Observe while it happens : catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations

Organisms use photo-receptors to react to light. The first step is usually the absorption of a photon by a prosthetic group embedded inside the photo-receptor, often a conjugated chromophore. The electronic changes in the chromophore induced by photo-absorption can trigger a cascade of structural or chemical transformations that culminate into a response to light. Understanding how these proteins have evolved to mediate their activation process has remained challenging because the required time and spacial resolutions are notoriously difficult to achieve experimentally. Therefore, mechanistic insights into photoreceptor activation have been predominantly obtained with computer simulations. …

Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

Many biological processes depend on detecting and responding to light. The response is often mediated by a structural change in a protein that begins when absorption of a photon causes isomerization of a chromophore bound to the protein. Pande et al. used x-ray pulses emitted by a free electron laser source to conduct time-resolved serial femtosecond crystallography in the time range of 100 fs to 3 ms. This allowed for the real-time tracking of the trans-cis isomerization of the chromophore in photoactive yellow protein and the associated structural changes in the protein.Science, this issue p. 725A variety of organisms have evolved mechanisms to detect and respond to light, in which the re…

Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that …

Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling

Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome from Deinococcus radiodurans (DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome from Agrobacterium fabrum (Agp1). Whereas Agp1 acts as a conventional histidine kinase, we identify DrBphP a…

The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The chan…

Weak intermolecular interactions promote blue luminescence of protonated 2,2′-dipyridylamine salts

In this work we demonstrate that protonation and π-stacking can be exploited to convert non-luminescent 2,2′-dipyridylamine into blue-emitting derivatives. We have synthesized a series of luminescent 2,2′-dipyridylamine (dpa) salts, i.e., (dpaH)X·nSolv (dpa = 2,2′-dipyridylamine, X = HF2, n = 0.5, Solv = H2O 1; X = Cl, n = 2, Solv = H2O 2; X = Br, n = 2, Solv = H2O 3; X = I n = 1, Solv = H2O 4a; X = I n = 1, Solv = CHCl34b), (dpaH)2[SiF6]·H2O 5 and (dpaH)X (X = I36; SbF67; BF48) and characterized their emission properties, both in the solid-state and in solution. To rationalize our observations and relate the luminescence properties to the structure in the solid state and in solution, we ha…

The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part I: gas phase.

The vibronic spectra of the green fluorescent protein chromophore analogues p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) and 3,5-tert-butyl-HBDI (35Bu) are similar in the vacuum, but very different in water or ethanol. To understand this difference, we have computed the vibrationally resolved solution spectra of these chromophores, using the polarizable continuum model (PCM) to account for solvent effects on the (harmonic) potential energy surfaces (PES). In agreement with experiment, we found that the vibrational progression increases with the polarity of the solvent, but we could neither reproduce the broadening, nor the large difference between the absorption spectra of HBDI and…

Solvated copper(I) hexafluorosilicate π-complexes based on [Cu2(amtd)2]2+ (amtd = 2-allylamino-5-methyl-1,3,4-thiadiazole) dimer

[Cu2(amdt)2]SiF6·C6H6 and [Cu2(amdt)2(H2O)2]SiF6·CH3CN·2H2O (amdt = 2-allylamino-5- methyl-1,3,4-thiadiazole) were obtained by alternating-current electrochemical synthesis, starting from water–acetonitrile–benzene mixtures containing 2-allylamino-5-methyl-1,3,4- thiadiazole and CuSiF6·4H2O. The electrochemical reduction of the saturated copper hexafluorosilicate water solution beneath the neatly poured layer of acetonitrile-benzene amdt solution resulted in the formation of crystalline [Cu2(amdt)2]SiF6·C6H6. The initial stirring of the same mixture before subjecting it to the electrochemical reduction resulted in the formation of [Cu2(amdt)2(H2O)2]SiF6·CH3CN·2H2O. A sluggish hydrolysis of …

Predictive First-principles Modeling of a Photosynthetic Antenna Protein : The Fenna-Matthews-Olson Complex

