Photoacoustic Calorimetry Studies of O2-Sensing FixL and (R200, I209) Variants from Sinorhizobium meliloti Reveal Conformational Changes Coupled to Ligand Photodissociation from the Heme-PAS Domain.

FixL is an oxygen-sensing heme-PAS protein that regulates nitrogen fixation in the root nodules of plants. In this paper, we present the first photothermal studies of the full-length wild-type FixL protein from Sinorhizobium meliloti and the first thermodynamic profile of a full-length heme-PAS protein. Photoacoustic calorimetry studies reveal a quadriphasic relaxation for SmFixL*WT and the five variant proteins (SmFixL*R200H, SmFixL*R200Q, SmFixL*R200E, SmFixL*R200A, and SmFixL*I209M) with four intermediates from <20 ns to ∼1.5 µs associated with the photodissociation of CO from the heme. The altered thermodynamic profiles of the full-length SmFixL* variant proteins confirm that the conserved heme domain residues R200 and I209 are important for signal transduction. In contrast, the truncated heme domain, SmFixLH128-264, shows only a single, fast monophasic relaxation at <50 ns associated with the fast disruption of a salt bridge and release of CO to the solvent, suggesting that the full-length protein is necessary to observe the conformational changes that propagate the signal from the heme domain to the kinase domain.

Molecular Mechanism of Protein Kinase Recognition and Sorting by the Hsp90 Kinome-Specific Cochaperone Cdc37.

Despite the essential functions of Hsp90, little is known about the mechanism that controls substrate entry into its chaperone cycle. We show that the role of Cdc37 cochaperone reaches beyond that of an adaptor protein and find that it participates in the selective recruitment of only client kinases. Cdc37 recognizes kinase specificity determinants in both clients and nonclients and acts as a general kinase scanning factor. Kinase sorting within the client-to-nonclient continuum relies on the ability of Cdc37 to challenge the conformational stability of clients by locally unfolding them. This metastable conformational state has high affinity for Cdc37 and forms stable complexes through a multidomain cochaperone interface. The interaction with nonclients is not accompanied by conformational changes of the substrate and results in substrate dissociation. Collectively, Cdc37 performs a quality control of protein kinases, where induced conformational instability acts as a "flag" for Hsp90 dependence and stable cochaperone association.

Confinement-guided photophysics in MOFs, COFs, and cages.

In this review, the dependence of the photophysical response of chromophores in the confined environments associated with crystalline scaffolds, such as metal-organic frameworks (MOFs), covalent-organic frameworks (COFs), and molecular cages, has been carefully evaluated. Tunability of the framework aperture, cavity microenvironment, and scaffold topology significantly affects emission profiles, quantum yields, or fluorescence lifetimes of confined chromophores. In addition to the role of the host and its effect on the guest, the methods for integration of a chromophore (e.g., as a framework backbone, capping linker, ligand side group, or guest) are discussed. The overall potential of chromophore-integrated frameworks for a wide-range of applications, including artificial biomimetic systems, white-light emitting diodes, photoresponsive devices, and fluorescent sensors with unparalleled spatial resolution are highlighted throughout the review.

Modulation of Osmium(II) Tris(2,2'-bipyridine) Photophysics through Encapsulation within Zinc(II) Trimesic Acid Metal Organic Frameworks.

The Os(II) tris(2,2'-bipyridine) (OsBpy) complex exhibits optical properties that are particularly attractive for light harvesting systems due to the broad absorption spectrum extending throughout the solar spectrum. However, the relatively short lifetime of the triplet metal to ligand charge transfer state (3MLCT) relative to the related Ru(II)tris(2,2'-bipyridine) (RuBpy) has limited applications. Here, the encapsulation of OsBpy within two distinct Zn(II)-trimesic acid MOFs, HKUST-1(Zn) and USF-2 is demonstrated in an effort to extend the 3MLCT lifetime. Encapsulation results in a hypsochromatic shift of the steady-state emission band in both frameworks resulting from a destabilization of the 3MLCT. The encapsulated OsBpy also exhibits extended emission lifetimes in both HKUST-1(Zn) (104 ns in MOF vs 50 ns in methanol) and USF-2 (81 ns in MOF vs 50 ns in methanol) arising from changes in the nonradiative decay constants in both systems. The data are also consistent with vibronic perturbations involved in mixing between higher energy 3MLCT* and ligand field states.

Time resolved calorimetry of photo-induced folding in horse heart cytochrome c at high pH.

