Dynamic determination of the functional state in photolyase and the implication for cryptochrome

Ultrafast Dynamics of Fatty Acid Photodecarboxylase in Anionic Semiquinone State

Fatty acid photodecarboxylase is a newly identified blue-light driven photoenzyme that catalyzes decarboxylation of fatty acids. The catalytic reaction involves a transient anionic semiquinone of flavin cofactor (FAD^•-) as an intermediate, but photochemical properties of this anionic radical are largely unknown. Here, we have anaerobically produced the wild-type FAP in the FAD^•- state and conducted femtosecond-resolved fluorescence and absorption measurements. We have observed the multiphasic deactivation dynamics of excited states on multiple time scales from a few picoseconds even to a few nanoseconds through conical intersections between various electronic states. Interestingly, the nanosecond components can only be observed from higher electronic excited states. Our results show the complexity of the energy landscapes of various excited states and rule out the occurrence of electron or proton transfer with nearby residue(s) in the active site.

Femtosecond Time-Resolved Absorption Study of Signaling State of a BLUF Protein PixD from the Cyanobacterium Synechocystis: Hydrogen-Bond Rearrangement Completes during Forward Proton-Coupled Electron Transfer

Femtosecond time-resolved absorption measurements were carried out for the dark and signaling states of a BLUF (Blue Light Using FAD) protein, PixD, from the cyanobacterium Synechocystis. When the dark state was excited, FAD semiquinone radical (FADH^•) was produced from the S₁ state, and FADH^• led to the signaling state. On the other hand, photoexcitation of the signaling state generated FADH^• and FAD anion radical (FAD^•-), and they decayed back to the original signaling state. In both cases, FADH^• was formed and decayed with a proton-coupled electron transfer (PCET) via the hydrogen-bond network that involves FAD, Gln50, and Tyr8, and hence the kinetics of FADH^• directly reflects the hydrogen-bond structure in the FAD-binding sites. It was found that the formation rate of FADH^• was significantly different between the dark and signaling states, whereas the decay rate was the same. This indicates that the hydrogen-bond network of FAD-Gln50-Tyr8 in the dark and signaling states is initially different but it becomes indistinguishable after FADH^• is formed, implying that the FAD-Gln50-Tyr8 hydrogen-bond network is rearranged during the PCET to generate FADH^•. The present results best agree with the model in which the Gln tautomerizes without rotation in the signaling-state formation.

Light-dependent reactions of animal circadian photoreceptor cryptochrome

Circadian rhythms are endogenous autonomous 24-h oscillations that are generated by a transcription-translation feedback loop (TTFL). In the positive arm of the TTFL, two transcription factors activate the expression of two genes of the negative arm as well as circadian clock-regulated genes. The circadian clocks are reset through photoreceptor proteins by sunlight in the early morning to keep synchrony with the geological clock. Among animal circadian photoreceptors, Drosophila Cryptochrome (DmCRY) has some unique properties because Drosophila has a single cryptochrome (CRY) that appears to have functions which are specific to organs or tissues, or even to a subset of cells. In mammals, CRYs are not photoreceptors but function in the TTFL, while insects have a light-insensitive mammalian-like CRY or a Drosophila-like photoreceptor CRY (or both). Here, we postulate that as being just one CRY in Drosophila, DmCRY might play different roles in different tissues/organs in a context-dependent manner. In addition to being a circadian photoreceptor/protein, attributing also a magnetoreception function to DmCRY has increased its workload. Considering that DmCRY senses photons as a photoreceptor but also can regulate many different events in a light-dependent manner, differential protein-protein interactions (PPIs) of DmCRY might play a critical role in the generation of such diverse outputs. Therefore, we need to add novel approaches in addition to the current ones to study multiple and context-dependent functions of DmCRY by adopting recently developed techniques. Successful identification of transient/fast PPIs on a scale of minutes would enhance our understanding of light-dependent and/or magnetoreception-associated reactions.

