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Fedorov VA, Kovalenko IB, Khruschev SS, Ustinin DM, Antal TK, Riznichenko GY, Rubin AB. Comparative analysis of plastocyanin-cytochrome f complex formation in higher plants, green algae and cyanobacteria. PHYSIOLOGIA PLANTARUM 2019; 166:320-335. [PMID: 30740703 DOI: 10.1111/ppl.12940] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
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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Affiliation(s)
- Vladimir A Fedorov
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Ilya B Kovalenko
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
- Institute of Physics and Mathematics, Astrakhan State University, Astrakhan, 414056, Russia
- Scientific and Technological Center of Unique Instrumentation of the Russian Academy of Sciences, Moscow, 117342, Russia
- Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russia
| | - Sergei S Khruschev
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Dmitry M Ustinin
- Keldysh Institute of Applied Mathematics RAS, Moscow, 125047, Russia
| | - Taras K Antal
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | | | - Andrei B Rubin
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
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Khruschev SS, Abaturova AM, Diakonova AN, Fedorov VA, Ustinin DM, Kovalenko IB, Riznichenko GY, Rubin AB. Brownian-dynamics simulations of protein–protein interactions in the photosynthetic electron transport chain. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915020086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Kovalenko IB, Knyazeva OS, Riznichenko GY, Rubin AB. Computer simulation of plastocyanin interaction with cytochrome f and photosystem I in cyanobacterium Phormidium laminosum. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350914010047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Gabdoulline RR, Wade RC. On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f: Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events. J Am Chem Soc 2009; 131:9230-8. [PMID: 19518050 DOI: 10.1021/ja809567k] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The factors that determine the extent to which diffusion and thermal activation processes govern electron transfer (ET) between proteins are debated. The process of ET between plastocyanin (PC) and cytochrome f (CytF) from the cyanobacterium Phormidium laminosum was initially thought to be diffusion-controlled but later was found to be under activation control (Schlarb-Ridley, B. G.; et al. Biochemistry 2005, 44, 6232). Here we describe Brownian dynamics simulations of the diffusional association of PC and CytF, from which ET rates were computed using a detailed model of ET events that was applied to all of the generated protein configurations. The proteins were modeled as rigid bodies represented in atomic detail. In addition to electrostatic forces, which were modeled as in our previous simulations of protein-protein association, the proteins interacted by a nonpolar desolvation (hydrophobic) force whose derivation is described here. The simulations yielded close to realistic residence times of transient protein-protein encounter complexes of up to tens of microseconds. The activation barrier for individual ET events derived from the simulations was positive. Whereas the electrostatic interactions between P. laminosum PC and CytF are weak, simulations for a second cyanobacterial PC-CytF pair, that from Nostoc sp. PCC 7119, revealed ET rates influenced by stronger electrostatic interactions. In both cases, the simulations imply significant contributions to ET from both diffusion and thermal activation processes.
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Affiliation(s)
- Razif R Gabdoulline
- Molecular and Cellular Modeling Group, EML Research gGmbH, Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany.
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Díaz-Moreno I, Muñoz-López FJ, Frutos-Beltrán E, De la Rosa MA, Díaz-Quintana A. Electrostatic strain and concerted motions in the transient complex between plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum. Bioelectrochemistry 2009; 77:43-52. [PMID: 19616485 DOI: 10.1016/j.bioelechem.2009.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 06/04/2009] [Accepted: 06/04/2009] [Indexed: 11/15/2022]
Abstract
Many fleeting macromolecular interactions, like those being involved in electron transport, are essential in biology. However, little is known about the behaviour of the partners and their dynamics within their short-lived complex. To tackle such issue, we have performed molecular dynamics simulations on an electron transfer complex formed by plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum. Besides simulations of the isolated partners, two independent trajectories of the complex were calculated, starting from the two different conformations in the NMR ensemble. The first one leads to a more stable ensemble with a shorter distance between the metal sites of the two partners. The second experiences a significant drift of the complex conformation. Analyses of the distinct calculations show that the conformation of cytochrome f is strained upon binding of its partner, and relaxes upon its release. Interestingly, the principal component analysis of the trajectories indicates that plastocyanin displays a concerted motion with the small domain of cytochrome f that can be attributed to electrostatic interactions between the two proteins.