Here the molar volume and enthalpy changes associated with the early events in the folding of ferrocytochrome c (Cc) at high pH have been examined using time resolved photoacoustic calorimetry (PAC). The data reveal an overall volume change of 1.3 ± 0.3 mL mol-1 and an enthalpy change of 13 ± 7 kcal mol -1 occurring subsequent to photodissociation of the unfolded CO bound Cc species in <∼20 ns. Two additional kinetic phases are observed that are associated with non-native His binding (ΔH and ΔV of 2 ± 4 kcal mol-1 and -0.5 mL mol-1, τ âˆ¼ 2.5 µs ) and Met binding (ΔH and ΔV -0.4 ± 2 kcal mol-1 and -0.1 ± 0.1 mL mol-1, τ∼ 660 ns). Considering only protein conformational changes (excluding volume and enthalpies associated with heme ligation events) the initial conformational event exhibits a ΔH and ΔV of 6 ± 3 kcal mol-1 and -3±0.1 mL mol-1, respectively, that are attributed to a small contraction of the unfolded protein. The corresponding enthalpy associated with both native and non-native ligand binding are found to be -5±4 kcal mol-1 (Fe-Met) and +20 ± 4 kcal mol-1 (Fe-His) with the change in volume for both phases being essential negligible. This would indicate that non-native ligand binding likely occurs from an already collapsed conformation.

Synthesis, characterization, and cellular localization of a fluorescent probe of the antimalarial 8-aminoquinoline primaquine.

Primaquine (PQ) is the only commercially available drug that clears dormant liver stages of malaria and blocks transmission to mosquito vectors. Although an old drug, much remains to be known about the mechanism(s) of action. Herein we develop a fluorescent tagged PQ to discover cellular localization in the human malaria parasite, Plasmodium falciparum. Successful synthesis and characterization of a primaquine-coumarin fluorescent probe (PQCP) demonstrated potency equivalent to the parent drug and the probe was not cytotoxic to HepG2 carcinoma cells. Cellular localization was found primarily in the cytosol of the asexual erythrocytic and gametocyte stages of parasite development.

Photoacoustic calorimetry studies of CO photo-dissociation from chloramine-T modified horse heart cytochrome-c.

Treatment of horse heart Cytochrome-c (Cc) with N-chloro-4-toluosulfonamide (Chloramine-t, CT) results in the oxidation of methionine (Met) residues to the corresponding sulfoxide including the distal heme ligand, Met80. The resulting Fe-sulfoxide coordination is sufficiently labile in the ferrous form to be displaced by gaseous ligands, including CO. Photolysis of the CO-CT-Cc complex provides an opportunity to examine ligand binding dynamics that are associated with a relatively rigid distal heme pocket. In this work, photoacoustic calorimetry (PAC) was utilized to obtain the kinetics as well as enthalpy and molar volume changes subsequent to CO photo-dissociation from CO-CT-Cc. Previous photolysis studies of CO-CT-Cc have led to a proposed model for ligand recombination in which the Met80-sulfoxide and CO recombine with the heme on relatively slow timescales (50 µs and ∼500 µs, respectively). The PAC data presented here reveals two additional kinetic phases with lifetimes of <20 ns and 534 ± 75 ns. The fast phase (<20 ns) is associated with an ΔH of 44 ± 5 kcal mol-1 and ΔV of -0.5 ± 0.5 mL mol-1, whereas the slower phase (534 ns) is associated with a small ΔH of 2 ± 3 kcal mol-1 and ΔV of 1 ± 0.5 mL mol-1.

Sulfono-γ-AApeptides as a new class of nonnatural helical foldamer.

Foldamers offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein we report a new class of nonnatural helical sulfono-γ-AApeptide foldamers of varying lengths. The crystal structure of the sulfono-γ-AApeptide monomer S6 illustrates the intrinsic folding propensity of sulfono-γ-AApeptides, which likely originates from the bulkiness of tertiary sulfonamide moiety. The two-dimensional solution NMR spectroscopy data for the longest sequence S1 demonstrates a 10/16 right-handed helical structure. Optical analysis using circular dichroism further supports well- defined helical conformation of sulfono-γ-AApeptides in solution containing as few as five building blocks. Future development of sulfono-γ-AApeptides may lead to new foldamers with discrete functions, enabling expanded application in chemical biology and biomedical sciences.

Ruthenium(II) tris(2,2'-bipyridine)-templated zinc(II) 1,3,5-tris(4-carboxyphenyl)benzene metal organic frameworks: structural characterization and photophysical properties.

