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

Visualizing the DNA repair process by a photolyase at atomic resolution

Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.

Time-resolved crystallography captures light-driven DNA repair

Photolyase is an enzyme that uses light to catalyze DNA repair. To capture the reaction intermediates involved in the enzyme's catalytic cycle, we conducted a time-resolved crystallography experiment. We found that photolyase traps the excited state of the active cofactor, flavin adenine dinucleotide (FAD), in a highly bent geometry. This excited state performs electron transfer to damaged DNA, inducing repair. We show that the repair reaction, which involves the lysis of two covalent bonds, occurs through a single-bond intermediate. The transformation of the substrate into product crowds the active site and disrupts hydrogen bonds with the enzyme, resulting in stepwise product release, with the 3' thymine ejected first, followed by the 5' base.

Reduced Flavin in Aqueous Solution Is Nonfluorescent

Flavins are blue-light-absorbing chromophores with rich redox activity. Biologically, the most important are riboflavin (vitamin B₂), flavin mononucleotide, and flavin adenine dinucleotide, the latter two of which are catalytic cofactors in enzymes. Flavins pivot between oxidized, one electron-, and two electron-reduced forms in different protonation states, depending on enzymatic requirements. Some flavoenzymes use light as a reagent for chemical bond formation, photoinduced electron transfer, or conformational changes required for light-sensitive signaling. Therefore, the photochemistry and photophysics of flavins have received wide attention. Fluorescence from oxidized flavin is often used to detect and track changes in flavin oxidation states. However, there have been conflicting reports over the past 45 years as to whether reduced flavin in solution has detectable fluorescence. Here, using single photon counting emission spectroscopy with rigorous sample preparation, we show definitively that reduced flavins are essentially nonfluorescent, having a quantum yield more than three orders of magnitude lower than oxidized flavin. This result will force a re-evaluation of experiments and models that assumed otherwise.

Excited-State Properties of Fully Reduced Flavins in Ferredoxin-NADP+ Oxidoreductase

The fully reduced flavin cofactor (FAD_red) in ferredoxin-NADP⁺ oxidoreductase (FNR) is a functional intermediate that displays different catalytic and steady-state spectral properties for enzymes from Bacillus subtilis (BsFNR), Chlorobaculum tepidum (CtFNR), and Rhodopseudomonas palustris (RpFNR). Using ultrafast spectroscopy, we reveal that at physiological pH, photoexcited FAD_red in BsFNR and RpFNR exhibits unprecedentedly fast decays (dominantly in 6 and 8 ps, respectively), whereas in CtFNR the decay is much slower (∼400 ps), as in other flavoproteins. Correlating these observations with the protonation states of FAD_red and the dynamic properties of the protein environment, we conclude that the excited state of neutral FAD_red can be intrinsically short-lived even in proteins, contrasting with the well-documented behavior of the anionic form that systematically displays markedly increased excited-state lifetime upon binding to proteins. This work provides new insight into the photochemistry of fully reduced flavins, which are emerging as functional initial states in bioengineered photocatalysts.

TiO2 as a Nanozyme Mimicking Photolyase to Repair DNA Damage

Cyclobutane pyrimidine dimer (CPD) is the most abundant DNA photolesion, and it can be repaired by photolyases based on electron-transfer mechanisms. However, photolyase is absent in the human body and lacks stability for applications. Can one develop natural enzyme mimetics utilizing nanoparticles (termed nanozymes) to mimic photolyase in repairing DNA damage? Herein, we observe the successful reversal of thymine dimer T<>T to normal T base by TiO₂ under UVA irradiation. Time-resolved spectroscopy provides direct evidence that the photogenerated electron of TiO₂ transfers to T<>T, causing structural instability and initiating the repair process. T-T^- would then undergo bond cleavage to form T and T^-, and T^- returns an electron to TiO₂, finishing the photocatalytic cycle. For the first time, TiO₂ is discovered to exhibit photocatalytic properties similar to those of natural enzymes, pointing to its extraordinary application potential as a nanozyme to mimic photolyase in repairing DNA damage.

