Characterization of photocycle intermediates in crystalline photoactive yellow protein

The photocycle in photoactive yellow protein (PYP) crystals was studied by single-crystal absorption spectroscopy with experimental setups for low-temperature and time-resolved measurements. Thin and flat PYP crystals, suitable for light absorption studies, were obtained using special crystallization conditions. Illumination of PYP crystals at 100 K led to the formation of a photostationary state, which includes at least one hypsochromic and one bathochromic photoproduct that resemble PYP(H) and PYP(B), respectively. The effect of temperature, light color and light pulse duration on the occupancy of these low-temperature photoproducts was determined and appeared similar to that observed in solution. At room temperature a blueshifted photocycle intermediate was identified that corresponds to the blueshifted state of PYP (pB). Kinetic studies show that the decay of this blueshifted intermediate is biphasic at -12 degrees C and 15-fold faster than that observed in solution at room temperature. These altered pB decay kinetics confirm a model that holds that the photocycle in crystals takes place in a shortcut version. In this version the key structural events of the photocycle, such as photoisomerization and reversible protonation of the chromophore, take place, but large conformational changes in the surrounding protein are limited by constraints imposed by the crystal lattice.     

Structural events in the photocycle of green fluorescent protein

Picosecond time-resolved mid-infrared absorption changes of the wild type green fluorescent protein from Aequorea victoria are reported on structural events during the photocycle. Concomitant with rapid H/D transfer following excitation of the neutral A state at 400 nm, a transient signal at 1721/1711 cm(-1) (H/D) developed belonging to protonated glutamate 222, which was definitively assigned using the E222D mutant from the altered proton-transfer kinetics to aspartate in addition to the altered band position and intensity in the spectra. A transient at 1697 cm(-1), assigned to a structural perturbation of glutamine 69, had a H/D kinetic isotope effect of >32, showing the conformational dynamics to be sensitive to the active site H/D vibrations. The kinetic data up to 2 ns after excitation in the 1250-1800 cm(-1) region in D2O provided 10 and 75 ps time constants for the excited-state deuteron transfer and the associated A1* - A1 and A2* - A2 difference spectra and showed the radiative intermediate I state vibrations and the transient accumulation of the long-lived ground-state intermediate I2. Assignments of chromophore modes for the A1, A2, and I2 ground states are proposed on the basis of published model compound studies (Esposito, A. P.; Schellenberg, P.; Parson, W. W.; Reid, P. J. J. Mol. Struct. 2001, 569, 25 and He, X.; Bell, A. F.; Tonge, P. J. J. Phys. Chem. B 2002, 106, 6056). Tentative assignments for the singlet-state intermediates A1*, A2*, and I* are discussed. An unexpected and unassigned band that may be a C=C chromophore vibration was observed in the ground state (1665 cm(-1)) as well as in all photocycle intermediates. Optical dumping of the transient I population was achieved using an additional 532 nm pulse and the directly obtained I2 - I* difference spectrum was highly similar to the I2 - I* photocycle spectrum. The pump-dump-probe spectrum differed from the pump-probe photocycle difference spectrum with respect to the intensity of the phenol 1 mode at 1578 cm(-1), suggesting stronger delocalization of the negative charge onto the phenolic ring of the anionic chromophore in the dumped I2 state. Indication for structural heterogeneity of the chromophore, Glu 222, and the chromophore environment was found in the two parallel proton-transfer reactions and their distinct associated ground- and intermediate-state vibrations. Vibrational spectral markers at 1695 cm(-1) assigned to Gln 69, at 1631 cm(-1) belonging to a C=C mode, and at 1354 cm(-1) belonging to a phenolate vibration further indicated the I2 and I* states to be unrelaxed.     

Protein type effects on steady-state crossflow membrane ultrafiltration fluxes and protein transmission

The permeate fluxes and percent protein transmission were evaluated for steady-state crossflow ultrafiltration of two proteins of different composition: bovine serum albumin (BSA), containing fatty acid, and “fatty-acid-poor” BSA, from which most of the fatty acids had been removed (BSA/FAP). The influences of protein concentration up to 6.5 percent w/v, transmembrane pressure, ionic environment and membrane type (i.e. nominal molecular weight cut-off) were investigated. For both BSA and BSA/FAP, the fluxes and the protein transmission were dependent on the amount of salt present. The higher fatty acid content in the BSA apparently enhanced protein-protein interaction, resulting in a more cohesive and resistant fouling layer; permeate fluxes were lower with BSA/FAP than with BSA at otherwise corresponding operating conditions. A hysteresis behaviour of the flux (J)-transmembrane pressure (TMP) relationship was observed whenever the ultrafiltration unit was operated at a TMP less than some higher value to which the membrane previously had been exposed.     

