Photoisomerization and proton transfer in photoactive yellow protein

Does the wavelength dependent photoisomerization process of the p‑coumaric acid come out from the electronic state dependent pathways?

Similar to the anion photoactive yellow protein (PYP) chromophore, the neutral form of the PYP chromophore was also found to exhibit a the wavelength-dependent photoisomerization quantum yield. The isomerization quantum yield increases with the increasing excitation energy on the S₁ state, while decreases when being excited to the S₂ state. Does this wavelength dependent product yield come out from the specific reaction pathways of the S₁ and S₂ states? This would mean that, the relaxation pathway of the S₂ state is distinct from that of the S₁ state and does not involve twisting motion. Does it break Kasha's rule by exhibiting a direct transition from the S₂ state to the ground state? The underlying mechanism needs further in. In this article, we employed the on-the-fly dynamics simulations and static electronic structure calculations to reveal the deactivation mechanism of the neutral form of the PYP chromophore. Our results indicated that the CC twisting motion dominates the S₁ state decay process. In contrast, for the decay process of the S₂ state, an ultrafast transition from the S₂ to the S₁ state through a planar conical intersection is observed, and the excess energy activates a new reaction channel to the ground state characterized by a puckering distortion of the ring. This pathway competes with the photoisomerization channel. No direct transition from S₂ to S₀ is observed, hence Kasha's rule is valid for this process. Our calcualtions can provide a reasonable explanation of the wavelength-dependent isomerization quantum yield of neutral PYP chromophore, and we hope it can provide theoretical foundations for comparing the effect of protonation state on the dynamcal behaviors of PYP chromophore.

Antioxidant flavone analog functionalized fluorescent silica nanoparticles: Synthesis and exploration of their possible use as biomolecule sensor

For the first time, a synthetic fluorescent antioxidant flavone analog was successfully anchored onto the surface of the APTES-modified mesoporous silica nanoparticles (NPs) through sulfonamide linkage. The surface chemistry and morphology of the flavone modified fluorescent silica (FMFS) NPs were studied in detail. The flavone moiety when attached onto the FMFS NP surface, imparted its characteristic fluorescence and antioxidant activities to these NPs. Moreover, the NPs are highly biocompatible as evidenced from their cytotoxicity assay on normal lung cell (L132). The fluorescence activity of these biocompatible NPs was further utilized to study their interaction with a biomolecule, BSA (Bovine Serum Albumin). It was interesting to note that the fluorescence behavior of FMFS NPs completely changed on their binding with BSA. On the other hand, the intrinsic fluorescence activity of BSA was also significantly modified due to its interaction with FMFS NPs. Thus, the sensing and detection of biomolecules like BSA in presence of FMFS NPs can be accomplished by monitoring changes in the fluorescence behavior of either FMFS NPs or BSA. Furthermore, these FMFS NPs retained their intrinsic fluorescence behavior in the cellular medium which opens up their possible use as biocompatible cell imaging agents in future.

Phytolatex synthesized gold nanoparticles as novel agent to enhance sun protection factor of commercial sunscreens

OBJECTIVE

To study the potential of phytolatex (latex of Jatropha gossypifolia) fabricated gold nanoparticles as promising candidate in sunscreen formulations for enhancement in sun protection factor.

METHODS

In this study, plant latex was used as reducing and capping agent to synthesize gold nanoparticles. Latex fabricated gold nanoparticles were characterized by different analytical techniques such as UV-Vis spectroscopy, Fourier transforms infrared spectroscopy, dynamic light scattering, zeta potential, transmission electron microscopy and X-ray diffraction. Potential of sunscreen preparations containing gold nanoparticles to protect skin from UV radiation was investigated by in vitro sun protection factor analysis. Transmission electron microscopy and UV-Vis spectroscopy techniques were used to get insight into mechanism by which AuNPs enhance sun protection factor of sunscreen.