Ultrafast dynamics of fully reduced flavin in catalytic structures of thymidylate synthase ThyX

Thymidylate is a vital DNA precursor synthesized by thymidylate synthases. ThyX is a flavin-dependent thymidylate synthase found in several human pathogens and absent in humans, which makes it a potential target for antimicrobial drugs. This enzyme methylates the 2'-deoxyuridine 5'-monophosphate (dUMP) to 2'-deoxythymidine 5'-monophosphate (dTMP) using a reduced flavin adenine dinucleotide (FADH^-) as prosthetic group and (6R)-N₅,N₁₀-methylene-5,6,7,8-tetrahydrofolate (CH₂THF) as a methylene donor. Recently, it was shown that ThyX-catalyzed reaction is a complex process wherein FADH^- promotes both methylene transfer and reduction of the transferred methylene into a methyl group. Here, we studied the dynamic and photophysics of FADH^- bound to ThyX, in several substrate-binding states (no substrate, in the presence of dUMP or folate or both) by femtosecond transient absorption spectroscopy. This methodology provides valuable information about the ground-state configuration of the isoalloxazine moiety of FADH^- and the rigidity of its local environment, through spectra shape and excited-state lifetime parameters. In the absence of substrate, the environment of FADH^- in ThyX is only mildly more constrained than that of free FADH^- in solution. The addition of dUMP however narrows the distribution of ground-state configurations and increases the constraints on the butterfly bending motion in the excited state. Folate binding results in the selection of new ground-state configurations, presumably located at a greater distance from the conical intersection where excited-state decay occurs. When both substrates are present, the ground-state configuration appears on the contrary rather limited to a geometry close to the conical intersection, which explains the relatively fast excited-state decay (100 ps on the average), even if the environment of the isoalloxazine is densely packed. Hence, although the environment of the flavin is dramatically constrained, FADH^- retains a dynamic necessary to shuttle carbon from folate to dUMP. Our study demonstrates the high sensitivity of FADH^- photophysics to the constraints exerted by its immediate surroundings.

UV-visible absorption spectrum of FAD and its reduced forms embedded in a cryptochrome protein

Cryptochromes are a class of flavoproteins proposed as candidates to explain magnetoreception of animals, plants and bacteria. The main hypothesis is that a biradical is formed upon blue-light absorption by flavin adenine dinucleotide (FAD). In a protein milieu, the oxidized form of FAD can be reduced, leading to four redox derivative forms: anionic and neutral semi-reduced radicals, and anionic and neutral fully reduced forms. All these forms have a characteristic electronic absorption spectrum, with a strong vibrational resolution. Here, we carried out a normal mode analysis at the electrostatic embedding QM/MM level of theory to compute the vibrationally resolved absorption spectra of the five redox forms of FAD embedded in a plant cryptochrome. We show that explicitly accounting for vibrational broadening contributions to electronic transitions is essential to reproduce the experimental spectra. In the case of the neutral radical form of FAD, the absorption spectrum is reproduced only if the presence of a tryptophan radical is considered.

Kinetic and structural insight into a role of the re-face Tyr328 residue of the homodimer type ferredoxin-NADP+ oxidoreductase from Rhodopseudomonas palustris in the reaction with NADP+/NADPH

Among the thioredoxin reductase-type ferredoxin-NAD(P)⁺ oxidoreductase (FNR) family, FNR from photosynthetic purple non‑sulfur bacterium Rhodopseudomonas palustris (RpFNR) is distinctive because the predicted residue on the re-face of the isoalloxazine ring portion of the FAD prosthetic group is a tyrosine. Here, we report the crystal structure of wild type RpFNR and kinetic analyses of the reaction of wild type, and Y328F, Y328H and Y328S mutants with NADP⁺/NADPH using steady state and pre-steady state kinetic approaches. The obtained crystal structure of wild type RpFNR confirmed the presence of Tyr328 on the re-face of the isoalloxazine ring of the FAD prosthetic group through the unique hydrogen bonding of its hydroxyl group. In the steady state assays, the substitution results in the decrease of K_d for NADP⁺ and K_M for NADPH in the diaphorase assay; however, the k_cat values also decreased significantly. In the stopped-flow spectrophotometry, mixing oxidized RpFNRs with NADPH and reduced RpFNRs with NADP⁺ resulted in rapid charge transfer complex formation followed by hydride transfer. The observed rate constants for the hydride transfer in both directions were comparable (>400 s^-1). The substitution did not drastically affect the rate of hydride transfer, but substantially slowed down the subsequent release and re-association of NADP⁺/NADPH in both directions. The obtained results suggest that Tyr328 stabilizes the stacking of C-terminal residues on the isoalloxazine ring portion of the FAD prosthetic group, which impedes the access of NADP⁺/NADPH on the isoalloxazine ring portions, in turn, enhancing the release of the NADP⁺/NADPH and/or reaction with electron transfer proteins.