Ion-exchange across a cationic membrane in concentrated solutions

Summary Equations have been derived, using the quasi-thermodynamic method, relating the diffusion potential, ion and solvent fluxes across a cation exchange membrane with its electrical conductivity and electro-osmotic permeability. A membrane separating two solutions of equal total concentration but containing different cations has been considered and the effect of sorbed anions taken into account. The membrane potential was calculated first and the fluxes of anions and solvent related very closely to this. The cation fluxes were calculated from the membrane potential and the electro-osmotic permeability.The theory has been tested with steady-state flux and potential measurements made using a cation exchange membrane and solutions of sodium and hydrogen chlorides at three temperatures, concentrations and membrane compositions. Excellent agreement was obtained between theory and experiment for the membrane potentials, anion fluxes and solvent fluxes. The cation fluxes were also in good agreement with the theory except when the membrane contained a high proportion of hydrogen ions; then the calculated fluxes were about 30% too small. The suggestion has been made that this may be due to a difference between the electrophoretic and relaxation corrections to the cationic mobilities in conduction and diffusion. These corrections were particularly large with the cations studied.

---

Zusammenfassung Mit einer quasithermodynamischen Methode wurden Gleichungen abgeleitet, die das Diffusionspotential und Ionen- und Lösungsmittelstrom durch eine Kationenaustauschermembran mit deren elektrischer Leitfähigkeit und elektroosmotischer Durchlässigkeit in Zusammenhang setzt. Eine Membran, die zwei Lösungen gleicher Gesamtkonzentration, aber verschiedene Kationen enthaltend, trennt, wird betrachtet und der Einfluß der sorbierten Anionen berücksichtigt. Das Membranpotential wurde zunächst berechnet und dann Anionenstrom und Lösungsmittelstrom in enge Beziehung hierzu gesetzt. Die Kationenströme wurden aus dem Membranpotential und der elektroosmotischen Permeabilität ermittelt.Die Theorie wurde am stationären Fall und durch Potentialmessungen an einer Kationenaustauschermembran geprüft mit Lösungen von Natriumchlorid und Salzzäure bei drei verschiedenen Temperaturen, Konzentrationen und Membranzusammensetzungen. Es ergab sich zwischen Theorie und Experiment ausgezeichnete Übereinstimmung für die Membranpotentiale, die Anionen und Lösungsmittelströme. Die Kationenströme waren ebenfalls in guter Übereinstimmung mit der Theorie, ausgenommen der Fall, daß die Membran einen hohen Anteil an Wasserstoffionen enthielt; dann waren die berechneten Ströme ungefähr 30% zu niedrig. Man kann vermuten, daß dies einer Differenz zwischen elektophoretischen und Relaxationskorrekturen auf die Kationenbeweglichkeiten bei Leitung und Diffusion zuzuschreiben ist. Diese Korrekturen waren für die untersuchten Kationen besonders hoch.

     

Computational characterization of reaction intermediates in the photocycle of the sensory domain of the AppA blue light photoreceptor

The AppA protein with the BLUF (blue light using flavin adenine dinucleotide) domain is a blue light photoreceptor that cycle between dark-adapted and light-induced functional states. We characterized possible reaction intermediates in the photocycle of AppA BLUF. Molecular dynamics (MD), quantum chemical and quantum mechanical-molecular mechanical (QM/MM) calculations were carried out to describe several stable structures of a molecular system modeling the protein. The coordinates of heavy atoms from the crystal structure (PDB code 2IYG) of the protein in the dark state served as starting point for 10 ns MD simulations. Representative MD frames were used in QM(B3LYP/cc-pVDZ)/MM(AMBER) calculations to locate minimum energy configurations of the model system. Vertical electronic excitation energies were estimated for the molecular clusters comprising the quantum subsystems of the QM/MM optimized structures using the SOS-CIS(D) quantum chemistry method. Computational results support the occurrence of photoreaction intermediates that are characterized by spectral absorption bands between those of the dark and light states. They agree with crystal structures of reaction intermediates (PDB code 2IYI) observed in the AppA BLUF domain. Transformations of the Gln63 side chain stimulated by photo-excitation and performed with the assistance of the chromophore and the Met106 side chain are responsible for these intermediates.     