Electron Transfer-Induced Active Site Structural Relaxation in 64-Photolyase of Drosophila melanogaster

While catalytic electron flow and photoreactivation of CPD-photolyases are increasingly understood, the microscopic details of the 64-photolyase repair mechanism are perpetually debated. Here, we investigate in long-time (μs) molecular dynamics simulations combined with extensive quantum mechanical/molecular mechanical (QM/MM) simulations the primary electron transfer (ET) reactions in 64-photolyase of Drosophila melanogaster (D. melanogaster). The characterization of the relative energetics of locally excited and charge separated states in the (6-4) photoproduct enzyme repair complex reveals a charge-separated state involving the adenine moiety of the FADH^- cofactor that facilitates reduction of the photoproduct. Microscopic details of the collective reaction coordinate of ET reactions are identified that involve the reorganization of the hydrogen bond network and structural relaxation of the active site. The simulations reveal complex active site relaxation dynamics involving distinguished amino acids (Lys246, His365, and His369), conformational reorganization of the hydroxyl group of the (6-4) photoproduct, and a strengthening of hydrogen bonds with immobilized water molecules. In particular, rotation of the Lys246 side chain is found to impose a double-well character along the reaction coordinate of the ET reaction. Our findings suggest that the primary ET reactions in the (6-4) photoproduct enzyme repair complex of D. melanogaster are governed by a complex multi-minima active site relaxation dynamics and potentially precede the equilibration of the protein. ET pathways mediated by the adenine moiety and the 5' side of the photoproduct are proposed to be relevant for triggering the catalytic (6-4) photoproduct reactivation.

Activation mechanism of Drosophila cryptochrome through an allosteric switch

Cryptochromes are signaling proteins activated by photoexcitation of the flavin adenine dinucleotide (FAD) cofactor. Although extensive research has been performed, the mechanism for this allosteric process is still unknown. We constructed three computational models, corresponding to different redox states of the FAD cofactor in Drosophila cryptochrome (dCRY). Analyses of the dynamics trajectories reveal that the activation process occurs in the semiquinone state FAD^-●, resulting from excited-state electron transfer. The Arg³⁸¹-Asp⁴¹⁰ salt bridge acts as an allosteric switch, regulated by the change in the redox state of FAD. In turn, Asp⁴¹⁰ forms new hydrogen bonds, connecting allosteric networks of the amino-terminal and carboxyl-terminal domains initially separated in the resting state. The expansion to a global dynamic network leads to enhanced protein fluctuations, an increase in the radius of gyration, and the expulsion of the carboxyl-terminal tail. These structural features are in accord with mutations and spectroscopic experiments.

Identification of the vibrational marker of tyrosine cation radical using ultrafast transient infrared spectroscopy of flavoprotein systems

Tryptophan and tyrosine radical intermediates play crucial roles in many biological charge transfer processes. Particularly in flavoprotein photochemistry, short-lived reaction intermediates can be studied by the complementary techniques of ultrafast visible and infrared spectroscopy. The spectral properties of tryptophan radical are well established, and the formation of neutral tyrosine radicals has been observed in many biological processes. However, only recently, the formation of a cation tyrosine radical was observed by transient visible spectroscopy in a few systems. Here, we assigned the infrared vibrational markers of the cationic and neutral tyrosine radical at 1483 and 1502 cm^-1 (in deuterated buffer), respectively, in a variant of the bacterial methyl transferase TrmFO, and in the native glucose oxidase. In addition, we studied a mutant of AppABLUF blue-light sensor domain from Rhodobacter sphaeroides in which only a direct formation of the neutral radical was observed. Our studies highlight the exquisite sensitivity of transient infrared spectroscopy to low concentrations of specific radicals.

A topologically distinct class of photolyases specific for UV lesions within single-stranded DNA

Photolyases are ubiquitously occurring flavoproteins for catalyzing photo repair of UV-induced DNA damages. All photolyases described so far have a bilobal architecture with a C-terminal domain comprising flavin adenine dinucleotide (FAD) as catalytic cofactor and an N-terminal domain capable of harboring an additional antenna chromophore. Using sequence-similarity network analysis we discovered a novel subgroup of the photolyase/cryptochrome superfamily (PCSf), the NewPHLs. NewPHL occur in bacteria and have an inverted topology with an N-terminal catalytic domain and a C-terminal domain for sealing the FAD binding site from solvent access. By characterizing two NewPHL we show a photochemistry characteristic of other PCSf members as well as light-dependent repair of CPD lesions. Given their common specificity towards single-stranded DNA many bacterial species use NewPHL as a substitute for DASH-type photolyases. Given their simplified architecture and function we suggest that NewPHL are close to the evolutionary origin of the PCSf.

