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.

Ultrafast photoreduction dynamics of a new class of CPD photolyases.

NewPHL is a recently discovered subgroup of ancestral DNA photolyases. Its domain architecture displays pronounced differences from that of canonical photolyases, in particular at the level of the characteristic electron transfer chain, which is limited to merely two tryptophans, instead of the "classical" three or four. Using transient absorption spectroscopy, we show that the dynamics of photoreduction of the oxidized FAD cofactor in the NewPHL begins similarly as that in canonical photolyases, i.e., with a sub-ps primary reduction of the excited FAD cofactor by an adjacent tryptophan, followed by migration of the electron hole towards the second tryptophan in the tens of ps regime. However, the resulting tryptophanyl radical then undergoes an unprecedentedly fast deprotonation in less than 100 ps in the NewPHL. In spite of the stabilization effect of this deprotonation, almost complete charge recombination follows in two phases of ~ 950 ps and ~ 50 ns. Such a rapid recombination of the radical pair implies that the first FAD photoreduction step, i.e., conversion of the fully oxidized to the semi-quinone state, should be rather difficult in vivo. We hence suggest that the flavin chromophore likely switches only between its semi-reduced and fully reduced form in NewPHL under physiological conditions.

Ultrafast Oxidation of a Tyrosine by Proton-Coupled Electron Transfer Promotes Light Activation of an Animal-like Cryptochrome.

The animal-like cryptochrome of Chlamydomonas reinhardtii (CraCRY) is a recently discovered photoreceptor that controls the transcriptional profile and sexual life cycle of this alga by both blue and red light. CraCRY has the uncommon feature of efficient formation and longevity of the semireduced neutral form of its FAD cofactor upon blue light illumination. Tyrosine Y373 plays a crucial role by elongating , as fourth member, the electron transfer (ET) chain found in most other cryptochromes and DNA photolyases, which comprises a conserved tryptophan triad. Here, we report the full mechanism of light-induced FADH• formation in CraCRY using transient absorption spectroscopy from hundreds of femtoseconds to seconds. Electron transfer starts from ultrafast reduction of excited FAD to FAD•- by the proximal tryptophan (0.4 ps) and is followed by delocalized migration of the produced WH•+ radical along the tryptophan triad (∼4 and ∼50 ps). Oxidation of Y373 by coupled ET to WH•+ and deprotonation then proceeds in ∼800 ps, without any significant kinetic isotope effect, nor a pH effect between pH 6.5 and 9.0. The FAD•-/Y373• pair is formed with high quantum yield (∼60%); its intrinsic decay by recombination is slow (∼50 ms), favoring reduction of Y373• by extrinsic agents and protonation of FAD•- to form the long-lived, red-light absorbing FADH• species. Possible mechanisms of tyrosine oxidation by ultrafast proton-coupled ET in CraCRY, a process about 40 times faster than the archetypal tyrosine-Z oxidation in photosystem II, are discussed in detail.

Ultrafast photoinduced flavin dynamics in the unusual active site of the tRNA methyltransferase TrmFO.

Flavoproteins often stabilize their flavin coenzyme by stacking interactions involving the isoalloxazine moiety of the flavin and an aromatic residue from the apoprotein. The bacterial FAD and folate-dependent tRNA methyltransferase TrmFO has the unique property of stabilizing its FAD coenzyme by an unusual H-bond-assisted π-π stacking interaction, involving a conserved tyrosine (Y346 in Bacillus subtilis TrmFO, BsTrmFO), the isoalloxazine of FAD and the backbone of a catalytic cysteine (C53). Here, the interaction between FAD and Y346 has been investigated by measuring the photoinduced flavin dynamics of BsTrmFO in the wild-type (WT) protein, C53A and several Y346 mutants by ultrafast transient absorption spectroscopy. In C53A, the excited FAD very rapidly (0.43 ps) abstracts an electron from Y346, yielding the FAD˙-/Y346OH˙+ radical pair, while relaxation of the local environment (1.3 ps) of the excited flavin produces a slight Stokes shift of its stimulated emission band. The radical pair then decays via charge recombination, mostly in 3-4 ps, without any deprotonation of the Y346OH˙+ radical. Presumably, the H-bond between Y346 and the amide group of C53 increases the pKa of Y346OH˙+ and slows down its deprotonation. The dynamics of WT BsTrmFO shows additional slow decay components (43 and 700 ps), absent in the C53A mutant, assigned to excited FADox populations not undergoing fast photoreduction. Their presence is likely due to a more flexible structure of the WT protein, favored by the presence of C53. Interestingly, mutations of Y346 canceling its electron donating character lead to multiple slower quenching channels in the ps-ns regime. These channels are proposed to be due to electron abstraction either (i) from the adenine moiety of FAD, a distribution of the isoalloxazine-adenine distance in the absence of Y346 explaining the multiexponential decay, or (ii) from the W286 residue, possibly accounting for one of the decays. This work supports the idea that H-bond-assisted π-π stacking controls TrmFO's active site dynamics, required for competent orientation of the reactive centers during catalysis.