High efficiency of light harvesting in photosynthetic pigment-protein complexes is governed by evolutionary-perfected protein-assisted tuning of individual pigment properties and inter-pigment interactions. Due to the large number of spectrally overlapping pigments in a typical photosynthetic complex, experimental methods often fail to unambiguously identify individual chromophore properties. Here we report a first principles-based modeling protocol capable of predicting properties of pigments in protein environment to a high precision. The technique was applied to successfully uncover electronic properties of the Fenna-Matthews-Olson (FMO) pigment-protein complex. Each of the three subunit…

Author response: The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila

Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics …

Excitation-Wavelength Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila

Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics …

Enhanced Excitation Energy Transfer under Strong Light-Matter Coupling: Insights from Multi-Scale Molecular Dynamics Simulations

Exciton transport can be enhanced in the strong coupling regime where excitons hybridise with confined light modes to form polaritons. Because polaritons have group velocity, their propagation should be ballistic and long-ranged. However, experiments indicate that organic polaritons propagate in a diffusive manner and more slowly than their group velocity. Here, we resolve this controversy by means of molecular dynamics simulations of Rhodamine molecules in a Fabry-P\'{e}rot cavity. Our results suggest that polariton propagation is limited by the cavity lifetime and appears diffusive due to reversible population transfers between polaritonic states that propagate ballistically at their grou…

Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with …

The Role of Small-Angle X-Ray Scattering and Molecular Simulations in 3D Structure Elucidation of a DNA Aptamer Against Lung Cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here we present a general optimization procedure for finding most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated aptamer LC-18t was developed. A three-dimensional shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and m…

Helix Inversion Controlled by Molecular Motors in Multistate Liquid Crystals.

Unravelling the rules of molecular motion is a contemporary challenge that promises to support the development of responsive materials and is likely to enhance the understanding of functional motion. Advances in integrating light‐driven molecular motors in soft matter have led to the design and realization of chiral nematic (cholesteric) liquid crystals that can respond to light with modification of their helical pitch, and also with helix inversion. Under illumination, these chiral liquid crystals convert from one helical geometry to another. Here, a series of light‐driven molecular motors that feature a rich configurational landscape is presented, specifically which involves three stable …

Tracking Polariton Relaxation with Multiscale Molecular Dynamics Simulations

When photoactive molecules interact strongly with confined light modes in optical cavities, new hybrid light–matter states form. They are known as polaritons and correspond to coherent superpositions of excitations of the molecules and of the cavity photon. The polariton energies and thus potential energy surfaces are changed with respect to the bare molecules, such that polariton formation is considered a promising paradigm for controlling photochemical reactions. To effectively manipulate photochemistry with confined light, the molecules need to remain in the polaritonic state long enough for the reaction on the modified potential energy surface to take place. To understand what determine…

Serial femtosecond crystallography reveals that photoactivation in a fluorescent protein proceeds via the hula twist mechanism

Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crys…

Predictive First-Principles Modeling of a Photosynthetic Antenna Protein: The Fenna–Matthews–Olson Complex

High efficiency of light harvesting in photosynthetic pigment–protein complexes is governed by evolutionary-perfected protein-assisted tuning of individual pigment properties and interpigment interactions. Due to the large number of spectrally overlapping pigments in a typical photosynthetic complex, experimental methods often fail to unambiguously identify individual chromophore properties. Here, we report a first-principles-based modeling protocol capable of predicting properties of pigments in protein environment to a high precision. The technique was applied to successfully uncover electronic properties of the Fenna–Matthews–Olson (FMO) pigment–protein complex. Each of the three subunit…

Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of Bacteriophytochrome

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that …

Hydrogen Bond Fluctuations Control Photochromism in a Reversibly Photo-Switchable Fluorescent Protein

Reversibly switchable fluorescent proteins (RSFPs) are essential for high-resolution microscopy of biological samples, but the reason why these proteins are photochromic is still poorly understood. To address this problem, we performed molecular dynamics simulations of the fast switching Met159Thr mutant of the RSFP Dronpa. Our simulations revealed a ground state structural heterogeneity in the chromophore pocket that consists of three populations with one, two, or three hydrogen bonds to the phenolate moiety of the chromophore. By means of non-adiabatic quantum mechanics/molecular dynamics simulations, we demonstrated that the subpopulation with a single hydrogen bond is responsible for of…