Light-induced chromophore and protein responses and mechanical signal transduction of BLUF proteins

Photoreceptor proteins have been used to study how protein conformational changes are induced by alterations in their environments and how their signals are transmitted to downstream factors to dictate physiological responses. These proteins are attractive models because their signal transduction aspects and structural changes can be precisely regulated in vivo and in vitro based on light intensity. Among the known photoreceptors, members of the blue light–using flavin (BLUF) protein family have been well characterized with regard to how they control various light-dependent physiological responses in several microorganisms. Herein, we summarize our current understanding of their photoactivation and signal-transduction mechanisms. For signal transduction, we review recent studies concerning how the BLUF protein, PixD, transmits a light-induced signal to its downstream factor, PixE, to modulate phototaxis of the cyanobacterium Synechocystis sp. PCC6803.

Photolyase: Dynamics and electron-transfer mechanisms of DNA repair

Photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) and pyrimidine-pyrimidone (6-4) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair. Here, we review our comprehensive characterization of the dynamics of flavin cofactor and its repair photocycles by different classes of photolyases on the most fundamental level. Using femtosecond spectroscopy and molecular biology, significant advances have recently been made to map out the entire dynamical evolution and determine actual timescales of all the catalytic processes in photolyases. The repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. The unified, bifurcated ET mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. For 6-4 photoproduct repair, a similar cyclic ET mechanism operates and a new cyclic proton transfer with a conserved histidine residue at the active site of (6-4) photolyases is revealed.

Bifurcating electron-transfer pathways in DNA photolyases determine the repair quantum yield

Photolyase is a blue-light-activated enzyme that repairs ultraviolet-induced DNA damage that occurs in the form of cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts. Previous studies on microbial photolyases have revealed an electron-tunneling pathway that is critical for the repair mechanism. In this study, we used femtosecond spectroscopy to deconvolute seven electron-transfer reactions in 10 elementary steps in all classes of CPD photolyases. We report a unified electron-transfer pathway through a conserved structural configuration that bifurcates to favor direct tunneling in prokaryotes and a two-step hopping mechanism in eukaryotes. Both bifurcation routes are operative, but their relative contributions, dictated by the reduction potentials of the flavin cofactor and the substrate, determine the overall quantum yield of repair.

Photolyase: Dynamics and Mechanisms of Repair of Sun-Induced DNA Damage

Photolyase, a photomachine discovered half a century ago for repair of sun-induced DNA damage of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs), has been characterized extensively in biochemistry (function), structure and dynamics since 1980s. The molecular mechanism and repair photocycle have been revealed at the most fundamental level. Using femtosecond spectroscopy, we have mapped out the entire dynamical evolution and determined all actual timescales of the catalytic processes. Here, we review our recent efforts in studies of the dynamics of DNA repair by photolyases. The repair of CPDs in three life kingdoms includes seven electron transfer (ET) reactions among 10 elementary steps through initial bifurcating ET pathways, a direct tunneling route and a two-step hopping path both through an intervening adenine from the cofactor to CPD, with a conserved folded structure at the active site. The repair of 6-4PPs is challenging and requires similar ET reactions and a new cyclic proton transfer with a conserved histidine residue at the active site of (6-4) photolyases. Finally, we also summarize our efforts on multiple intraprotein ET of photolyases in different redox states and such mechanistic studies are critical to the functional mechanism of homologous cryptochromes of blue-light photoreceptors.

Overlapping Electronic States with Nearly Parallel Transition Dipole Moments in Reduced Anionic Flavin Can Distort Photobiological Dynamics