Probing the primary event in the photocycle of photoactive yellow protein using photochemical hole-burning technique

Photochemical hole-burning spectroscopy was used to study the excited-state electronic structure of the 4-hydroxycinnamyl chromophore in photoactive yellow protein (PYP). This system is known to undergo a trans-to-cis isomerization process on a femtosecond-to-picosecond time scale, similar to membrane-bound rhodopsins, and is characterized by a broad featureless absorbance at 446 nm. Resolved vibronic structure was observed for the hole-burned spectra obtained when PYP in phosphate buffer at pH 7 was frozen at low temperature and irradiated with narrow bandwidth laser light at 431 nm. The approximate homogeneous width of 752 cm-1 could be calculated from the deconvolution of the hole-burned spectra leading to an estimated dephasing time of approximately 14 fs for the PYP excited-state structure. The resolved vibronic structure also enabled us to obtain an estimated change in the C=C stretching frequency, from 1663 cm-1 in the ground state to approximately 1429 cm-1 upon photoexcitation. The results obtained allowed us to speculate about the excited-state structure of PYP. We discuss the data for PYP in relation to the excited-state model proposed for the photosynthetic membrane protein bacteriorhodopsin, and use it to explain the primary event in the function of photoactive biological protein systems. Photoexcitation was also carried out at 475 nm. The vibronic structure obtained was quite different both in terms of the frequencies and Franck-Condon envelope. The origin of this spectrum was tentatively assigned.     

Additivity of noise propagation in a protein cascade

Stochastic fluctuations in a protein synthetic cascade are investigated using standard Omega-expansion technique. For the steady-state sensitivity, we show the conditions that result in the ultrasensitive "all-or-none" behavior, and for the noise propagation, we show clearly that (i) for any one given protein species in this cascade, the contributions of fluctuations in upstream proteins to its noise should be additive; and (ii) the output noise levels can vary as a function of the input concentrations and cascade length. Our results provide a possible theoretical explanation for the previous experimental studies.     

CO2 laser-controlled transmission of visible light in N-isopropylacrylamide gel

The transmission of visible laser light through the N-isopropylacrylamide (NIPA) gel has been measured under the influence of an applied co-axial CO₂ infrared laser beam. It is found that the transmission can be controlled by adjusting the infrared laser power. The change of the transmission of the visible light as the infrared laser is turned on and off is completely reversible. The response time required for the change of the transmission is much faster than that required for the change of gel volume. Since the response time is short, the sample cell temperature remains almost constant during the infrared laser on-and-off cycles. The experimental results have been explained in terms of spinodal decomposition theory.     

Anharmonic vibrational calculations modeling the raman spectra of intermediates in the photoactive yellow protein (PYP) photocycle

The role of anharmonic effects in the vibrational spectroscopy of the dark state and two major chromophore intermediates of the photoactive yellow protein (PYP) photocycle is examined via ab initio vibrational self-consistent field (VSCF) calculations and time-resolved resonance Raman spectroscopy. For the first time, anharmonicity is considered explicitly in calculating the vibrational spectra of an ensemble consisting of the PYP chromophore surrounded by model compounds used as mimics of the important active-site residues. Predictions of vibrational frequencies on an ab initio corrected semiempirical potential energy surface show remarkable agreement with experimental frequencies for all three states, thus shedding light on the potential along the reaction path. For example, calculated frequencies for vibrational modes of the red-shifted intermediate, PYPL, exhibit an overall average error of 0.82% from experiment. Upon analysis of anharmonicity patterns in the PYP modes we observe a decrease in anharmonicity in the C8-C9 stretching mode nu29 (trans-cis isomerization marker mode) with the onset of the cis configuration in PYPL. This can be attributed to the loss of the hydrogen-bonding character of the adjacent C9-O2 to the methylamine (Cys69 backbone). For several of the modes, the anharmonicity is mostly due to mode-mode coupling, while for others it is mostly intrinsic. This study shows the importance of the inclusion of anharmonicity in theoretical spectroscopic calculations, and the sensitivity of experiments to anharmonicity. The characterization of protein active-site residues by small molecular mimics provides an acceptable chemical structural representation for biomolecular spectroscopy calculations.     