RESULTS

Monodisperse gold nanoparticles were synthesized using plant latex without need of hazardous chemical reducing and capping agents. Gold nanoparticles showed surface plasmon resonance peak at 550 nm in UV-Vis spectroscopic study. Gold nanoparticles were spherical and triangular in shape with size range of 30-50 nm. The zeta potential of gold nanoparticles was found to be -9.39 ± 0.19 mV. XRD analysis confirmed face-centred cubic (fcc) structure of gold nanoparticles. Incorporation of latex synthesized gold nanoparticles (2 and 4 [% w/w]) into commercial sunscreens increased the sun protection factor from 2.43 ± 0.74 to 24.11 ± 0.46% than sunscreen devoid of gold nanoparticles. From UV-Vis absorption spectroscopy and TEM analysis, it was observed that gold nanoparticles enhance the sun protection factor of commercial sunscreens due to reflection and scattering of UV radiation.

CONCLUSION

Phytolatex synthesized gold nanoparticle is novel agent to enhance sun protection factor of commercial sunscreens. Gold nanoparticles aggregation in commercial sunscreen was the main factor behind SPF enhancement. This study showed that gold nanoparticles are potent alternative to traditionally used hazardous titanium dioxide and zinc oxide nanoparticles in sunscreen.

A comprehensive study of isomerization and protonation reactions in the photocycle of the photoactive yellow protein

A comprehensive picture of the overall photocycle was obtained to reveal a wide range of structural signals in the photoactive yellow protein.

Experimental and theoretical study of enol–keto prototropic tautomerism and photophysics of azomethine–BODIPY dyads

Enol ↔ keto prototropic tautomerism can be exploited to modulate the photophysics of BODIPY chromophores based on proton-coupled photoinduced electron transfer processes.

Simulations of Two-dimensional Infrared and Stimulated Resonance Raman Spectra of Photoactive Yellow Protein

We present simulations of one and two-dimensional infrared (2DIR) and stimulated resonance Raman (SRR) spectra of the dark state (pG) and early red-shifted intermediate (pR) of photoactive yellow protein (PYP). Shifts in the amide I and Glu46 COOH stretching bands distinguish between pG and pR in the IR absorption and 2DIR spectra. The one-dimensional SRR spectra are similar to the spontaneous RR spectra. The two-dimensional SRR spectra show large changes in cross peaks involving the C=O stretch of the two species and are more sensitive to the chromophore structure than 2DIR spectra.

Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein

We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.

Ab initio, density functional theory, and semi-empirical calculations

This chapter introduces the theory and applications of commonly used methods of electronic structure calculation, with particular emphasis on methods applicable for modelling biomolecular systems. This chapter is sectioned as follows. We start by presenting ab initio methods, followed by a treatment of density functional theory (DFT) and some recent advances in semi-empirical methods. Treatment of excited states as well as basis sets are also presented.

Mössbauer properties of the diferric cluster and the differential iron(II)-binding affinity of the iron sites in protein R2 of class Ia Escherichia coli ribonucleotide reductase: a DFT/electrostatics study

The R2 subunit of class-Ia ribonucleotide reductase (RNR) from Escherichia coli (E. coli) contains a diiron active site. Starting from the apo-protein and Fe(II) in solution at low Fe(II)/apoR2 ratios, mononuclear Fe(II) binding is observed indicating possible different Fe(II) binding affinities for the two alternative sites. Further, based on their Mössbauer spectroscopy and two-iron-isotope reaction experiments, Bollinger et al. (J. Am. Chem. Soc., 1997, 119, 5976-5977) proposed that the site Fe1, which bonds to Asp84, should be associated with the higher observed (57)Fe Mössbauer quadrupole splitting (2.41 mm s(-1)) and lower isomer shift (0.45 mm s(-1)) in the Fe(III)Fe(III) state, site Fe2, which is further from Tyr122, should have a greater affinity for Fe(II) binding than site Fe1, and Fe(IV) in the intermediate X state should reside at site Fe2. In this paper, using density functional theory (DFT) incorporated with the conductor-like screening (COSMO) solvation model and with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) methodologies, we have demonstrated that the observed large quadrupole splitting for the diferric state R2 does come from site Fe1(III) and it is mainly caused by the binding position of the carboxylate group of the Asp84 sidechain. Further, a series of active site clusters with mononuclear Fe(II) binding at either site Fe1 or Fe2 have been studied, which show that with a single dielectric medium outside the active site quantum region, there is no energetic preference for Fe(II) binding at one site over another. However, when including the explicit extended protein environment in the PB-SCRF model, the reaction field favors the Fe(II) binding at site Fe2 rather than at site Fe1 by ~9 kcal mol(-1). Therefore our calculations support the proposal of the previous Mössbauer spectroscopy and two-iron-isotope reaction experiments by Bollinger et al.