Chromophoric biomolecules are exploited as reporters of a diverse set of phenomena, acting as internal distance monitors, environment and redox sensors, and endogenous imaging probes. The extent to which they can be exploited is dependent on an accurate knowledge of their fundamental electronic properties. Arguably of greatest importance is a precise knowledge of the direction(s) of the absorption transition dipole moment(s) (TDMs) in the molecular frame of reference. Such is the case for flavins, fluorescent redox cofactors utilized for ground- and excited-state redox and photochemical processes. The directions of the TDMs in oxidized and semiquinone flavins were characterized decades ago, and the details of charge redistribution in these forms have also been studied by Stark spectroscopy. The electronic structure of the fully reduced hydroquinone anionic state, FlH^-, however, has been the subject of unfounded assumptions and estimates about the number and direction of TDMs in FlH^-, as well the electronic structure changes that occur upon light absorption. Here we have used Stark spectroscopy to measure the magnitude and direction of charge redistribution in FlH^- upon optical excitation. These data were analyzed using TD-DFT calculations. The results show unequivocally that not one but two nearly orientation-degenerate electronic transitions are required to explain the 340-500 nm absorption spectral range, demolishing the commonly held assumption of a single transition. The difference dipole moments for these states show that electron density shifts toward the xylene ring for both transitions. These measurements force a reappraisal of previous studies that have used erroneous assumptions and unsubstantiated estimates of these quantities. The results put future optical studies of reduced flavins/flavoproteins on a firm photophysical footing.

Coexistence of Different Electron-Transfer Mechanisms in the DNA Repair Process by Photolyase

DNA photolyase has been the topic of extensive studies due to its important role of repairing photodamaged DNA, and its unique feature of using light as an energy source. A crucial step in the repair by DNA photolyase is the forward electron transfer from its cofactor (FADH(-) ) to the damaged DNA, and the detailed mechanism of this process has been controversial. In the present study, we examine the forward electron transfer in DNA photolyase by carrying out high-level ab initio calculations in combination with a quantum mechanical/molecular mechanical (QM/MM) approach, and by measuring fluorescence emission spectra at low temperature. On the basis of these computational and experimental results, we demonstrate that multiple decay pathways exist in DNA photolyase depending on the wavelength at excitation and the subsequent transition. This implies that the forward electron transfer in DNA photolyase occurs not only by superexchange mechanism but also by sequential electron transfer.

Characterization of the Intermediate in and Identification of the Repair Mechanism of (6-4) Photolesions by Photolyases

Quantum mechanics/molecular mechanics calculations are employed to assign previously recorded experimental spectroscopic signatures of the intermediates occurring during the photo-induced repair of (6-4) photolesions by photolyases to specific molecular structures. Based on this close comparison of experiment and theory it is demonstrated that the acting repair mechanism involves proton transfer from the protonated His365 to the N3' nitrogen of the lesion, which proceeds simultaneously with intramolecular OH transfer along an oxetane-like transition state.

Photochemistry of Wild-Type and N378D Mutant E. coli DNA Photolyase with Oxidized FAD Cofactor Studied by Transient Absorption Spectroscopy

DNA photolyases (PLs) and evolutionarily related cryptochrome (CRY) blue-light receptors form a widespread superfamily of flavoproteins involved in DNA photorepair and signaling functions. They share a flavin adenine dinucleotide (FAD) cofactor and an electron-transfer (ET) chain composed typically of three tryptophan residues that connect the flavin to the protein surface. Four redox states of FAD are relevant for the various functions of PLs and CRYs: fully reduced FADH(-) (required for DNA photorepair), fully oxidized FADox (blue-light-absorbing dark state of CRYs), and the two semireduced radical states FAD(.-) and FADH(.) formed in ET reactions. The PL of Escherichia coli (EcPL) has been studied for a long time and is often used as a reference system; however, EcPL containing FADox has so far not been investigated on all relevant timescales. Herein, a detailed transient absorption study of EcPL on timescales from nanoseconds to seconds after excitation of FADox is presented. Wild-type EcPL and its N378D mutant, in which the asparagine facing the N5 of the FAD isoalloxazine is replaced by aspartic acid, known to protonate FAD(.-) (formed by ET from the tryptophan chain) in plant CRYs in about 1.5 μs, are characterized. Surprisingly, the mutant protein does not show this protonation. Instead, FAD(.-) is converted in 3.3 μs into a state with spectral features that are different from both FADH(.) and FAD(.-) . Such a conversion does not occur in wild-type EcPL. The chemical nature and formation mechanism of the atypical FAD radical in N378D mutant EcPL are discussed.