The ability to confine photoactive catalysts within metal organic framework (MOF) materials affords the opportunity to expand the functional diversity of these materials into solar-based applications. Here, two new Ru(II) tris(2,2'-bipyridine) (RuBpy)-based photoactive materials derived from reactions between Zn(II) ions and 1,3,5-tris(4-carboxyphenyl)benzene and templated by the presence of RuBpy (RWLC-1 and RWLC-2) are described with regard to structure and RuBpy photophysics. RuBpy cations have been successfully encapsulated within the cavities (RWLC-1) and channels (RWLC-2) of the new negatively charged frameworks, both of which are synthesized simultaneously in a single reaction vial. Single-crystal X-ray diffraction studies allowed for determination of the RuBpy position within crystal voids. RuBpy encapsulated in each of the two new MOFs exhibits biphasic triplet metal to ligand charge transfer ((3)MLCT) emission decay lifetimes (τRWLC-1-fast = 237 ns, τRWLC-1-slow = 1.60 µs, τRWLC-2-fast = 171 ns, and τRWLC-2-slow = 797 ns at 25 °C) consistent with two populations of RuBpy complexes, one being encapsulated in highly space-restricted cavities giving rise to a longer (3)MLCT lifetime, while the second is encapsulation within a larger nonperiodic pore or defect with a coencapsulated quencher giving rise to short emission lifetimes. Taken together, these results represent examples of the templating ability of RuBpy to produce novel materials with distinct photophysical environments of the encapsulated guests.

Spectroscopic investigation of the noncovalent association of the nerve agent simulant diisopropyl methylphosphonate (DIMP) with zinc(II) porphyrins.

Organophosphonates pose a significant threat as chemical warfare agents, as well as environmental toxins in the form of pesticides. Thus, methodologies to sense and decontaminate these agents are of significant interest. Porphyrins and metalloporphyrins offer an excellent platform to develop chemical threat sensors and photochemical degradation systems. These highly conjugated planar molecules exhibit relatively long-lived singlet and triplet states with high quantum yields and also form self-associated complexes with a wide variety of molecules. A significant aspect of porphyrins is the ability to functionalize the peripheral ring system either directly to the pyrrole rings or to the bridging methine carbons. In this report, steady-state absorption and fluorescence are utilized to probe binding affinities of a series of symmetric and asymmetric zinc(II) metalloporphyrins for the nerve agent simulant diisopropyl methylphosphonate (DIMP) in hexane. The red shifts in the absorption and emission spectra observed for all of the metalloporphyrins probed are discussed in the frame of Gouterman's four orbital model and a common binding motif involving coordination between the metalloporphyrin and DIMP via interaction between the zinc metal center of the porphyrin and phosphoryl oxygen of DIMP (Zn-O═P) is proposed.

Time resolved thermodynamics associated with ligand photorelease in heme peroxidases and globins: Open access channels versus gated ligand release.

Heme proteins represent a diverse class of biomolecules responsible for an extremely diverse array of physiological functions including electron transport, monooxygenation, ligand transport and storage, cellular signaling, respiration, etc. An intriguing aspect of these proteins is that such functional diversity is accomplished using a single type of heme macrocycle based upon iron protoporphyrin IX. The functional diversity originates from a delicate balance of inter-molecular interactions within the protein matrix together with well choreographed dynamics that modulate the heme electronic structure as well as ligand entry/exit pathways from the bulk solvent to the active site. Of particular interest are the dynamics and energetics associated with the entry/exit of ligands as this process plays a significant role in regulating the rates of heme protein activity. Time-resolved photoacoustic calorimetry (PAC) has emerged as a powerful tool through which to probe the underlying energetics associated with small molecule dissociation and release to the bulk solvent in heme proteins on time scales from tens of nanoseconds to several microseconds. In this review, the results of PAC studies on various classes of heme proteins are summarized highlighting how different protein structures affect the thermodynamics of ligand migration. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.

How can proteins enter the interior of a MOF? Investigation of cytochrome c translocation into a MOF consisting of mesoporous cages with microporous windows.

It has been demonstrated for the first time that the heme protein cytochrome c (Cyt c) can enter the interior of a MOF despite the larger molecular dimension of the protein relative to the access pore sizes. Mechanistic studies suggest that the Cyt c molecules must undergo a significant conformational change during translocation into the MOF interior through the relatively small nanopores.

Understanding ion sensing in Zn(II) porphyrins: spectroscopic and computational studies of nitrite/nitrate binding.