Density functional theory analysis of structure, energetics, and spectroscopy for the Mn-Fe active site of Chlamydia trachomatis ribonucleotide reductase in four oxidation states

Models for the Mn-Fe active site structure of ribonucleotide reductase (RNR) from pathogenic bacteria Chlamydia trachomatis (Ct) in different oxidation states have been studied in this paper, using broken-symmetry density functional theory (DFT) incorporated with the conductor like screening (COSMO) solvation model and also with finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) calculations. The detailed structures for the reduced Mn(II)-Fe(II), the met Mn(III)-Fe(III), the oxidized Mn(IV)-Fe(III) and the superoxidized Mn(IV)-Fe(IV) states are predicted. The calculated properties, including geometries, (57)Fe Mossbauer isomer shifts and quadrupole splittings, and (57)Fe and (55)Mn electron nuclear double resonance (ENDOR) hyperfine coupling constants, are compared with the available experimental data. The Mössbauer and energetic calculations show that the (mu-oxo, mu-hydroxo) models better represent the structure of the Mn(IV)-Fe(III) state than the di-mu-oxo models. The predicted Mn(IV)-Fe(III) distances (2.95 and 2.98 A) in the (mu-oxo, mu-hydroxo) models are in agreement with the extended X-ray absorption fine structure (EXAFS) experimental value of 2.92 A (Younker et al. J. Am. Chem. Soc. 2008, 130, 15022-15027). The effect of the protein and solvent environment on the assignment of the Mn metal position is examined by comparing the relative energies of alternative mono-Mn(II) active site structures. It is proposed that if the Mn(II)-Fe(II) protein is prepared with prior addition of Mn(II) or with Mn(II) richer than Fe(II), Mn is likely positioned at metal site 2, which is further from Phe127.

Chromophore packing leads to hysteresis in GFP

Green fluorescent protein (GFP) possesses a unique folding landscape with a dual basin leading to the hysteretic folding behavior observed in experiment. While theoretical data do not have the resolution necessary to observe details of the chromophore during refolding, experimental results point to the chromophore as the cause of the observed hysteresis. With the use of NMR spectroscopy, which probes at the level of the individual residue, the hysteretic intermediate state is further characterized in the context of the loosely folded isomerized native-like state {N(iso)} predicted in simulation. In the present study, several residues located in the lid of GFP indicate heterogeneity of the native states. Some of these residues show chemical shifts when the native-like intermediate {N(iso)} responsible for GFP's hysteretic folding behavior is trapped. Observed changes in the chromophore are consistent with increased flexibility or isomerization in {N(iso)} as predicted in recent theoretical work. Here, we observed that multiple chromophore environments within the native state are averaged in the trapped intermediate, linking chromophore flexibility to mispacking in the trapped intermediate. The present work is experimental evidence for the proposed final "locking" mechanism in GFP folding forming an incorrectly or loosely packed barrel under intermediate (hysteretic) folding conditions.

Electronic Structure of the PYP Chromophore in Its Native Protein Environment

We report on supermolecular ab initio calculations which clarify the role of the local amino acid environment in determining the unique electronic structure properties of the photoactive yellow protein (PYP) chromophore. The extensive ab initio calculations, at the level of the CC2 and EOM-CCSD methods, allow us to explicitly address how the interactions between the deprotonated p-coumaric thio-methyl ester (pCTM-) chromophore and the surrounding amino acids act together to create a specifically stabilized pCTM- species. Particularly noteworthy is the role of the Arg52 amino acid in stabilizing the chromophore against autoionization, and the role of the Tyr42 and Glu46 amino acids in determining the hydrogen-bonding properties that carry the dominant energetic effects.