Electron transfer mechanisms of DNA repair by photolyase

Photolyase is a flavin photoenzyme that repairs two DNA base damage products induced by ultraviolet (UV) light: cyclobutane pyrimidine dimers and 6-4 photoproducts. With femtosecond spectroscopy and site-directed mutagenesis, investigators have recently made significant advances in our understanding of UV-damaged DNA repair, and the entire enzymatic dynamics can now be mapped out in real time. For dimer repair, six elementary steps have been characterized, including three electron transfer reactions and two bond-breaking processes, and their reaction times have been determined. A unique electron-tunneling pathway was identified, and the critical residues in modulating the repair function at the active site were determined. The dynamic synergy between the elementary reactions for maintaining high repair efficiency was elucidated, and the biological nature of the flavin active state was uncovered. For 6-4 photoproduct repair, a proton-coupled electron transfer repair mechanism has been revealed. The elucidation of electron transfer mechanisms and two repair photocycles is significant and provides a molecular basis for future practical applications, such as in rational drug design for curing skin cancer.

The molecular origin of high DNA-repair efficiency by photolyase

The primary dynamics in photomachinery such as charge separation in photosynthesis and bond isomerization in sensory photoreceptor are typically ultrafast to accelerate functional dynamics and avoid energy dissipation. The same is also true for the DNA repair enzyme, photolyase. However, it is not known how the photoinduced step is optimized in photolyase to attain maximum efficiency. Here, we analyse the primary reaction steps of repair of ultraviolet-damaged DNA by photolyase using femtosecond spectroscopy. With systematic mutations of the amino acids involved in binding of the flavin cofactor and the cyclobutane pyrimidine dimer substrate, we report our direct deconvolution of the catalytic dynamics with three electron-transfer and two bond-breaking elementary steps and thus the fine tuning of the biological repair function for optimal efficiency. We found that the maximum repair efficiency is not enhanced by the ultrafast photoinduced process but achieved by the synergistic optimization of all steps in the complex repair reaction.

Ultrafast photoinduced electron transfer in green fluorescent protein bearing a genetically encoded electron acceptor

Electron transfer (ET) is widely used for driving the processes that underlie the chemistry of life. However, our abilities to probe electron transfer mechanisms in proteins and design redox enzymes are limited, due to the lack of methods to site-specifically insert electron acceptors into proteins in vivo. Here we describe the synthesis and genetic incorporation of 4-fluoro-3-nitrophenylalanine (FNO2Phe), which has similar reduction potentials to NAD(P)H and ferredoxin, the most important biological reductants. Through the genetic incorporation of FNO2Phe into green fluorescent protein (GFP) and femtosecond transient absorption measurement, we show that photoinduced electron transfer (PET) from the GFP chromophore to FNO2Phe occurs very fast (within 11 ps), which is comparable to that of the first electron transfer step in photosystem I, from P700* to A0. This genetically encoded, low-reduction potential unnatural amino acid (UAA) can significantly improve our ability to investigate electron transfer mechanisms in complex reductases and facilitate the design of miniature proteins that mimic their functions.

Dynamics and mechanisms of DNA repair by photolyase

Photolyases, a class of flavoproteins, use blue light to repair two types of ultraviolet-induced DNA damage, a cyclobutane pyrimidine dimer (CPD) and a pyrimidine-pyrimidone (6-4) photoproduct (6-4PP). In this perspective, we review the recent progress in the repair dynamics and mechanisms of both types of DNA restoration by photolyases. We first report the spectroscopic characterization of flavin in various redox states and the active-site solvation dynamics in photolyases. We then systematically summarize the detailed repair dynamics of damaged DNA by photolyases and a biomimetic system through resolving all elementary steps on ultrafast timescales, including multiple intermolecular electron- and proton-transfer reactions and bond-breaking and -making processes. We determined the unique electron tunneling pathways, identified the key functional residues and revealed the molecular origin of high repair efficiency, and thus elucidate the molecular mechanisms and repair photocycles at the most fundamental level. We finally conclude that the active sites of photolyases, unlike the aqueous solution for the biomimetic system, provide a unique electrostatic environment and local flexibility and thus a dedicated synergy for all elementary dynamics to maximize the repair efficiency. This repair photomachine is the first enzyme that the entire functional evolution is completely mapped out in real time.