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Affiliation(s)
- Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla and C.S.I.C.), Spain
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Rubin A, Riznichenko G. Modeling of the Primary Processes in a Photosynthetic Membrane. PHOTOSYNTHESIS IN SILICO 2009. [DOI: 10.1007/978-1-4020-9237-4_7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Hart SE, Howe CJ, Mizuguchi K, Fernandez-Recio J. Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum. Protein Eng Des Sel 2008; 21:689-98. [DOI: 10.1093/protein/gzn051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Gross EL. A Brownian Dynamics computational study of the interaction of spinach plastocyanin with turnip cytochrome f: the importance of plastocyanin conformational changes. PHOTOSYNTHESIS RESEARCH 2007; 94:411-422. [PMID: 17972160 DOI: 10.1007/s11120-007-9192-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 05/01/2007] [Indexed: 05/25/2023]
Abstract
Brownian Dynamics (BD) computer simulations were used to study electrostatic interactions between turnip cytochrome f (cyt f) and spinach plastocyanin (PC). Three different spinach PC structures were studied: The X-ray crystal structure of Xue and coworkers [(1998) Protein Sci 7:2099-2105] and the NMR structure of Musiani et al. [(2005) J Biol Chem 280:18833-18841] and Ubbink and co-workers [(1998) Structure 6:323-335]. Significant differences exist in the backbone conformation between the PC taken from Ubbink and coworkers and the other two PC structures particularly the regions surrounding G10, E59-E60, and D51. Complexes formed in BD simulations using the PC of Ubbink and colleagues had a smaller Cu-Fe distance than the other two. These results suggest that different PC conformations may exist in solution with different capabilities of forming electron-transfer-active docks. All three types of complexes show electrostatic contacts between D42, E43, and D44 on PC and K187 on cyt f as well as between E59 on PC and K58 on cyt f. However, the PC of Ubbink and coworkers reveals additional contacts between D51 and cyt f as a result of the difference in backbone configuration. A second minor complex component was observed for the PC of Ubbink and co-workers and Xue and co-workers which had contacts between K187 on cyt f and E59 and E60 on PC rather than between K187 on cyt f and D42-D44 on PC as observed for the major components. This second type of complex may represent an earlier complex which rearranges to form a final complex capable of electron transfer.
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Affiliation(s)
- Elizabeth L Gross
- Department of Biochemistry, The Ohio State University, 484 W. 12th. Ave, Columbus, OH 43235, USA.
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Ermakova E. Brownian dynamics simulation of the competitive reactions: binase dimerization and the association of binase and barstar. Biophys Chem 2007; 130:26-31. [PMID: 17651890 DOI: 10.1016/j.bpc.2007.06.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 06/26/2007] [Accepted: 06/28/2007] [Indexed: 11/28/2022]
Abstract
A comparative study of the competitive reactions-the association reaction of binase with polypeptide inhibitor barstar and the reaction of binase dimerization-has been performed by the Brownian dynamics simulation method. It was shown that three types of the binase dimers could be formed and the dimerization reaction could compete with the inhibition reaction. The first type of the dimers leaves the active centre of binase free. During the formation of the dimers of the second and the third types the active centre of one or both binase molecules is blocked and ribonuclease becomes partially or fully inactive. Brownian dynamics simulation shown, that the ratio of competitive reaction rates depends on pH and ionic strength of solution.
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Affiliation(s)
- E Ermakova
- Kazan Institute of Biochemistry and Biophysics RAS, 420111, Kazan, P.B. 30, Russia.