Model for proton transport coupled to protein conformational change: application to proton pumping in the bacteriorhodopsin photocycle

A modeling method is presented for protein systems in which proton transport is coupled to conformational change, as in proton pumps and in motors driven by the proton-motive force. Previously developed methods for calculating pKa values in proteins using a macroscopic dielectric model are extended beyond the equilibrium case to a master-equation model for the time evolution of the system through states defined by ionization microstate and a discrete set of conformers. The macroscopic dielectric model supplies free energy changes for changes of protonation microstate, while the method for obtaining the energetics of conformational change and the relaxation rates, the other ingredients needed for the master equation, are system dependent. The method is applied to the photoactivated proton pump, bacteriorhodopsin, using conformational free energy differences from experiment and treating relaxation rates through three adjustable parameters. The model is found to pump protons with an efficiency relatively insensitive to parameter choice over a wide range of parameter values, and most of the main features of the known photocycle from very early M to the return to the resting state are reproduced. The boundaries of these parameter ranges are such that short-range proton transfers are faster than longer-range ones, which in turn are faster than conformational changes. No relaxation rates depend on conformation. The results suggest that an "accessibility switch", while not ruled out, is not required and that vectorial proton transport can be achieved through the coupling of the energetics of ionization and conformational states.     

Characteristic features of the crystallization of carbonate precipitates in alkaline solutions

The results of studies of the mechanism of action of sodium polyacrylate on the nucleation and crystal growth for carbonate salts under precipitation-simulating conditions are considered.     

Coalescence in crude oil emulsions investigated by a light transmission method

Using a strong light source and a sensitive detector the light transmission of crude oil emulsions can be measured. A semi-empirical theory describes how the measured optical density results from the interaction of absorption and scattering. Changes in the scattering can be used to investigate the coalescence effects caused by demulsifiers. The method is of use in testing demulsifier effectiveness.     

Folding and self-association of atTic20 in lipid membranes: implications for understanding protein transport across the inner envelope membrane of chloroplasts

Background

We have previously shown that the P. gingivalis HmuY hemophore-like protein binds heme and scavenges heme from host hemoproteins to further deliver it to the cognate heme receptor HmuR. The aim of this study was to characterize structural features of HmuY variants in the presence and absence of heme with respect to roles of tryptophan residues in conformational stability.

Results

HmuY possesses tryptophan residues at positions 51 and 73, which are conserved in HmuY homologs present in a variety of bacteria, and a tryptophan residue at position 161, which has been found only in HmuY identified in P. gingivalis strains. We expressed and purified the wildtype HmuY and its protein variants with single tryptophan residues replaced by alanine or tyrosine residues. All HmuY variants were subjected to thermal denaturation and fluorescence spectroscopy analyses. Replacement of the most buried W161 only moderately affects protein stability. The most profound effect of the lack of a large hydrophobic side chain in respect to thermal stability is observed for W73. Also replacement of the W51 exposed on the surface results in the greatest loss of protein stability and even the large aromatic side chain of a tyrosine residue has little potential to substitute this tryptophan residue. Heme binding leads to different exposure of the tryptophan residue at position 51 to the surface of the protein. Differences in structural stability of HmuY variants suggest the change of the tertiary structure of the protein upon heme binding.

Conclusions

Here we demonstrate differential roles of tryptophan residues in the protein conformational stability. We also propose different conformations of apo- and holoHmuY caused by tertiary changes which allow heme binding to the protein.     

Characteristic features of phase diagrams describing condensation of adsorbate in narrow pores

The phase diagrams describing condensation of adsorbate in micro- and mesoporous adsorbents having slit-shaped and cylindrical pores whose size varied from 1 to 20 monolayers were constructed. The study was performed using the lattice-gas model in the quasichemical approximation to take into account the intermolecular interactions. The phase diagrams for various values of the potential arising from different types of adsorbate--adsorbent interaction were analyzed for adsorption of helium, neon, methane, and carbon tetrachloride in graphite pores. Other adsorption systems are considered and the relationship between the pressure and temperature of adsorbate condensation is discussed. A nonmonotonic variation of the critical densities for pore widths from 3 to 10 molecular diameters was found. The pattern of this variation depends on the ratio of the energy of lateral interactions of the adsorbate molecules to the energy of interaction of the adsorbate molecules with pore walls. The critical temperature decreases monotonically with a decrease in the pore width. The stronger the adsorbate interaction with the pore walls, the greater the decrease in the critical temperature.     