Photoinduced Electron Transfer in DNA: Charge Shift Dynamics Between 8-Oxo-Guanine Anion and Adenine

Femtosecond time-resolved IR spectroscopy is used to investigate the excited-state dynamics of a dinucleotide containing an 8-oxoguanine anion at the 5'-end and neutral adenine at the 3'-end. UV excitation of the dinucleotide transfers an electron from deprotonated 8-oxoguanine to its π-stacked neighbor adenine in less than 1 ps, generating a neutral 8-oxoguanine radical and an adenine radical anion. These species are identified by the excellent agreement between the experimental and calculated IR difference spectra. The quantum efficiency of this ultrafast charge shift reaction approaches unity. Back electron transfer from the adenine radical anion to the 8-oxguanine neutral radical occurs in 9 ps, or approximately 6 times faster than between the adenine radical anion and the 8-oxoguanine radical cation (Zhang, Y. et al. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 11612-11617). The large asymmetry in forward and back electron transfer rates is fully rationalized by semiclassical nonadiabatic electron transfer theory. Forward electron transfer is ultrafast because the driving force is nearly equal to the reorganization energy, which is estimated to lie between 1 and 2 eV. Back electron transfer is highly exergonic and takes place much more slowly in the Marcus inverted region.

Photochemistry of flavoprotein light sensors

Three major classes of flavin photosensors, light oxygen voltage (LOV) domains, blue light sensor using FAD (BLUF) proteins and cryptochromes (CRYs), regulate diverse biological activities in response to blue light. Recent studies of structure, spectroscopy and chemical mechanism have provided unprecedented insight into how each family operates at the molecular level. In general, the photoexcitation of the flavin cofactor leads to changes in redox and protonation states that ultimately remodel protein conformation and molecular interactions. For LOV domains, issues remain regarding early photochemical events, but common themes in conformational propagation have emerged across a diverse family of proteins. For BLUF proteins, photoinduced electron transfer reactions critical to light conversion are defined, but the subsequent rearrangement of hydrogen bonding networks key for signaling remains highly controversial. For CRYs, the relevant photocycles are actively debated, but mechanistic and functional studies are converging. Despite these challenges, our current understanding has enabled the engineering of flavoprotein photosensors for control of signaling processes within cells.

Signaling-State Formation Mechanism of a BLUF Protein PapB from the Purple Bacterium Rhodopseudomonas palustris Studied by Femtosecond Time-Resolved Absorption Spectroscopy

We studied the signaling-state formation of a BLUF (blue light using FAD) protein, PapB, from the purple bacterium Rhodopseudomonas palustris, using femtosecond time-resolved absorption spectroscopy. Upon photoexcitation of the dark state, FADH(•) (neutral flavin semiquinone FADH radical) was observed as the intermediate before the formation of the signaling state. The kinetic analysis based on singular value decomposition showed that FADH(•) mediates the signaling-state formation, showing that PapB is the second example of FADH(•)-mediated formation of the signaling state after Slr1694 (M. Gauden et al. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 10895-10900). The mechanism of the signaling-state formation is discussed on the basis of the comparison between femtosecond time-resolved absorption spectra of the dark state and those obtained by exciting the signaling state. FADH(•) was observed also with excitation of the signaling state, and surprisingly, the kinetics of FADH(•) was indistinguishable from the case of exciting the dark state. This result suggests that the hydrogen bond environment in the signaling state is realized before the formation of FADH(•) in the photocycle of PapB.

Excited-state proton coupled electron transfer between photolyase and the damaged DNA through water wire: a photo-repair mechanism

The photolyase enzyme absorbs blue light to repair damaged DNA through a cyclic electron transfer reaction. A description of the underlying mechanism has proven to be a challenging issue for both experimental and theoretical studies. In the present work, combined CASPT2//CASSCF/AMBER (QM/MM) calculations have been performed for damaged DNA in photolyase. A proton-coupled electron transfer (PCET) mechanism has been determined for restoring cyclobutane pyrimidine dimer (CPD) to two normal thymine bases by irradiation of photolyase. A well-defined water wire between FADH(-) and CPD was determined as a bridge to assist the PCET process within FADH(-) and thereby trigger the forward electron transfer to CPD. The subsequent CPD splitting and the alternation of the H-bond pattern proceed in a concerted way, which makes the productive backward electron transfer occur on an ultrafast timescale. A local minimum of SCT((1)ππ*)-LMin was identified on the pathway of the futile backward electron transfer (BET), which is stabilized by the strong H-bond interaction between the water wire and CPD. As a result, the futile BET process is endothermic by ∼18.0 kcal mol(-1), which is responsible for a 2.4 ns timescale inferred experimentally for the futile BET process. Besides the unbiased interpretation for the majority of the experimental findings, the present study provides a new excited-state PCET mechanism, which leads to a significant step toward a deeper understanding of the photo-repair process of damaged-DNA by the photolyase enzyme.

