculty. The main idea of this approach and the results obtained are presented in the papers [4,[6][7][8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

“…Models of Brownian dynamics (see review [12]) simulate the diffusion and mutual orientation of protein molecules in the formation of a preliminary complex. The distinctive feature of our models is that they are multi-particulate and allow us to simulate not only the processes of interaction of proteins in solution, but also to study the behavior of ensembles of interacting macromolecules in the complex interior of the photosynthetic membrane and to take into account the structural features of the membrane organization [14,16,17].…”

Section: Introductionmentioning

confidence: 99%

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Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling

et al. 2019

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The paper presents the review of works on modeling the interaction of photosynthetic proteins using the multiparticle Brownian dynamics method developed at the Department of Biophysics, Biological Faculty, Lomonosov Moscow State University. The method describes the displacement of individual macromolecules – mobile electron carriers, and their electrostatic interactions between each other and with pigment-protein complexes embedded in photosynthetic membrane. Three-dimensional models of the protein molecules were constructed on the basis of the data from the Protein Data Bank. We applied the Brownian methods coupled to molecular dynamic simulations to reveal the role of electrostatic interactions and conformational motions in the transfer of an electron from the cytochrome complex Cyt b6f) membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and to the molecule of the mobile carrier plastocyanin (Pc) in plants, green algae and cyanic bacteria. Taking into account the interior of photosynthetic membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and Cyt b6f, embedded in photosynthetic membrane, electron transfer and complex dissociation. Multiparticle Brownian simulation method can be used to consider the processes of protein interactions in subcellular systems in order to clarify the role of individual stages and the biophysical mechanisms of these processes.

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“…Its structure is variable, as one of the molecules undergoes rotational and linear motions relative to the other one without any noticeable changes in the interaction energy. In our previous studies, we used BD simulations and hierarchical cluster analysis to determine the energetically favorable states during the diffusional encounter of spinach Pc and turnip Cyt f (Khruschev et al ). We identified two ensembles of mutual orientations that differ considerably from each other with respect to the orientation of the Pc molecule relative to Cyt f .…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of plastocyanin–cytochrome f complex formation in higher plants, green algae and cyanobacteria

Fedorov

Kovalenko

Khruschev

et al. 2019

Physiologia Plantarum

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Mechanisms of the complex formation between plastocyanin and cytochrome f in higher plants (Spinacia oleracea and Brassica rapa), green microalgae Chlamydomonas reinhardtii and two species of cyanobacteria (Phormidium laminosum and Nostoc sp.) were investigated using combined Brownian and molecular dynamics simulations and hierarchical cluster analysis. In higher plants and green algae, electrostatic interactions force plastocyanin molecule close to the heme of cytochrome f. In the subsequent rotation of plastocyanin molecule around the point of electrostatic contact in the vicinity of cytochrome f, copper (Cu) atom approaches cytochrome heme forming a stable configuration where cytochrome f molecule behaves as a rather rigid body without conformational changes. In Nostoc plastocyanin molecule approaches cytochrome f in a different orientation (head‐on) where the stabilization of the plastocyanin–cytochrome f complex is accompanied by the conformational changes of the G188E189D190 loop that stabilizes the whole complex. In cyanobacterium P. laminosum, electrostatic preorientation of the approaching molecules was not detected, thus indicating that random motions rather than long‐range electrostatic interactions are responsible for the proper mutual orientation. We demonstrated that despite the structural similarity of the investigated electron transport proteins in different photosynthetic organisms, the complexity of molecular mechanisms of the complex formation increases in the following sequence: non‐heterocystous cyanobacteria – heterocystous cyanobacteria – green algae – flowering plants.

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Brownian-dynamics simulations of protein–protein interactions in the photosynthetic electron transport chain

Cited by 11 publications

References 121 publications

α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics

α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics

Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling

Comparative analysis of plastocyanin–cytochrome f complex formation in higher plants, green algae and cyanobacteria

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