The development of effective sensor elements relies on the ability of a chromophore to bind an analyte selectively and then study the binding through changes in spectroscopic signals. In this report the ability of Zn(II) Tetraphenyl Porphyrin (ZnTPP) to selectively bind nitrite over nitrate ions is examined. The results of Benesi-Hildebrand analysis reveals that ZnTPP binds NO(2)(-) and NO(3)(-) ions with association constants of 739 ± 70 M(-1) and 134 ± 15 M(-1), respectively. Interestingly, addition of a pyridine ligand to the fifth coordination site of the Zn(II) center enhances ion binding with the association constants increasing to 71,300 ± 8,000 M(-1) and 18,900 ± 3,000 M(-1) for nitrite and nitrate, respectively. Density functional theory calculations suggest a binding mechanism through which Zn(II)-porphyrin interactions are disrupted by ligand and base coordination to Zn(II), with Zn(II) having more favorable overlap with nitrite orbitals, which are less delocalized than nitrate orbitals. Overall, these provide new insights into the ability to tune the affinity and selectivity of porphyrin based sensors utilizing electronic factors associated with the central Zn(II) ion.

Fluorescent properties and resonance energy transfer of 3,4-bis(2,4-difluorophenyl)-maleimide.

A fluorescent compound 3,4-bis(2,4-difluorophenyl)-maleimide from the 3,4-diaryl-substituted maleimides was synthesized and determined to have a Stokes shift of 140 nm (λ(abs) 341 nm, λ(em) 481 nm), a high fluorescent quantum yield (Φ(fl) 0.61) and an extinction coefficient ε((340)) of 48 400 M(-1) cm(-1) in dichloromethane. For the first time we demonstrated the successful implementation of a 3,4-diaryl-substituted maleimide molecule as a donor component in FRET experiments.

Photophysical studies of Ru(II)tris(2,2'-bipyridine) confined within a Zn(II)-trimesic acid polyhedral metal-organic framework.

The ability to confine photoactive catalysts within metal-organic framework (MOF) materials affords the opportunity to expand the functional diversity of these materials into solar based applications. Here, the confinement of Ru(II)tris(2,2'-bipyridine) (RuBpy) by a MOF material derived from Zn(II) ions and trimesic acid (hereafter, USF2) is examined. Although the encapsulated RuBpy could not be crystallographically resolved within the MOF framework, the photophysical properties of the complex are characteristic of confinement including extended triplet metal-to-ligand ((3)MLCT) lifetime (τethanol = 614 ns and τUSF2 = 1.2 µs at 25 °C) and a slight hypsochromic shift in the steady-state emission spectrum relative to RuBpy in ethanol. The extended lifetime is attributed to a deactivation of a nonradiative (3)dd that is antibonding with respect to the Ru(II)-bipyridine due to a confined molecular environment. These results represent one of the first examples of RuBpy encapsulation and photophysical characterization within a polyhedral MOF material.

Photophysical comparison of Zn(II) phthalocyanaine tetrasulfonate and Zn(II) tetrakis(4-sulfonatophenyl)porphyrin encapsulated within the Zn-polyhedral metal organic framework, HKUST-1(Zn).

Porphyrins and phthalocyanines are ideal candidates for the development of photoactive porous metal organic frameworks (MOFs) due to their broad absorption spectra in the visible and near UV regions, high molar extinction coefficients and long triplet state lifetimes. An important factor in the development of porphyrin/phthalocyanine based MOFs is the extent to which the pore modulates the photophysical properties of the guest. Here, two structurally related guests, Zn(II)tetra(4-sulfonatophenyl)porphyrin (Zn4SP) and Zn(II)phthalocyanine tetrasulfonate (ZnPcS4) have been encapsulated within the pores of the MOF HKUST-1(Zn). Both the ZnPcS4@HKUST-1(Zn) and Zn4SP@HKUST-1(Zn) display bathochromic shifts in the Soret absorption band and steady state emission spectra as well as biphasic emissions lifetimes, relative to the chromophores in solution. These results are consistent with the pore modulating the excited state conformations of both chromophores. Interestingly, rotational control of the phenyl groups associated with Zn4SP@HKUST-1(Zn) appears to have a moderate impact on the photophysics.

Mimicking heme enzymes in the solid state: metal-organic materials with selectively encapsulated heme.

To carry out essential life processes, nature has had to evolve heme enzymes capable of synthesizing and manipulating complex molecules. These proteins perform a plethora of chemical reactions utilizing a single iron porphyrin active site embedded within an evolutionarily designed protein pocket. We herein report the first class of metal-organic materials (MOMs) that mimic heme enzymes in terms of both structure and reactivity. The MOMzyme-1 class is based upon a prototypal MOM, HKUST-1, into which catalytically active metalloporphyrins are selectively encapsulated in a "ship-in-a-bottle" fashion within one of the three nanoscale cages that exist in HKUST-1. MOMs offer unparalleled levels of permanent porosity and their modular nature affords enormous diversity of structures and properties. The MOMzyme-1 class could therefore represent a new paradigm for heme biomimetic catalysis since it combines the activity of a homogeneous catalyst with the stability and recyclability of heterogeneous catalytic systems within a single material.

