Plastocyanin: Structure, Location, Diffusion and Electron Transfer Mechanisms

Gross, Elizabeth

doi:10.1007/0-306-48127-8_21

Cited by 17 publications

(36 citation statements)

References 94 publications

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“…PC is an 11 kDa ''blue'' copper, b-sheet protein that has two clusters of negatively charged residues called the upper and lower cluster, respectively (7,10,(12)(13)(14). The upper cluster consists of residue Nos.…”

Section: Introductionmentioning

confidence: 99%

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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

Haddadian

Gross

2006

Biophysical Journal

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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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Section: Introductionmentioning

confidence: 99%

“…The upper cluster consists of residue Nos. 59-61, but it should be noted that PCs from all algae and some species of higher plants have a two-residue deletion in this region (13). For example, C. reinhardtii PC has only two negatively charged residues at positions No.…”

Section: Introductionmentioning

confidence: 99%

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

Haddadian

Gross

2006

Biophysical Journal

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“…For a more detailed discussion of the evidence for electrostatic interaction between PC and cyt f, see Gross (1996) and Haddadian and Gross (2005). But see Soriano et al (1996) for evidence against electrostatic interactions in C. reinhardtii.…”

Section: Introductionmentioning

confidence: 97%

“…Plastocyanin is a 10 kDa, ''blue'' copper protein (Freeman 1981;Sykes 1991;Gross 1996;Redinbo et al 1994;Sigfridsson 1998;Hope 2000). The Cu atom is coordinated to four ligands (H37, H87, C84 and M92) in a distorted tetrahedral geometry.…”

Section: Introductionmentioning

confidence: 99%

A Brownian dynamics computational study of the interaction of spinach plastocyanin with turnip cytochrome f: the importance of plastocyanin conformational changes

Gross

2007

Photosynth Res

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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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“…Молекулы пластоцианина окисляют цитохром f и восстанавливают реакционный центр PS I, диффундируя в люминальном пространстве на довольно большие расстояния (сотни нм) и перенося электроны между гранальными и стромальными областями в тилакоидах [Мокроносов, Гавриленко, 1992;Hope, 1993;Gross, 1996]. В нативном хлоропласте толщина люмена (4-10 нм [Mehta et al, 1999]) сравнима с размерами пластоцианина, а люмен заполнен выступающими частями трансмембранных мультиферментных комплексов [Hope, 2000], концентрация которых в тилакоидной мембране очень высока [Albertsson, 2001].…”

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Combination of different simulation techniques in the complex model of photosynthetic membrane

Ustinin¹,

Kovalenko²,

Riznichenko³

et al. 2013

CRM

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Получено 18 декабря 2012 г., после доработки 01 марта 2013 г.Необходимость корректного учета деталей пространственной и функциональной организации клеточных структур требует поиска новых подходов к моделированию субклеточных процессов, в том числе первичных процессов фотосинтеза в тилакоидной мембране. Эти подходы должны интегрировать физические и биологические представления о конкретных механизмах, которые объединяются в общую картину на уровне компьютерной модели. В работе предлагается новый подход к моделированию, в котором воспроизводится трехмерная пространственная структура фотосинтетической мембраны. Разные стадии переноса зарядов при фотосинтезе моделируются с использованием разного математического аппарата и объединяются в единую компьютерную модель. Разработанные алгоритмы реализованы в виде программного комплекса, использующего параллельные вычисления на высокопроизводительных кластерах и графических процессорах. Ключевые слова: компьютерное моделирование, броуновская динамикаAbstract. -Complex geometric organization of subcellular structures such as photosynthetic or mitochondrial membranes determines mechanism of electron and proton transfer processes. We propose new approach in modeling processes, where geometric shape of membranes is accurately taken into account. Different stages of charge transfer process are simulated using different approaches, which are integrated into a combined model. We implemented this model as software which utilizes parallel computations on high-performance clusters and GPUs for better performance.

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Plastocyanin: Structure, Location, Diffusion and Electron Transfer Mechanisms

Cited by 17 publications

References 94 publications

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

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

A Brownian dynamics computational study of the interaction of spinach plastocyanin with turnip cytochrome f: the importance of plastocyanin conformational changes

Combination of different simulation techniques in the complex model of photosynthetic membrane

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