Characteristic features of excess charge localization in stepwise three-electron reduction of Ni-octaethylporphin

We have investigated the electronic structure of Ni-octaethylporphin anions (NiOEP) by¹H NMR. We have established that in (NiOEP)–, the excess electron is localized in the orbital of the nickel, while the second and third extra electrons in (NiOEP)^2- and (NiOEP)^3- are localized in the orbitals of the ligand. We conclude that spin density is transferred between the d orbitals of the Ni and the orbitals of the porphyrin ligand.Institute of Molecular and Atomic Physics, Academy of Sciences of Belarus, 70 Prospekt Frantsiska Skoriny, Minsk 220072, Belarus. Translated from Teoreticheskaya i Éksperimental'naya Khimiya, No. 6, pp. 345–347, November–December, 1996. Original article submitted February 22, 1996.     

Hydration and interfacial water in Nafion membrane probed by transmission infrared spectroscopy

Infrared spectroscopy was applied to probe water inside pores and channels of Nafion membrane exchanged with either proton (H+) or sodium ions (Na+). Transmission measurements were performed on freestanding Nafion 112 (approximately 50 microm thickness) in a cell that enabled adjustment of the relative humidity. Experiments that employed Na+-exchanged Nafion focused on relative humidity environments at or below about 32% generated through the use of humectants. Under these conditions, narrow features in the O-H stretching spectral region near 3650-3720 cm(-1), previously attributed to interfacial water, were detected and matched to bands in vibrational sum frequency (VSF) spectra of water/air, water/organic, and salt-solution/air interfaces. The features correspond to the stretching mode of the "free" OH group of water oriented with one hydrogen atom toward other water molecules and interacting through hydrogen bonding and the other straddling the interface extending into fluorocarbon-rich regions (approximately 3668 cm(-1)) or air-filled segments (approximately 3700 cm(-1)) in the membrane. For membrane exchanged with H+, -SO3- groups were easily shifted to -SO3H as water was removed upon exposure to a few Torr of vacuum at 95 degrees C. In contrast, residual water was retained by membrane exchanged with Na+ after exposure to these conditions for up to 72 h. The permeation of methanol and acetone into Na+-exchanged Nafion 112 was also examined. The C-H and O-H stretching modes of methanol were perturbed in a manner that suggests the polymer disrupts hydrogen bonding interactions within the solvent, similar to the effect it exerts on pure water. For acetone, the C-H stretching modes were not shifted appreciably compared to those of the bulk liquid. However, the carbonyl band was affected, indicating the likely importance of dipolar interactions between solvent molecules and polar groups on the polymer. Control experiments performed with poly(hexafluoropropylene-co-tetrafluoroethylene) (FEP) membrane did not show evidence for water or methanol permeation, which demonstrates the critical role played by the ion-filled channels and pores in facilitating solvent transport within Nafion membrane.     

Structure determination of a membrane protein in proteoliposomes

An NMR method for determining the three-dimensional structures of membrane proteins in proteoliposomes is demonstrated by determining the structure of MerFt, the 60-residue helix-loop-helix integral membrane core of the 81-residue mercury transporter MerF. The method merges elements of oriented sample (OS) solid-state NMR and magic angle spinning (MAS) solid-state NMR techniques to measure orientation restraints relative to a single external axis (the bilayer normal) from individual residues in a uniformly (13)C/(15)N labeled protein in unoriented liquid crystalline phospholipid bilayers. The method relies on the fast (>10(5) Hz) rotational diffusion of membrane proteins in bilayers to average the static chemical shift anisotropy and heteronuclear dipole-dipole coupling powder patterns to axially symmetric powder patterns with reduced frequency spans. The frequency associated with the parallel edge of such motionally averaged powder patterns is exactly the same as that measured from the single line resonance in the spectrum of a stationary sample that is macroscopically aligned parallel to the direction of the applied magnetic field. All data are collected on unoriented samples undergoing MAS. Averaging of the homonuclear (13)C/(13)C dipolar couplings, by MAS of the sample, enables the use of uniformly (13)C/(15)N labeled proteins, which provides enhanced sensitivity through direct (13)C detection as well as the use of multidimensional MAS solid-state NMR methods for resolving and assigning resonances. The unique feature of this method is the measurement of orientation restraints that enable the protein structure and orientation to be determined in unoriented proteoliposomes.