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Haddadian EJ, Gross EL. A Brownian dynamics study of the interactions of the luminal domains of the cytochrome b6f complex with plastocyanin and cytochrome c6: the effects of the Rieske FeS protein on the interactions. Biophys J 2006; 91:2589-600. [PMID: 16844750 PMCID: PMC1562394 DOI: 10.1529/biophysj.106.085936] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Accepted: 06/21/2006] [Indexed: 11/18/2022] Open
Abstract
The availability of the structures of the cytochrome b6f complex (cyt b6f), plastocyanin (PC), and cytochrome c6 (cyt c6) from Chlamydomonas reinhardtii allowed us, for the first time, to model electron transfer interactions between the luminal domains of this complex (including cyt f and the Rieske FeS protein) and its redox partners in the same species. We also generated a model structure in which the FeS center of the Rieske protein was positioned closer to the heme of cyt f than observed in the crystal structure and studied its interactions with both PC and cyt c6. Our data showed that the Rieske protein in both the original crystal structure and in our modeled structure of the cyt b6f complex did not physically interfere with binding position or orientation of PC or cyt c6 on cyt f. PC docked on cyt f with the same orientation in the presence or the absence of the Rieske protein, which matched well with the previously reported NMR structures of complexes between cyt f and PC. When the FeS center of the Rieske protein was moved close to the heme of cyt f, it even enhanced the interaction rates. Studies using a cyt f modified in the 184-191 loop showed that the cyt f structure is a more important factor in determining the rate of complex formations than is the presence or the absence of the Rieske protein or its position with respect to cyt f.
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Affiliation(s)
- Esmael J Haddadian
- Biophysics Program and Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Ermakova EA. A comparative study of the interaction of Bacillus amyloliquefaciens ribonuclease (barnase) and Bacillus intermedius ribonuclease (binase) with barstar by brownian dynamics simulation. Biophysics (Nagoya-shi) 2006. [DOI: 10.1134/s0006350906020072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Haddadian EJ, Gross EL. A Brownian dynamics study of the effects of cytochrome f structure and deletion of its small domain in interactions with cytochrome c6 and plastocyanin in Chlamydomonas reinhardtii. Biophys J 2006; 90:566-77. [PMID: 16239335 PMCID: PMC1367061 DOI: 10.1529/biophysj.105.067058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Accepted: 09/13/2005] [Indexed: 11/18/2022] Open
Abstract
The availability of seven different structures of cytochrome f (cyt f) from Chlamydomonas reinhardtii allowed us, using Brownian dynamics simulations, to model interactions between these molecules and their redox partners, plastocyanin (PC) and cytochrome c6 (cyt c6) in the same species to study the effect of cyt f structure on its function. Our results showed that different cyt f structures, which are very similar, produced different reaction rates in interactions with PC and cyt c6. We were able to attribute this to structural differences among these molecules, particularly to a small flexible loop between A-184 and G-191 (which has some of the highest crystallographic temperature factors in all of the cyt f structures) on the cyt f small domain. We also showed that deletion of the cyt f small domain affected cyt c6 more than PC, due to their different binding positions on cyt f. One function of the small domain in cyt f may be to guide PC or cyt c6 to a uniform dock with cyt f, especially due to electrostatic interactions with K-188 and K-189 on this domain. Our results could serve as a good guide for future experimental work on these proteins to understand better the electron transfer process between them. Also, these results demonstrated the sensitivity and the power of the Brownian dynamics simulations in the study of molecular interactions.
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Affiliation(s)
- Esmael J Haddadian
- Biophysics Program and Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Gross EL, Rosenberg I. A Brownian dynamics study of the interaction of Phormidium cytochrome f with various cyanobacterial plastocyanins. Biophys J 2006; 90:366-80. [PMID: 16214856 PMCID: PMC1367034 DOI: 10.1529/biophysj.105.065185] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Accepted: 09/13/2005] [Indexed: 11/18/2022] Open
Abstract
Brownian dynamics simulations were used to study the role of electrostatic forces in the interactions of cytochrome f from the cyanobacterium Phormidium laminosum with various cyanobacterial plastocyanins. Both the net charge on the plastocyanin molecule and the charge configuration around H92 (H87 in higher plants) are important in determining the interactions. Those plastocyanins (PCs) with a net charge more negative than -2.0, including those from Synechococcus sp. PCC7942, Synechocystis sp. 6803, and P. laminosum showed very little complex formation. On the other hand, complex formation for those with a net charge more positive than -2.0 (including Nostoc sp. PCC7119 and Prochlorothrix hollandica) as well as Nostoc plastocyanin mutants showed a linear dependence of complex formation upon the net charge on the plastocyanin molecule. Mutation of charged residues on the surface of the PC molecules also affected complex formation. Simulations involving plastocyanin mutants K35A, R93A, and K11A (when present) showed inhibition of complex formation. In contrast, D10A and E17A mutants showed an increase in complex formation. All of these residues surround the H92 (H87 in higher plant plastocyanins) ligand to the copper. An examination of the closest electrostatic contacts shows that these residues interact with D63, E123, R157, D188, and the heme on Phormidium cytochrome f. In the complexes formed, the long axis of the PC molecule lies perpendicular to the long axis of cytochrome f. There is considerable heterogeneity in the orientation of plastocyanin in the complexes formed.
