Biomedical subjects

Michael Wulff

Publications and source records attributed to Michael Wulff.

15 recordsLinked to original sources

PubMed2006

Structure of the photodissociation products of CCl4, CBr4, and CI4 in solution studied by DFT and ab initio calculations.

Various molecular species that can be populated during the photoreaction of carbon tetrahalides CX(4) (X = Cl, Br, I) in the gas phase and in solution have been studied by ab initio and density functional theory (DFT) calculations. Geometries, energies, and vibrational frequencies of CX(4), CX(3), CX(2), C(2)X(6), C(2)X(5), C(2)X(4), X(2), and the isomer X(2)CX-X were calculated and transition states connecting these species were characterized. Spin-orbit DFT (SODFT) computations were also performed to include the relativistic effects, which cannot be neglected for Br and I atoms. The calculated potential energy surfaces satisfactorily describe the reactions of the photoexcited CX(4) molecules. In the gas phase, the initial C-X bond rupture in CX(4) is followed by secondary C-X breakage in the CX(3) radical, leading to CX(2) and 2X, and the formation of C(2)X(6) or C(2)X(4) through bimolecular recombination of the CX(3) or CX(2) radicals is favored thermodynamically. In solution, by contrast, the X(2)CX-X isomer is formed via X-X binding, and two CX(3) radicals recombine nongeminately to form C(2)X(6), which then dissociates into C(2)X(4) and X(2) through C(2)X(5). The Raman intensities and the vibrational frequencies, as well as the absorption spectra and oscillator strengths of the Br(2)CBr-Br isomer in the gas phase and in various solvents were computed and the calculated absorption and Raman spectra of the Br(2)CBr-Br isomer in various solutions are in good agreement with the experimental data. The natural population analysis indicates that the Br(2)CBr-Br isomer corresponds to the recently reported solvent-stabilized solvated ion pair (CBr(3)(+)//Br(-))(solv) in the highly polar alcohol solvent. The singlet-triplet energy separations of the CX(2) radicals in the gas phase and in solution were evaluated with high level computational methods, and the optimized geometric parameters are in good agreement with the experimental results. The geometric and energetic differences between the singlet and triplet states were explained by the electronic properties of the CX(2) radicals. C(2)X(4), C(2)X(5), and C(2)X(6) (X = Br, I) in the gas phase and in solution were optimized at different computational levels, and the optimized geometric parameters of C(2)I(4) are in very good agreement with the experimental data.

Journal Article↗

PubMed2006

Spatiotemporal reaction kinetics of an ultrafast photoreaction pathway visualized by time-resolved liquid x-ray diffraction.

We have studied the reaction dynamics for HgI(2) in methanol by using time-resolved x-ray diffraction (TRXD). Although numerous time-resolved spectroscopic studies have provided ample information about the early dynamics of HgI(2), a comprehensive reaction mechanism in the solution phase spanning from picoseconds up to microseconds has been lacking. Here we show that TRXD can provide this information directly and quantitatively. Picosecond optical pulses triggered the dissociation of HgI(2), and 100-ps-long x-ray pulses from a synchrotron probed the evolving structures over a wide temporal range. To theoretically explain the diffracted intensities, the structural signal from the solute, the local structure around the solute, and the hydrodynamics of bulk solvents were considered in the analysis. The results in this work demonstrate that the determination of transient states in solution is strongly correlated with solvent energetics, and TRXD can be used as an ultrafast calorimeter. It also is shown that a manifold of structural channels can be resolved at the same time if the measurements are accurate enough and that global analysis is applied. The rate coefficients for the reactions were obtained by fitting our model against the experimental data in one global fit including all q-values and time delays. The comparison between all putative reaction channels confirms that two-body dissociation is the dominant dissociation pathway. After this primary bond breakage, two parallel channels proceed. Transient HgI associates nongeminately with an iodine atom to form HgI(2), and I(2) is formed by nongeminate association of two iodine atoms.

Journal Article↗

PubMed2005

Photodissociation reaction of 1,2-diiodoethane in solution: a theoretical and X-ray diffraction study.