Ground- and excited-state properties of Zn(II) tetrakis(4-tetramethylpyridyl) pophyrin specifically encapsulated within a Zn(II) HKUST metal-organic framework.

We have examined the photophysical properties of Zn(II) tetramethylpyridyl porphyrin (ZnT4MPyP) specifically encapsulated within the cubioctahedral cavities of a ZnHKUST metal- organic framework. The encapsulated ZnT4MPyP exhibits a Soret maxima at ∼458 nm that is bathochromically shifted relative to ZnT4PyP in ethanol solution (Soret maxima centered at 440 nm). The corresponding emission spectra of the encapsulated porphyrin exhibit resolvable bands centered at 636 and 677 nm relative to a single broad emission band of the ZnT4MPyP in ethanol solution centered at 636 nm with a shoulder situated near ∼660 nm. The fluorescence lifetime of the encapsulated porphyrin is also perturbed relative to that of the free porphyrin in solution (1.88 ns for the encapsulated porphyrin relative to 1.2 ns in solution). These results are consistent with the ZnT4MPyP being in a more constrained environment in which the peripheral pyridyl groups have restricted rotational motion. The ZnT4MPyP triplet lifetime is also affected by encapsulation, giving rise to a longer lifetime (τ ≈ 3.3 ms) relative to that for the free porphyrin in solution (τ ≈ 1 ms). The triplet-state results indicate that nonplanar vibrational modes of the porphyrin leading to intersystem crossing are retained by encapsulation of the porphyrin but that either the density of vibrational states or the specific nonplanar modes coupling the singlet and triplet states may be perturbed, resulting in the longer observed lifetime.

Photothermal studies of CO photodissociation from peroxidases from horseradish and soybean.

In this work, the results of photoacoustic calorimetry (PAC) studies involving CO photodissociation from horseradish peroxidase (HRP) and soybean peroxidase (SBP) are discussed. Both proteins contain Fe-protoporphyrin IX active sites and relatively open distal heme pockets (i.e., direct solvent access). In addition, it has been shown previously that SBP binds a Tris molecule in the distal pocket near the heme group potentially regulating ligand binding to the heme iron. Results of PAC studies indicate a fast (< approximately 50 ns) relaxation for both HRP and SBP subsequent to CO photolysis in both phosphate and Tris buffers and with varying concentrations of Tris. However, the molar volume/enthalpy changes associated with CO release are distinct between the two proteins. In the case of HRP, CO photolysis results in an enthalpy change of approximately 2 kcal mol(-1) and volume change of approximately -12 mL mol(-1) attributed to solvation/structural changes regardless of buffer conditions. In contrast, SBP exhibits buffer and ionic strength dependent enthalpy changes ranging from approximately -23 kcal mol(-1) in 50 mM phosphate buffer to approximately 6 kcal mol(-1) in Tris buffer with volume changes similar to those observed in HRP. The results are consistent with a model in which photodissociation of CO from ferrous HRP or SBP leads to CO migration from the distal heme pocket to the bulk solvent with a corresponding input of a water molecule all occurring in < approximately 50 ns. The differences in enthalpies are attributed to variations in hydrogen bond formation between the incoming water molecule(s) and the protein matrix in both HRP and SBP.

Framework induced deformation modulates the photophysical properties of ZnTetra(4-pyridyl)porphyrin incorporated within a new metal organic framework, RWLAA-1.

Porphyrin based metal organic frameworks (MOFs) have provided a broad platform through which a wide variety of light harvesting applications have been developed. Of particular interest within light harvesting MOFs containing porphyrin chromophores is the extent to which the both environment of the porphyrin and the porphyrin conformation modulate the photophysical properties. With this in mind, a new MOF (RWLAA-1) has been synthesized based on zinc cations linked by zinc(ii) tetra(4-pyridyl)porphyrin (ZnTPyP) and benzene tricarboxylate (H3BTC) linkers in which the porphyrin exhibits significant conformational distortions that have a profound effect on the photophysics of the material including bathochromic shifts in both the optical (Soret and visible bands) and emission bands, reduction in the energy separation between the Q(0,0) and Q(0,1) emission bands and shorter singlet and triplet state lifetimes. These effects are consistent with the porphyrin deformation resulting in changes in the porphyrin electronic structure and excited state conformational dynamics that alter the vibronic coupling between the excited states (S1 and T1) and the S0 ground state.