Delocalized hole transport coupled to sub-ns tryptophanyl deprotonation promotes photoreduction of class II photolyases.

Class II photolyases utilize for the photoreduction of their flavin cofactor (FAD) a completely different tryptophan triad than most other photolyases and cryptochromes. To counter sped-up back electron transfer, they evolved an unusually fast deprotonation of the distal tryptophanyl radical cation (WH˙+) that is produced after excitation of the flavin. We studied the primary aspects of oxidized FAD photoreduction by ultrafast transient absorption spectroscopy, using the class II photolyase from Methanosarcina mazei. With a time constant of 9.2 ps, the initial reduction step of the excited flavin by the proximal W381 tryptophan proceeds almost twentyfold slower than in other photolyases carrying oxidized FAD, most likely because of the larger distance between the flavin and the proximal tryptophan. The thus formed W381H˙+ radical is tracked by transient anisotropy measurements to migrate in 29 ps with delocalization over several members of the tryptophan triad. This 29 ps phase also includes the decay of a small fraction of excited flavin, reacting on a slower timescale, and partial recombination of the FAD˙-/WH˙+ radical pair. A final kinetic phase in 230 ps is assigned to the deprotonation of W388H˙+ that occurs in competition with partial charge recombination. Interestingly, we show by comparison with the Y345F mutant that this last phase additionally involves oxidation of the Y345 phenolic group by W388H˙+, producing a small amount of neutral tyrosyl radical (YO˙). The rate of this electron transfer step is about six orders of magnitude faster than the corresponding oxidation of Y345 by the deprotonated W388˙ radical. Unlike conventional photolyases, where the electron hole accumulates on the distal tryptophan before the much slower tryptophanyl deprotonation, our data show that delocalized hole transport is concomitantly concluded by ultrafast deprotonation of W388H˙+.

Ultrafast flavin photoreduction in an oxidized animal (6-4) photolyase through an unconventional tryptophan tetrad.

Photolyases are flavoenzymes repairing UV-induced lesions in DNA, which may be activated by a photoreduction of their FAD cofactor. In most photolyases, this photoreduction proceeds by electron transfer along a chain of three tryptophan (Trp) residues, connecting the flavin to the protein surface. Much less studied, animal (6-4) photolyases (repairing pyrimidine-pyrimidone (6-4) photoproducts) are particularly interesting as they were recently shown to have a longer electron transfer chain, counting four Trp residues. Using femtosecond polarized transient absorption spectroscopy, we performed a detailed analysis of the photoactivation reaction in the (6-4) photolyase of Xenopus laevis with oxidized FAD. We showed that the excited flavin is very quickly reduced (∼0.5 ps) by a nearby tryptophan residue, yielding FAD˙- and WH˙+ radicals. Subsequent kinetic steps in the picosecond regime were assigned to the migration of the positive charge along the Trp tetrad, in competition with charge recombination. We propose that the positive charge is actually delocalized over various Trp residues during most of the dynamics and that charge recombination essentially occurs through the proximal tryptophanyl radical. Oxidation of the fourth tryptophan is thought to be reached about as fast as that of the third one (∼40 ps), based on a comparison with a mutant protein lacking the distal Trp, implying ultrafast electron transfer between these two residues. This unusual mechanism sheds light on the rich diversity of electron transfer pathways found in various photolyases, and evolution-related cryptochromes alike.

Photo-induced cation translocation in a molecular shuttle based on a calix[4]-biscrown including DCM and DMABN chromophores.

We present a new molecular shuttle, consisting of a calixarene core attached to two different photoactive centers, DCM and DMABN. We show that a K(+) ion bound to the DCM-grafted crown is translocated towards the other site of the molecule upon photoexcitation, but not released to the bulk.

Real-time monitoring of chromophore isomerization and deprotonation during the photoactivation of the fluorescent protein Dronpa.