ATP binding and aspartate protonation enhance photoinduced electron transfer in plant cryptochrome

Cryptochromes are flavoproteins encountered in most vegetal and animal species. They play a role of blue-light receptors in plants and in invertebrates. The putative resting state of the FAD cofactor in these proteins is its fully oxidized form, FADox. Upon blue-light excitation, the isoalloxazine ring (ISO) may undergo an ultrafast reduction by a nearby tryptophan residue W400. This primary reduction triggers a cascade of electron and proton transfers, ultimately leading to the formation of the FADH° radical. A recent experimental study has shown that the yield of FADH° formation in Arabidopsis cryptochrome can be strongly modulated by ATP binding and by pH, affecting the protonation state of D396 (proton donor to FAD°(-)). Here we provide a detailed molecular analysis of these effects by means of combined classical molecular dynamics simulations and time-dependent density functional theory calculations. When ATP is present and D396 protonated, FAD remains in close contact with W400, thereby enhancing electron transfer (ET) from W400 to ISO*. In contrast, deprotonation of D396 and absence of ATP introduce flexibility to the photoactive site prior to FAD excitation, with the consequence of increased ISO-W400 distance and diminished tunneling rate by almost two orders of magnitude. We show that under these conditions, ET from the adenine moiety of FAD becomes a competitive relaxation pathway. Overall, our data suggest that the observed effects of ATP and pH on the FAD photoreduction find their roots in the earliest stage of the photoreduction process; i.e., ATP binding and the protonation state of D396 determine the preferred pathway of ISO* relaxation.

Direct determination of resonance energy transfer in photolyase: structural alignment for the functional state

Photoantenna is essential to energy transduction in photoinduced biological machinery. A photoenzyme, photolyase, has a light-harvesting pigment of methenyltetrahydrofolate (MTHF) that transfers its excitation energy to the catalytic flavin cofactor FADH¯ to enhance DNA-repair efficiency. Here we report our systematic characterization and direct determination of the ultrafast dynamics of resonance energy transfer from excited MTHF to three flavin redox states in E. coli photolyase by capturing the intermediates formed through the energy transfer and thus excluding the electron-transfer quenching pathway. We observed 170 ps for excitation energy transferring to the fully reduced hydroquinone FADH¯, 20 ps to the fully oxidized FAD, and 18 ps to the neutral semiquinone FADH^•, and the corresponding orientation factors (κ²) were determined to be 2.84, 1.53 and 1.26, respectively, perfectly matching with our calculated theoretical values. Thus, under physiological conditions and over the course of evolution, photolyase has adopted the optimized orientation of its photopigment to efficiently convert solar energy for repair of damaged DNA.

ATP binding turns plant cryptochrome into an efficient natural photoswitch

Cryptochromes are flavoproteins that drive diverse developmental light-responses in plants and participate in the circadian clock in animals. Plant cryptochromes have found application as photoswitches in optogenetics. We have studied effects of pH and ATP on the functionally relevant photoreduction of the oxidized FAD cofactor to the semi-reduced FADH^· radical in isolated Arabidopsis cryptochrome 1 by transient absorption spectroscopy on nanosecond to millisecond timescales. In the absence of ATP, the yield of light-induced radicals strongly decreased with increasing pH from 6.5 to 8.5. With ATP present, these yields were significantly higher and virtually pH-independent up to pH 9. Analysis of our data in light of the crystallographic structure suggests that ATP-binding shifts the pK_a of aspartic acid D396, the putative proton donor to FAD·⁻, from ~7.4 to >9, and favours a reaction pathway yielding long-lived aspartate D396⁻. Its negative charge could trigger conformational changes necessary for signal transduction.