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Affiliation(s)
- Elizabeth L Gross
- Department of Biochemistry, The Ohio State University, Columbus, Ohio, USA.
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Ermakova E. Lysozyme dimerization: Brownian dynamics simulation. J Mol Model 2005; 12:34-41. [PMID: 16133093 DOI: 10.1007/s00894-005-0001-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2004] [Accepted: 05/12/2005] [Indexed: 10/25/2022]
Abstract
The lysozyme dimerization reaction has been studied within the framework of encounter-complex (EC) formation theory using the MacroDox software package. Two types of energetically favorite ECs were determined. In the first of them, active-center amino acids of lysozyme take part in the complex formation or the second molecule blocks accessibility to active center sterically. Epitope amino-acid residues are involved in the complex of type II. The existence of both types of complexes does not contradict experimental data. Dimer-formation rate constants for different kinds of EC were calculated. Increasing the pH from 2.0 to 10.0 decreases the total positive lysozyme charge and eliminates the unfavorable repulsive electrostatic interaction. The rate constant of EC formation is inversely proportional to the protein total charge. The association rate constant was also enhanced by an increase of ionic strength that screened repulsive electrostatic interaction between positively charged proteins.
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Affiliation(s)
- Elena Ermakova
- Kazan Institute of Biochemistry and Biophysics RAS, 420111 Kazan, P.O. Box 30, Russia.
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Haddadian EJ, Gross EL. Brownian dynamics study of cytochrome f interactions with cytochrome c6 and plastocyanin in Chlamydomonas reinhardtii plastocyanin, and cytochrome c6 mutants. Biophys J 2005; 88:2323-39. [PMID: 15626695 PMCID: PMC1305281 DOI: 10.1529/biophysj.104.053561] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2004] [Accepted: 12/17/2004] [Indexed: 11/18/2022] Open
Abstract
Using Brownian dynamics simulations, all of the charged residues in Chlamydomonas reinhardtii cytochrome c(6) (cyt c(6)) and plastocyanin (PC) were mutated to alanine and their interactions with cytochrome f (cyt f) were modeled. Systematic mutation of charged residues on both PC and cyt c(6) confirmed that electrostatic interactions (at least in vitro) play an important role in bringing these proteins sufficiently close to cyt f to allow hydrophobic and van der Waals interactions to form the final electron transfer-active complex. The charged residue mutants on PC and cyt c(6) displayed similar inhibition classes. Our results indicate a difference between the two acidic clusters on PC. Mutations D44A and E43A of the lower cluster showed greater inhibition than do any of the mutations of the upper cluster residues. Replacement of acidic residues on cyt c(6) that correspond to the PC's lower cluster, particularly E70 and E69, was observed to be more inhibitory than those corresponding to the upper cluster. In PC residues D42, E43, D44, D53, D59, D61, and E85, and in cyt c(6) residues D2, E54, K57, D65, R66, E70, E71, and the heme had significant electrostatic contacts with cyt f charged residues. PC and cyt c(6) showed different binding sites and orientations on cyt f. As there are no experimental cyt c(6) mutation data available for algae, our results could serve as a good guide for future experimental work on this protein. The comparison between computational values and the available experimental data (for PC-cyt f interactions) showed overall good agreement, which supports the predictive power of Brownian dynamics simulations in mutagenesis studies.
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Affiliation(s)
- Esmael J Haddadian
- Biophysics Program and Department of Biochemistry, The Ohio State University, 484 W. 12th Ave., Columbus, OH 43210, USA
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Ermakova EA, Zuev YF. Brownian dynamics study of the selective orientation of a guest molecule in the surfactant shell of a reverse micelle. MENDELEEV COMMUNICATIONS 2005. [DOI: 10.1070/mc2005v015n04abeh002062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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