Dronpa is a photochromic green fluorescent protein (GFP) homologue used as a probe in super-resolution microscopy. It is known that the photochromic reaction involves cis/trans isomerization of the chromophore and protonation/deprotonation of its phenol group, but the sequence in time of the two steps and their characteristic time scales are still the subject of much debate. We report here a comprehensive UV-visible transient absorption spectroscopy study of the photoactivation mechanism of Dronpa, covering all relevant time scales from ∼100 fs to milliseconds. The Dronpa-2 variant was also studied and showed the same behavior. By carefully controlling the excitation energy to avoid multiphoton processes, we could measure both the spectrum and the anisotropy of the first photoactivation intermediate. We show that the observed few nanometer blue-shift of this intermediate is characteristic for a neutral cis chromophore, and that its anisotropy of ∼0.2 is in good agreement with the reorientation of the transition dipole moment expected upon isomerization. These data constitute the first clear evidence that trans → cis isomerization of the chromophore precedes its deprotonation and occurs on the picosecond time scale, concomitantly to the excited-state decay. We found the deprotonation step to follow in ∼10 µs and lead directly from the neutral cis intermediate to the final state.

Visible luminescence spectroscopy of free-base and zinc phthalocyanines isolated in cryogenic matrices.

The absorption, emission and excitation spectra of ZnPc and H(2)Pc trapped in Ne, N(2), Ar, Kr and Xe matrices have been recorded in the region of the Q states. A comparison of the matrix fluorescence spectra with Raman spectra recorded in KBr pellets reveals very strong similarities. This is entirely consistent with the selection rules and points to the occurrence of only fundamental vibrational transitions in the emission spectra. Based on this behaviour, the vibronic modes in emission have been assigned using results obtained recently on the ground state with large basis-set DFT calculations [Murray et al. PCCP, 12, 10406 (2010)]. Furthermore, the very strong mirror symmetry between excitation and emission has allowed these assignments to be extended to the excitation (absorption) bands. While this approach works well for ZnPc, coupling between the band origin of the S(2)(Q(Y)) state and vibrationally excited levels of S(1)(Q(X)), limits the range of its application in H(2)Pc. The Q(X)/Q(Y) state coupling is analysed from data obtained from site-selective excitation spectra, revealing pronounced matrix and site effects. From this analysis, the splitting of the Q(X) and Q(Y) states has been determined more accurately than in any previous attempts.

Infra-red and Raman spectroscopy of free-base and zinc phthalocyanines isolated in matrices.

The infrared absorption spectra of matrix-isolated zinc phthalocyanine (ZnPc) and free-base phthalocyanine (H(2)Pc) have been recorded in the region from 400 to 4000 cm(-1) in solid N(2), Ar, Kr and Xe. Raman spectra have been recorded in doped KBr pellets. The isotopomers HDPc and D(2)Pc have been synthesised in an attempt to resolve the conflicting assignments that currently exist in the literature for the N-H bending modes in H(2)Pc spectra. A complete correlation between the vibrational modes of the three free-base isotopomers and ZnPc has been achieved. Comparison of the IR and Raman spectroscopic results, obtained with isotopic substitution and with predictions from large basis set ab initio calculations, allows identification of the in-plane (IP) and out-of-plane (OP) N-H bending modes. The largest IP isotope shift is observed in the IR at 1046 cm(-1) and at 1026 cm(-1) in Raman spectra while the largest effect in the OP bending modes is at 764 cm(-1). OP bending modes are too weak to be observed in the experimental Raman data. The antisymmetric N-H stretching mode is observed at approximately 3310 cm(-1) in low temperature solids slightly blue shifted from, but entirely consistent with the literature KBr data. With the exception of the N-H stretches, the recorded H/D isotope shifts in all the N-H vibrations are complex, with the IP bending modes exhibiting small nu(H)/nu(D) ratios (the largest value is 1.089) while one of the observed OP modes has a ratio < 1. DFT results reveal that the small ratios arise in particular from strong coupling of the N-H IP bending modes with IP stretching modes of C-N bonds. The unexpected finding of a nu(H)/nu(D) ratio smaller than one was analysed theoretically by examining the evolution of the frequencies of the free base by increasing the mass from H to D in a continuous manner. A consequence of this frequency increase in the heavier isotopomer is that the direction of the N-D OP bend is reversed from the N-H OP bend.

Amplified emission of phthalocyanine isolated in cryogenic matrices.

