Surface residues dynamically organize water bridges to enhance electron transfer between proteins

Lande, Aurélien de la; Babcock, Nathan S.; Řezáč, Jan; Sanders, Barry C.; Salahub, Dennis R.

doi:10.1073/pnas.0914457107

Cited by 57 publications

(64 citation statements)

References 43 publications

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“…The first point concerns the active role played by FAD intrinsic dynamics which shows that high coupling structures are obtained due to FAD movement and presence of water molecules that bridge the ET path between both domains (FBD and GD). The key role of structural bridging waters for FHb ET paths is consistent with previous results reported by several groups who showed that water molecules are able to adapt protein contact surfaces of ET transfer complexes significantly enhancing the corresponding rate [62,[69][70][71][72][73]. Other relevant point concerns the electron entry point on the GD.…”

Section: Electron Transfer Pathwayssupporting

confidence: 87%

“…The computed H AB values should be considered only as an estimation of the real coupling values, but, as shown in previous works from our group [60,61] and others [58,59,62,[69][70][71][72][73], are accurate enough to distinguish and characterize different possible ET paths in the same protein, and/or preferred ET conformations, in remarkable consistency with experimental measurements of the ET rates [58,59,62,[69][70][71][72][73]. Moreover, since in the present case donor and acceptor states are the same for all studied cases, since we are dealing with the same protein, the other factors governing ET, like the reorganization energy, and ET reaction free energy, remain constant.…”

Section: Electron Transfer Pathwaysmentioning

confidence: 97%

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The key role of water in the dioxygenase function of Escherichia coli flavohemoglobin

Ferreiro

Boechi

Estrin

et al. 2013

Journal of Inorganic Biochemistry

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Section: Electron Transfer Pathwayssupporting

confidence: 87%

Section: Electron Transfer Pathwaysmentioning

confidence: 97%

The key role of water in the dioxygenase function of Escherichia coli flavohemoglobin

Ferreiro

Boechi

Estrin

et al. 2013

Journal of Inorganic Biochemistry

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“…The peptide backbone may mediate charge movement along the PPII helix or even allow transient localization, and explicitly including these effects could lead to higher predicted transfer rates. Furthermore, it has been shown that bridging water molecules can serve to enhance electron transfer pathways in proteins, 142,143 and a similar effect seems to be important in solvated peptides. This effect is already present in our results, seen in the importance of considering water molecules in the couplings in Table 4.…”

Section: ■ Discussionmentioning

confidence: 99%

Charge Transfer in Model Peptides: Obtaining Marcus Parameters from Molecular Simulation

et al. 2012

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Charge transfer within and between biomolecules remains a highly active field of biophysics. Due to the complexities of real systems, model compounds are a useful alternative to study the mechanistic fundamentals of charge transfer. In recent years, such model experiments have been underpinned by molecular simulation methods as well. In this work, we study electron hole transfer in helical model peptides by means of molecular dynamics simulations. A theoretical framework to extract Marcus parameters of charge transfer from simulations is presented. We find that the peptides form stable helical structures with sequence dependent small deviations from ideal PPII helices. We identify direct exposure of charged side chains to solvent as a cause of high reorganization energies, significantly larger than typical for electron transfer in proteins. This, together with small direct couplings, makes long-range superexchange electron transport in this system very slow. In good agreement with experiment, direct transfer between the terminal amino acid side chains can be dicounted in favor of a two-step hopping process if appropriate bridging groups exist. ■ INTRODUCTIONCharge transfer is a fundamental phenomenon in physical chemistry, enjoying strong and consistent scientific interest for more than fifty years. 1 Understanding charge transfer in complex and flexible biomolecules is crucial for a huge variety of processes, from cellular respiration and photosynthesis to DNA damage and repair. 2−4 Describing it accurately has turned out to be particularly challenging, both to experimentalists and theoreticians. Biochemical charge transfer involves the directed movement of electrons over large distances (multiple nanometers) through macromolecules, typically proteins or large heterogeneous multiprotein assemblies. These processes involve dynamical changes that occur on a time scale spanning multiple orders of magnitude, from subpicosecond changes in electronic structure to microsecond or even slower conformational changes. Only recently has the complicated interplay between atomic structural fluctuations and electron dynamics become a focus for charge transfer studies in biochemical systems, 5−9 building onto earlier work on model systems. 10−15 This fact, combined with the large system dimensions and difficult experimental conditions, explains why many open questions on electron transfer (ET) in biomolecules remain. Therefore, simpler model systems to study some aspects of ET have gained popularity, and theoretical models based on computer simulations have become important tools to help interpret experiments and gain a better understanding of the structure and function of the involved molecules. 16−22 An important model system in the study of charge transfer processes has always been peptide systems. Extensive experimental work was done by Isied et al., who have studied ET over distances of 8−32 Å via spectroscopical techniques and determined the properties of polyproline II helices as ET bridges. 27−34 This wo...

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“…de la Lande et al reported an investigation of the tunneling pathways between a quinol cofactor of the protein MADH (methylamine dehydrogenase) and a blue copper center contained in amicyanin [176]. The results from MD simulation coupled to PM analyses indicated that the protein interface favors the establishment of efficient water mediated ET pathways between the proteins.…”

Section: Water Mediated Electron Transfersmentioning

confidence: 94%

Progress and challenges in simulating and understanding electron transfer in proteins

Lande

Gillet

Chen

et al. 2015

Archives of Biochemistry and Biophysics

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Surface residues dynamically organize water bridges to enhance electron transfer between proteins

Cited by 57 publications

References 43 publications

The key role of water in the dioxygenase function of Escherichia coli flavohemoglobin

The key role of water in the dioxygenase function of Escherichia coli flavohemoglobin

Charge Transfer in Model Peptides: Obtaining Marcus Parameters from Molecular Simulation

Progress and challenges in simulating and understanding electron transfer in proteins

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