Protonation of the chromophore in the photoactive yellow protein

The photoactive yellow protein (PYP) acts as a light sensor to its bacterial host: it responds to light by changing shape. After excitation by blue light, PYP undergoes several transformations, to partially unfold into its signaling state. One of the crucial steps in this photocycle is the protonation of p-coumaric acid after excitation and isomerization of this chromophore. Experimentalists still debate on the nature of the proton donor and on whether it donates the hydrogen directly or indirectly. To obtain better knowledge of the mechanism, we studied this proton transfer using Car-Parrinello molecular dynamics, classical molecular dynamics, and computer simulations combining these two methods (quantum mechanics/molecular mechanics, QMMM). The simulations reproduce the chromophore structure and hydrogen-bond network of the protein measured by X-ray crystallography and NMR. When the chromophore is protonated, it leaves the assumed proton donor, glutamic acid 46, with a negative charge in a hydrophobic environment. We show that the stabilization of this charge is a very important factor in the mechanism of protonation. Protonation frequently occurs in simplified ab initio simulations of the chromophore binding pocket in vacuum, where amino acids can easily hydrogen bond to Glu46. When the complete protein environment is incorporated in a QMMM simulation on the complete protein, no proton transfer is observed within 14 ps. The hydrogen-bond rearrangements in this time span are not sufficient to stabilize the new protonation state. Force field molecular dynamics simulations on a much longer time scale have shown which internal rearrangements of the protein are needed. Combining these simulations with more QMMM calculations enabled us to check the stability of protonation states and clarify the initial requirements for the proton transfer in PYP.

Proton Transfer and Associated Molecular Rearrangements in the Photocycle of Photoactive Yellow Protein: Role of Water Molecular Migration on the Proton Transfer Reaction

The mechanism of the proton transfer and the concomitant molecular structural and hydrogen bond rearrangements after the photoisomerization of the chromophore in the photocycle of photoactive yellow protein are theoretically investigated by using the QM/MM method and molecular dynamics calculations. The free energy surface along this proton-transfer process is determined. This work suggests the important role of the water molecular migration into the moiety of chromophore, which facilitates proton transfer by the hydrogen bond rearrangement and the hydration of the pB' state.

Excited-State Charge Transfer at a Conical Intersection: Effects of an Environment

The influence of a polar and polarizable environment on charge transfer processes at a conical intersection (CI) can be described by a diabatic free energy model yielding coupled surfaces as a function of both molecular coordinates and a solvent coordinate. We extend and apply this model for the S1-S0 CI in protonated Schiff bases, representing a model for retinal isomerization (Faraday Discuss. 2004, 127, 395, 2004). A dielectric continuum description of the solvent is combined with a minimal, two-electron-two-orbital electronic structure model according to Bonacić-Koutecký, Koutecký, and Michl (Angew. Chem. 1987, 26, 170), which characterizes the charge translocation effects at the CI. The model predicts that the nonequilibrium solvent state resulting from the S0-->S1 Franck-Condon transition can entail the disappearance of the CI, such that solvent motion is necessary to reach the CI seam. The concerted evolution of the intramolecular coordinates and the solvent coordinate is illustrated by an excited-state minimum energy path.

N-salicylideneanilines: tautomers for formation of hydrogen-bonded capsules, clefts, and chains

[structure: see text] The synthesis, characterization, and solid-state structures of new salicylaldimines are reported. Bis(N-salicylideneaniline)s (BSANs) and tris(N-salicylideneaniline)s (TSANs) are sterically encumbered compounds featuring a central six-membered ring in the keto-enamine tautomer. When extended with additional functional groups, these molecules may form hydrogen-bonded capsules, clefts, and extended structures. A TSAN with N-(t)()BOC-o-phenylenediamine groups has been structurally investigated. The complementary hydrogen-bonding motif in this molecule leads it to form dimers in solution and in the solid state. A BSAN with N-(t)()BOC-o-phenylenediamine substituents forms a hydrogen-bonded cleft in solution but forms an extended hydrogen-bonded ladder assembly of cofacial dimers in the solid state. When N-(t)()BOC-1,8-naphthalenediamine was utilized to extend the cleft, an unusual perimidine structure was obtained with the central core in the enol tautomer. In addition, ab initio calculations have been used to support the assignment of the keto-enamine or enol-imine tautomers of the BSANs and TSANs and to predict tautomerization in related BSANs and TSANs.

Structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein

We have studied the structural changes induced by optical excitation of the chromophore in wild-type photoactive yellow protein (PYP) in liquid solution with a combined approach of polarization-sensitive ultrafast infrared spectroscopy and density functional theory calculations. We identify the nuC8-C9 marker modes for solution phase PYP in the P and I0 states, from which we derive that the first intermediate state I0 that appears with a 3 ps time constant can be characterized to have a cis geometry. This is the first unequivocal demonstration that the formation of I0 correlates with the conversion from the trans to the cis state. For the P and I0 states we compare the experimentally measured vibrational band patterns and anisotropies with calculations and find that for both trans and cis configurations the planarity of the chromophore has a strong influence. The C7=C8-(C9=O)-S moiety of the chromophore in the dark P state has a trans geometry with the C=O group slightly tilted out-of-plane, in accordance with the earlier reported structure obtained in an X-ray diffraction study of PYP crystals. In the case of I0, experiment and theory are only in agreement when the C7=C8-(C9=O)-S moiety has a planar configuration. We find that the carboxylic side group of Glu46 that is hydrogen-bonded to the chromophore phenolate oxygen does not alter its orientation on going from the electronic ground P state, via the electronic excited P state to the intermediate I0 state, providing conclusive experimental evidence that the primary stages of PYP photoisomerization involve flipping of the enone thioester linkage without significant relocation of the phenolate moiety.

Solvent Effect on the Excited-State Dynamics of Analogues of the Photoactive Yellow Protein Chromophore

We previously reported that two analogues of the Photoactive Yellow Protein chromophore, trans-p-hydroxycinnamic acid (pCA(2-)) and its amide derivative (pCM-) in their deprotonated forms, undergo a trans-cis photoisomerization whereas the thioester derivative, trans-p-hydroxythiophenyl cinnamate (pCT-), does not. pCT- is also the only one to exhibit a short-lived intermediate on its excited-state deactivation pathway. We here further stress the existence of two different relaxation mechanisms for these molecules and examine the reaction coordinates involved. We looked at the effect of the solvent properties (viscosity, polarity, solvation dynamics) on their excited-state relaxation dynamics, probed by ultrafast transient absorption spectroscopy. Sensitivity to the solvent properties is found to be larger for pCT- than for pCA(2-) and pCM-. This difference is considered to reveal that either the relaxation pathway or the reaction coordinate is different for these two classes of analogues. It is also found to be correlated to the electron donor-acceptor character of the molecule. We attribute the excited-state deactivation of analogues bearing a weaker acceptor group, pCA(2-) and pCM-, to a stilbene-like photoisomerization mechanism with the concerted rotation of the ethylenic bond and one adjacent single bond. For pCT-, which contains a stronger acceptor group, we consider a photoisomerization mechanism mainly involving the single torsion of the ethylenic bond. The excited-state deactivation of pCT- would lead to the formation of a ground-state intermediate at the "perp" geometry, which would return to the initial trans conformation without net isomerization.

Primary steps of the photoactive yellow protein: isolated chromophore dynamics and protein directed function

The cycle of the photoactive yellow protein (PYP) has been extensively studied, but the dynamics of the isolated chromophore responsible for transduction is unknown. Here, we present real-time observation of the dynamics of the negatively charged chromophore and detection of intermediates along the path of trans-to-cis isomerization using femtosecond mass selection/electron detachment techniques. The results show that the role of the protein environment is not in the first step of double-bond twisting (barrier crossing) but in directing efficient conversion to the cis-structure and in impeding radical formation within the protein.

Ultrafast Electron Diffraction: Dynamical Structures on Complex Energy Landscapes

In this contribution, we report studies in ultrafast electron diffraction (UED), with the aim of exploring new directions. The main focus is on the determination of complex structures and their dynamics with spatial and temporal resolutions sufficient to give an atomic-scale picture for the evolution in chemical or biological change. We also provide the theoretical framework for UED, and compare the experimental findings of UED to those predicted by density functional and charge density calculations. Selected applications are given in order to highlight phenomena related to concepts such as bifurcation of trajectories in dynamics, far-from-equilibrium coherent structures, and conformational robustness in biological structures. For the former two cases, we consider chemical systems, and, for the latter, we examine proteins of 200 atoms (angiotensin I) or more.