Laser induced fluorescence spectroscopy of free-base (H(2)Pc) and zinc (ZnPc) phthalocyanines trapped in rare gas and nitrogen matrices reveals a quite unexpected phenomenon with a moderate increase in the laser intensity. In all matrices except Xe, a huge increase occurs in the intensity of an emission band near 755 nm when pumping the S(1) <-- S(0) transition. The band involves a vibrational mode of the ground state, located at 1550 and 1525 cm(-1) for H(2)Pc and ZnPc, respectively. Many of the characteristics of amplified emission (AE) are exhibited by this vibronic transition. Excitation scans recorded for the AE band yield greatly enhanced site selectivity compared to what is obtained in normal fluorescence excitation scans.

Vibrational spectra and structure of CH3Cl:(H2O)2 and CH3Cl:(D2O)2 complexes. IR matrix isolation and ab initio calculations.

The infrared spectra of CH3Cl + H2O isolated in solid neon at low temperature have been investigated. High concentration studies of water (0.01%-4%) and subsequent annealing lead to the formation of the ternary CH3Cl:(H2O)2 complex. Detailed vibrational assignments were made on the observed spectra of water and deuterated water engaged in the complex. In parallel, structural, energetic, and vibrational properties of the complex have been studied at the second-order Møller-Plesset perturbation theory using several basis sets. Anaharmonic correction to the vibrational frequencies has been done with the standard second-order perturbation approach. It was shown that the ground state of the complex has a cyclic form for which the nonadditive three-body contribution was found to be around 10% of the interaction energy.

Vibrational spectra and structures of H2O-NO, HDO-NO, and D2O-NO complexes. An IR matrix isolation and DFT study.

The IR spectra of H2O+NO, HDO+NO, and D2O+NO, isolated in solid neon at low temperature have been investigated. Concentration effects and detailed vibrational analysis of deuterated and partially deuterated species allowed identification of three 1:1 HDO-NO species, two 1:1 D2O-NO species, and only one 1:1 H2O-NO complex. From comparison between the experimental spectra and the results of DFT calculations, it appeared that two different types of weakly bound complexes between water and nitric oxide can be formed in a neon matrix. The first species is a 1:1 complex where bonding occurs between water hydrogen and nitric oxide nitrogen, in which OH-N and OD-N intermolecular bonds are engaged. For this complex only DOD-NO, HOD-NO, and DOH-NO isotopic species have been experimentally detected and no IR bands of HOH-NO were observed. This result could be explained by the fact that the dissociation energy of HOH-NO is lower than those of DOD-NO, HOD-NO and DOH-NO. For the second detected 1:1 H2O-NO complex and its isotopic variants, the H2O-NO potential surface was explored systematically at the B3LYP level, but no stable species corresponding to the complex could be calculated. The structure of the second observed 1:1 H2O-NO complex results from columbic attractions between water and nitric oxide and could be stabilized only in matrix, probably by interaction between NO, water and (Ne)n.

Vibrational spectra and structure of CH3Cl:NO complex: IR matrix isolation and DFT study.

Infrared spectra of the CH(3)Cl:NO complex isolated in solid neon have been investigated. Most of the vibrational modes of the complex have been detected. The weak interaction between NO and CH(3)Cl in CH(3)Cl:NO is responsible for small shifts of the vibrational mode frequencies of both CH(3)Cl and NO molecules. The measured shifts range between -3.2 and + 3.8 cm(-1). On the basis of DFT calculations, different geometries have been explored for the complex, and it has been shown that the most stable structure is of C(1) symmetry. The calculated frequency shifts match well the experimental data.

Vibrational spectra and structure of CH3Cl:H2O, CH3Cl:HDO, and CH3Cl:D2O complexes. IR matrix isolation and ab initio calculations.

The infrared spectra of CH3Cl + H2O isolated in solid neon at low temperatures have been investigated. The CH3Cl + H2O system is remarkable because of its propensity to form CH3Cl:H2O and CH3Cl:(H2O)n (n > or = 2) complexes. We focus here on the CH3Cl:H2O species. Low concentration studies (0.01-0.5%) and subsequent annealing lead to formation of the 1:1 CH3Cl:H2O complex with O-H. . .Cl-C or O. . .H-C intermolecular hydrogen bonds. Vibrational modes of this complex have been detected. In addition, spectra of D2O + CH3Cl and HDO + CH3Cl have also been recorded. A detailed vibrational analysis of partially deuterated species shows that HDO is exclusively D bonded to CH3Cl. This is a consequence of the preference for HDO to form a deuterium bonding complex rather than a hydrogen bonding one.