Measuring electronic structure properties of flavins and flavoproteins by electronic Stark spectroscopy

The optical spectrum of a flavoprotein is one of its signature properties. No two flavoprotein absorption spectra are exactly alike as each encodes the details of the interaction of the flavin cofactor electronic structure with the specific protein binding pocket. Electronic Stark spectroscopy has the potential to elucidate these interactions with high sensitivity, at low cost, and requiring minimal technical sophistication. In this chapter we will outline the theoretical basis for Stark spectroscopy and describe the construction of the Stark spectrometer. Step-by-step instructions are given for acquiring and interpreting Stark spectra to retrieve difference moments of the flavin ground versus excited state charge distributions.

Multispectral multidimensional spectrometer spanning the ultraviolet to the mid-infrared

Multidimensional spectroscopy is the optical analog to nuclear magnetic resonance, probing dynamical processes with ultrafast time resolution. At optical frequencies, the technical challenges of multidimensional spectroscopy have hindered its progress until recently, where advances in laser sources and pulse-shaping have removed many obstacles to its implementation. Multidimensional spectroscopy in the visible and infrared (IR) regimes has already enabled respective advances in our understanding of photosynthesis and the structural rearrangements of liquid water. A frontier of ultrafast spectroscopy is to extend and combine multidimensional techniques and frequency ranges, which have been largely restricted to operating in the distinct visible or IR regimes. By employing two independent amplifiers seeded by a single oscillator, it is straightforward to span a wide range of time scales (femtoseconds to seconds), all of which are often relevant to the most important energy conversion and catalysis problems in chemistry, physics, and materials science. Complex condensed phase systems have optical transitions spanning the ultraviolet (UV) to the IR and exhibit dynamics relevant to function on time scales of femtoseconds to seconds and beyond. We describe the development of the Multispectral Multidimensional Nonlinear Spectrometer (MMDS) to enable studies of dynamical processes in atomic, molecular, and material systems spanning femtoseconds to seconds, from the UV to the IR regimes. The MMDS employs pulse-shaping methods to provide an easy-to-use instrument with an unprecedented spectral range that enables unique combination spectroscopies. We demonstrate the multispectral capabilities of the MMDS on several model systems.

Determinants of Photolyase's DNA Repair Mechanism in Mesophiles and Extremophiles

Light-driven DNA repair by extremophilic photolyases is of tremendous importance for understanding the early development of life on Earth. The mechanism for flavin adenine dinucleotide repair of DNA lesions is the subject of debate and has been studied mainly in mesophilic species. In particular, the role of adenine in the repair process is poorly understood. Using molecular docking, molecular dynamics simulations, electronic structure calculations, and electron tunneling pathways analysis, we examined adenine's role in DNA repair in four photolyases that thrive at different temperatures. Our results indicate that the contribution of adenine to the electronic coupling between the flavin and the cyclobutane pyrimidine dimer lesion to be repaired is significant in three (one mesophilic and two extremophilic) of the four enzymes studied. Our analysis suggests that thermophilic and hyperthermophilic photolyases have evolved structurally to preserve the functional position (and thus the catalytic function) of adenine at their high temperatures of operation. Water molecules can compete with adenine in establishing the strongest coupling pathway for the electron transfer repair process, but the adenine contribution remains substantial. The present study also reconciles prior seemingly contradictory conclusions on the role of adenine in mesophile electron transfer repair reactions, showing how adenine-mediated superexchange is conformationally gated.