Impact of Sulfur vs Oxygen on the Low-Lying Excited States oftrans-p-Coumaric Acid andtrans-p-Coumaric Thio Acid

The low-lying excited singlet states of trans-p-coumaric acid (CA) and trans-p-coumaric thio acid (CTA) are investigated in view of characterizing the chromophore of the photoactive yellow protein (PYP), with particular regard to the impact of sulfur on the chromophore's electronic structure. The comparative ab initio study, performed with the highly accurate EOM-CCSD method, shows that the electronic state ordering upon vertical excitation and following in-plane geometry relaxation indeed depends in a very sensitive fashion on the presence of either sulfur or oxygen. The study identifies three relevant excited singlet states, two of which are of pi-pi type while the third state is of n-pi character. The study highlights the role of the latter n-pi state which is shown to be the lowest-lying excited state of CTA at all in-plane geometries under consideration, whereas this is not the case for CA.

Dynamical transition and proteinquake in photoactive yellow protein

Conformational dynamics in protein functioning covers a wide range of time scales from nanosecond fluctuations around a conformation to the large-amplitude conformational changes of milliseconds or longer. We illustrate a picture of cooperative coupling among such motions of different time scales in a model protein, photoactive yellow protein, by proposing a model that can consistently explain the experimental results on the photocycle of photoactive yellow protein. The model provides a scenario in which the global collective motion induced by the unfolding of the N-terminal domain promotes the loosening of the atomistic packing around the chromophore, which produces the favorable molecular environment for the photoexcited chromophore, thereby stabilizing the partially unfolded intermediate in the photocycle. The proteinquake, the large conformational change triggered by the local structural disturbance, plays a decisive role in controlling the kinetics of functioning.

Initial events in the photocycle of photoactive yellow protein

The light-induced isomerization of a double bond is the key event that allows the conversion of light energy into a structural change in photoactive proteins for many light-mediated biological processes, such as vision, photosynthesis, photomorphogenesis, and photo movement. Cofactors such as retinals, linear tetrapyrroles, and 4-hydroxy-cinnamic acid have been selected by nature that provide the essential double bond to transduce the light signal into a conformational change and eventually, a physiological response. Here we report the first events after light excitation of the latter chromophore, containing a single ethylene double bond, in a low temperature crystallographic study of the photoactive yellow protein. We measured experimental phases to overcome possible model bias, corrected for minimized radiation damage, and measured absorption spectra of crystals to analyze the photoproducts formed. The data show a mechanism for the light activation of photoactive yellow protein, where the energy to drive the remainder of the conformational changes is stored in a slightly strained but fully cis-chromophore configuration. In addition, our data indicate a role for backbone rearrangements during the very early structural events.

Highly Stable Keto-Enamine Salicylideneanilines

[reaction: see text] Highly stable NH salicylideneanilines have been prepared by reaction of 1,3,5-triformylphloroglucinol with aniline derivatives. The NH form was confirmed by X-ray crystallographic data, as well as by NMR studies. A convenient one-step synthesis of triformylphloroglucinol is also reported.

Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation

Protein photoreceptors use small-molecule cofactors called chromophores to detect light. Only under the influence of the receptors' active sites do these chromophores adopt spectral and photochemical properties that suit the receptors' functional requirements. This protein-induced change in chromophore properties is called photochemical tuning and is a prime example for the general--but poorly understood--process of chemical tuning through which proteins shape the reactivity of their active-site groups. Here we report the 0.82-A resolution X-ray structure of the bacterial light receptor photoactive yellow protein (PYP). The unusually precise structure reveals deviations from expected molecular geometries and anisotropic atomic displacements in the PYP active site. Our analysis of these deviations points directly to the intramolecular forces and active-site dynamics that tune the properties of PYP's chromophore to absorb blue light, suppress fluorescence, and favor the required light-driven double-bond isomerization.