Molecular Mechanism of Flavin Photoprotection by Archaeal Dodecin: Photoinduced Electron Transfer and Mg<sup>2+</sup>-Promoted Proton Transfer

Scheurer, Maximilian; Brisker-Klaiman, Daria; Dreuw, Andreas

doi:10.1021/acs.jpcb.7b08597

Cited by 6 publications

(18 citation statements)

References 46 publications

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“…PyContact has been thoroughly tested on several diverse examples, including protein-protein, protein-membrane, and protein-small molecule systems (45). To illustrate the versatile applicability and capabilities of PyContact, we per-formed case studies on two different systems previously investigated with MD simulations (18,46,47).…”

Section: Case Studiesmentioning

confidence: 99%

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations

Scheurer

Rodenkirch

Siggel

et al. 2018

Biophysical Journal

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109

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Molecular dynamics (MD) simulations have become ubiquitous in all areas of life sciences. The size and model complexity of MD simulations are rapidly growing along with increasing computing power and improved algorithms. This growth has led to the production of a large amount of simulation data that need to be filtered for relevant information to address specific biomedical and biochemical questions. One of the most relevant molecular properties that can be investigated by all-atom MD simulations is the time-dependent evolution of the complex noncovalent interaction networks governing such fundamental aspects as molecular recognition, binding strength, and mechanical and structural stability. Extracting, evaluating, and visualizing noncovalent interactions is a key task in the daily work of structural biologists. We have developed PyContact, an easy-to-use, highly flexible, and intuitive graphical user interface-based application, designed to provide a toolkit to investigate biomolecular interactions in MD trajectories. PyContact is designed to facilitate this task by enabling identification of relevant noncovalent interactions in a comprehensible manner. The implementation of PyContact as a standalone application enables rapid analysis and data visualization without any additional programming requirements, and also preserves full in-program customization and extension capabilities for advanced users. The statistical analysis representation is interactively combined with full mapping of the results on the molecular system through the synergistic connection between PyContact and VMD. We showcase the capabilities and scientific significance of PyContact by analyzing and visualizing in great detail the noncovalent interactions underlying the ion permeation pathway of the human P2X receptor. As a second application, we examine the protein-protein interaction network of the mechanically ultrastable cohesin-dockering complex.

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Section: Case Studiesmentioning

confidence: 99%

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations

Scheurer

Rodenkirch

Siggel

et al. 2018

Biophysical Journal

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109

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“…385 For example, in archaea and bacteria dodecins sequester free flavins that are liable to photo-induced degradation and ROS production; once the flavins are bound to dodecins, the excitation energy of absorbed light quanta can be rapidly dissipated via ultrafast proton and electron transfer mechanisms. 386 Similar mechanisms might be operating in BL photoreceptors as well. Essentially, the generation of reactive oxygen species by photosensitizers proceeds via one of two general mechanisms: in type I, a PS donates an electron to O 2 thereby forming the superoxide anion radical (O 2 −.…”

Section: Off-label Use Of Photoreceptorsmentioning

confidence: 97%

Blue-Light Receptors for Optogenetics

2018

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Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.

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“…The other dominant amplitudes show a mixture of CT and local excitation (LE) 43 (data not illustrated), where HOMO→LUMO exhibits the most prominent fragment separation. Since…”

Section: Lumiflavin In Bulk Solventmentioning

confidence: 99%

“…From an MD trajectory obtained in previous work, 43 From the ten QM/MM MD simulations, ten snapshots were extracted per trajectory, and embedding potentials were generated for the extracted snapshots using PyFraME. 72 The dodecin environment setup is graphically illustrated in Figure 2a.…”

Section: Lumiflavin Embedded In Dodecin Environmentmentioning

confidence: 99%

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Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems

Scheurer

Herbst

Reinholdt

et al. 2018

J. Chem. Theory Comput.

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We present a variant of the algebraic diagrammatic construction (ADC) scheme by combining ADC with the polarizable embedding (PE) model. The presented PE-ADC method is implemented through second and third order and is designed with the aim of performing accurate calculations of excited states in large molecular systems. Accuracy and large-scale applicability are demonstrated with three case studies, and we further analyze the importance of both state-specific and linear-response-type corrections to the excitation energies in the presence of the polarizable environment. We demonstrate how our combined method can be readily applied to study photoinduced biochemical processes as we model the charge-transfer (CT) excitation which is key to the photoprotection mechanism in the dodecin protein with PE-ADC(2). Through direct access to state-of-the-art excited state analysis, we find that the polarizable environment plays a decisive role by significantly increasing the CT character of the electronic excitation in dodecin. PE-ADC is thus suited to decipher photoinduced processes in complex, biomolecular systems at high precision and at reasonable computational cost.

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Molecular Mechanism of Flavin Photoprotection by Archaeal Dodecin: Photoinduced Electron Transfer and Mg²⁺-Promoted Proton Transfer

Cited by 6 publications

References 46 publications

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations

Blue-Light Receptors for Optogenetics

Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems

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Molecular Mechanism of Flavin Photoprotection by Archaeal Dodecin: Photoinduced Electron Transfer and Mg2+-Promoted Proton Transfer

Cited by 6 publications

References 46 publications

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations

Blue-Light Receptors for Optogenetics

Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems

Contact Info

Product

Resources

About

Molecular Mechanism of Flavin Photoprotection by Archaeal Dodecin: Photoinduced Electron Transfer and Mg²⁺-Promoted Proton Transfer