Illuminating a Phytochrome Paradigm – a Light-Activated Phosphatase in Two-Component Signaling Uncovered

ABSTRACTBacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome fromDeinococcus radiodurans(DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome fromAgrobacterium fabrum(AgP1). Whereas AgP1 acts as a conventional histidine kinase, we identify DrBp…

The first copper(I)-olefin complexes bearing a 1,3,4-oxadiazole core: Alternating-current electrochemical crystallization, X-ray experiment and DFT study

By means of alternating-current electrochemical technique, four new π-complexes, namely [Cu2(C11H10N2OS)2Br1.91Cl0.09] (1), [Cu(C11H10N2OS)NO3] (2), [Cu2(C11H10N2OS)2(H2O)2](BF4)2 (3) and [Cu2(C11H10N2OS)2(H2O)2](ClO4)2 (4), were obtained using copper(II) salts and the 2-(allylthio)-5-phenyl-1,3,4-oxadiazole (C11H10N2OS) ligand. The metal and halogen centers in 1 form Cu2X2 dimers; the N-atom from the oxadiazole ring and the Cdouble bond; length as m-dashC bond of the allyl group from the same ligand complete the copper coordination environment, giving [Cu(C11H10N2OS)X]2 isolated fragments. The ligand plays the same chelating role in 2, whereas the O (NO3) atom occupies the third position i…

Steering the excited state dynamics of a photoactive yellow protein chromophore analogue with external electric fields

Abstract The first excited state of the Photoactive Yellow Protein chromophore exhibits a strong charge transfer character and the dipole moments of the excited and ground states differ significantly. Furthermore, the excited state charge distribution changes during the isomerization of this chromophore. These observations suggest that external electric fields can be used to control photo-isomerization, providing a new concept for developing photochromic devices, such as e-paper or optical memory. To test this idea, we performed excited state dynamics simulations and static calculations of a PYP chromophore analogue (pCK − ) in an external electric field. By adjusting direction and strength…

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering…

Photoactive Yellow Protein Chromophore Photoisomerizes around a Single Bond if the Double Bond Is Locked

Photoactivation in the Photoactive Yellow Protein, a bacterial blue light photoreceptor, proceeds via photo-isomerization of the double C=C bond in the covalently attached chromophore. Quantum chemistry calculations, however, have suggested that in addition to double bond photo-isomerization, the isolated chromophore and many of its analogues, can isomerize around a single C-C bond as well. Whereas double bond photo-isomerization has been observed with x-ray crystallography, experimental evidence for single bond photo-isomerization is currently lacking. Therefore, we have synthesized a chromophore analogue, in which the formal double bond is covalently locked in a cyclopentenone ring and ca…

Identifying Vibrations that Control Non-adiabatic Relaxation of Polaritons in Strongly Coupled Molecule-Cavity Systems

The strong light–matter coupling regime, in which excitations of materials hybridize with excitations of confined light modes into polaritons, holds great promise in various areas of science and technology. A key aspect for all applications of polaritonic chemistry is the relaxation into the lower polaritonic states. Polariton relaxation is speculated to involve two separate processes: vibrationally assisted scattering (VAS) and radiative pumping (RP), but the driving forces underlying these two mechanisms are not fully understood. To provide mechanistic insights, we performed multiscale molecular dynamics simulations of tetracene molecules strongly coupled to the confined light modes of an…

The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization.