Dynamic Determination of Active-Site Reactivity in Semiquinone Photolyase by the Cofactor Photoreduction

Photolyase contains a flavin cofactor in a fully reduced form as its functional state to repair ultraviolet-damaged DNA upon blue light absorption. However, after purification, the cofactor exists in its oxidized or neutral semiquinone state. Such oxidization eliminates the repair function, but it can be reverted by photoreduction, a photoinduced process with a series of electron-transfer (ET) reactions. With femtosecond absorption spectroscopy and site-directed mutagenesis, we completely recharacterized such photoreduction dynamics in the semiquinone state. Comparing with all previous studies, we identified a new intramolecular ET pathway, determined stretched ET behaviors, refined all ET time scales, and finally evaluated the driving forces and reorganization energies for eight elementary ET reactions. Combined with the oxidized-state photoreduction dynamics, we elucidated the different active-site properties of the reduction ability and structural flexibility in the oxidized and semiquinone states, leading to the dramatically different ET dynamics and photoreduction efficiency in the two states.

From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World

Flavin-based photoreceptor proteins of the LOV (Light, Oxygen, and Voltage) and BLUF (Blue Light sensing Using Flavins) superfamilies are ubiquitous among the three life domains and are essential blue-light sensing systems, not only in plants and algae, but also in prokaryotes. Here we review their biological roles in the prokaryotic world and their evolution pathways. An unexpected large number of bacterial species possess flavin-based photosensors, amongst which are important human and plant pathogens. Still, few cases are reported where the activity of blue-light sensors could be correlated to infectivity and/or has been shown to be involved in the activation of specific genes, resulting in selective growth patterns. Metagenomics and bio-informatic analysis have only recently been initiated, but signatures are beginning to emerge that allow definition of a bona fide LOV or BLUF domain, aiming at better selection criteria for novel blue-light sensors. We also present here, for the first time, the phylogenetic tree for archaeal LOV domains that have reached a statistically significant number but have not at all been investigated thus far.

Mechanism of photosignaling by Drosophila cryptochrome: role of the redox status of the flavin chromophore

Cryptochrome (CRY) is the primary circadian photoreceptor in Drosophila. Upon light absorption, dCRY undergoes a conformational change that enables it to bind to Timeless (dTIM), as well as to two different E3 ligases that ubiquitylate dTIM and dCRY, respectively, resulting in their proteolysis and resetting the phase of the circadian rhythm. Purified dCRY contains oxidized flavin (FADox), which is readily photoreduced to the anionic semiquinone through a set of 3 highly conserved Trp residues (Trp triad). The crystal structure of dCRY has revealed a fourth Trp (Trp-536) as a potential electron donor. Previously, we reported that the Trp triad played no role in photoinduced proteolysis of dCRY in Drosophila cells. Here we investigated the role of the Trp triad and Trp-536, and the redox status of the flavin on light-induced proteolysis of both dCRY and dTIM and resetting of the clock. We found that both oxidized (FADox) and reduced (FAD) forms of dCRY undergo light-induced conformational change in vitro that enable dCRY to bind JET and that Trp triad and Trp-536 mutations that block known or presumed intraprotein electron transfer reactions do not affect dCRY phototransduction under bright or dim light in vivo as measured by light-induced proteolysis of dCRY and dTIM in Drosophila S2R+ cells. We conclude that both oxidized and reduced forms of dCRY are capable of photosignaling.

Femtosecond dynamics of short-range protein electron transfer in flavodoxin

Intraprotein electron transfer (ET) in flavoproteins is important for understanding the correlation of their redox, configuration, and reactivity at the active site. Here, we used oxidized flavodoxin as a model system and report our complete characterization of a photoinduced redox cycle from the initial charge separation in 135-340 fs to subsequent charge recombination in 0.95-1.6 ps and to the final cooling relaxation of the product(s) in 2.5-4.3 ps. With 11 mutations at the active site, we observed that these ultrafast ET dynamics, much faster than active-site relaxation, mainly depend on the reduction potentials of the electron donors with minor changes caused by mutations, reflecting a highly localized ET reaction between the stacked donor and acceptor at a van der Waals distance and leading to a gas-phase type of bimolecular ET reaction confined in the active-site nanospace. Significantly, these ultrafast ET reactions ensure our direct observation of vibrationally excited reaction product(s), suggesting that the back ET barrier is effectively reduced because of the decrease in the total free energy in the Marcus inverted region, leading to the accelerated charge recombination. Such vibrationally coupled charge recombination should be a general feature of flavoproteins with similar configurations and interactions between the cofactor flavin and neighboring aromatic residues.

Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions

Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.