Photoactivation of bacteriophytochrome involves a cis–trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the c…

Ultrafast structural changes within a photosynthetic reaction centre

Nature <London> / Physical science 589, 310 - 314 (2021). doi:10.1038/s41586-020-3000-7

A new tetranuclear copper(I) complex based on allyl(5-phenyl-1,3,4-thiadiazol-2-yl)azanide ligand: Synthesis and structural characterization

Abstract By means of alternating current electrochemical technique a new tetranuclear crystalline copper(I) complex [Cu I 4 ( L − ) 4 ] ( L −  – allyl(5-phenyl-1,3,4-thiadiazol-2-yl)azanide ion) has been obtained and characterized by X-ray single crystal diffraction ( Sp. gr. I 4 1 / a ) and Raman spectroscopy. The metal center adopts linear arrangement, composed of one thiadiazole N atom from the one L − anion and one azanide N atom of the other L − ligand. A bridged Cu atoms stitch four L − ligands into the firstly observed tetranuclear copper(I) azanide complex with intramolecular Cu(I)⋯Cu(I) interactions at the distance of 2.7451(6) A. Molecular structure and Raman spectrum of the compo…

CCDC 1004968: Experimental Crystal Structure Determination

Related Article: Alexander N. Chernyshev, Dmitry Morozov, Jarkko Mutanen, Vadim Yu Kukushkin, Gerrit Groenhof, Matti Haukka|2014|J.Mater.Chem.C|2|8285|doi:10.1039/C4TC01165A

CCDC 1004967: Experimental Crystal Structure Determination

Related Article: Alexander N. Chernyshev, Dmitry Morozov, Jarkko Mutanen, Vadim Yu Kukushkin, Gerrit Groenhof, Matti Haukka|2014|J.Mater.Chem.C|2|8285|doi:10.1039/C4TC01165A

CCDC 1004972: Experimental Crystal Structure Determination

Related Article: Alexander N. Chernyshev, Dmitry Morozov, Jarkko Mutanen, Vadim Yu Kukushkin, Gerrit Groenhof, Matti Haukka|2014|J.Mater.Chem.C|2|8285|doi:10.1039/C4TC01165A

CCDC 1004969: Experimental Crystal Structure Determination

Related Article: Alexander N. Chernyshev, Dmitry Morozov, Jarkko Mutanen, Vadim Yu Kukushkin, Gerrit Groenhof, Matti Haukka|2014|J.Mater.Chem.C|2|8285|doi:10.1039/C4TC01165A

CCDC 1004974: Experimental Crystal Structure Determination

Related Article: Alexander N. Chernyshev, Dmitry Morozov, Jarkko Mutanen, Vadim Yu Kukushkin, Gerrit Groenhof, Matti Haukka|2014|J.Mater.Chem.C|2|8285|doi:10.1039/C4TC01165A

CCDC 1004971: Experimental Crystal Structure Determination

Related Article: Alexander N. Chernyshev, Dmitry Morozov, Jarkko Mutanen, Vadim Yu Kukushkin, Gerrit Groenhof, Matti Haukka|2014|J.Mater.Chem.C|2|8285|doi:10.1039/C4TC01165A

CCDC 1004975: Experimental Crystal Structure Determination

Related Article: Alexander N. Chernyshev, Dmitry Morozov, Jarkko Mutanen, Vadim Yu Kukushkin, Gerrit Groenhof, Matti Haukka|2014|J.Mater.Chem.C|2|8285|doi:10.1039/C4TC01165A

CCDC 1004970: Experimental Crystal Structure Determination

Related Article: Alexander N. Chernyshev, Dmitry Morozov, Jarkko Mutanen, Vadim Yu Kukushkin, Gerrit Groenhof, Matti Haukka|2014|J.Mater.Chem.C|2|8285|doi:10.1039/C4TC01165A

CCDC 1004973: Experimental Crystal Structure Determination

Related Article: Alexander N. Chernyshev, Dmitry Morozov, Jarkko Mutanen, Vadim Yu Kukushkin, Gerrit Groenhof, Matti Haukka|2014|J.Mater.Chem.C|2|8285|doi:10.1039/C4TC01165A

CCDC 1004976: Experimental Crystal Structure Determination

Related Article: Alexander N. Chernyshev, Dmitry Morozov, Jarkko Mutanen, Vadim Yu Kukushkin, Gerrit Groenhof, Matti Haukka|2014|J.Mater.Chem.C|2|8285|doi:10.1039/C4TC01165A