Various molecular species are known to form during the photoreaction of C2H4I2 in the gas phase and in solution. We have studied all species involved in this reaction by ab initio and density functional theory (DFT) calculations: Geometries, energies, and vibrational frequencies of C2H4I2, bridged C2H4I*, anti C2H4I*, C4H4, I2, I3-, and the isomer C2H4I-I were calculated. The absorption peaks and oscillator strengths of selected species along the potential energy surface (PES) were calculated using time-dependent DFT and were compared with available experimental results. The calculated PES satisfactorily describes the observed reactions of the photoexcited C2H4I2 molecule. In the gas phase, there is only one reaction pathway: the first C-I bond ruptures followed by a secondary C-I breakage in the haloethyl radical C2H4I*. In solution, by contrast, another reaction channel, which is energetically more favored over the secondary dissociation, is switched on due to a solvation effect: the bridged C2H4I* can bind to the free iodine atom to form a C2H4I-I isomer without any energy barrier. The isomer can then break into C2H4 and I2. The rotational barriers in the gas phase and in solution were also calculated and compared. To provide experimental data on the structure of C2H4I2 in solution, the ground state structure of C2H4I2 in methanol was determined from static X-ray diffraction data using 88 keV (lambda = 0.14 A) X-rays. The structural parameters are compared with those from the theoretical results.

Computer Simulation↗

PubMed2005

Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.

Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use time-resolved Laue crystallography to extract short-lived intermediate structures and thereby unveil signal transduction in the blue light photoreceptor photoactive yellow protein (PYP) from Halorhodospira halophila. By analyzing a comprehensive set of Laue data during the PYP photocycle (forty-seven time points from one nanosecond to one second), we track all atoms in PYP during its photocycle and directly observe how absorption of a blue light photon by its p-coumaric acid chromophore triggers a reversible photocycle. We identify a complex chemical mechanism characterized by five distinct structural intermediates. Structural changes at the chromophore in the early, red-shifted intermediates are transduced to the exterior of the protein in the late, blue-shifted intermediates through an initial "volume-conserving" isomerization of the chromophore and the progressive disruption of hydrogen bonds between the chromophore and its surrounding binding pocket. These results yield a comprehensive view of the PYP photocycle when seen in the light of previous biophysical studies on the system.

Bacterial Proteins↗

PubMed2004

Visualizing chemical reactions in solution by picosecond x-ray diffraction.

We present a time-resolved x-ray diffraction study to monitor the recombination of laser-dissociated iodine molecules dissolved in CCl4. The change in structure of iodine is followed during the whole recombination process. The deexcitation of solute molecules produces a heating of the solvent and induces tiny changes in its structure. The variations in the distance between pairs of chlorine atoms in adjacent CCl4 molecules are probed on the mA length scale. However, the most striking outcome of the present work is the experimental determination of temporally varying atom-atom pair distribution functions. Variations of the mean density of the solution during thermal expansion are also followed in real time. One concludes that not only time-resolved optical spectroscopy but also time-resolved x-ray diffraction can be used to monitor atomic motions in liquids.

Carbon Tetrachloride↗

PubMed2004

Picosecond time-resolved X-ray crystallography: probing protein function in real time.

A detailed mechanistic understanding of how a protein functions requires knowledge not only of its static structure, but also how its conformation evolves as it executes its function. The recent development of picosecond time-resolved X-ray crystallography has allowed us to visualize in real time and with atomic detail the conformational evolution of a protein. Here, we report the photolysis-induced structural evolution of wild-type and L29F myoglobin over times ranging from 100 ps to 3 micros. The sub-ns structural rearrangements that accompany ligand dissociation in wild-type and the mutant form differ dramatically, and lead to vastly different ligand migration dynamics. The correlated protein displacements provide a structural explanation for the kinetic differences. Our observation of functionally important protein motion on the sub-ns time scale was made possible by the 150-ps time resolution of the measurement, and demonstrates that picosecond dynamics are relevant to protein function. To visualize subtle structural changes without modeling, we developed a novel method for rendering time-resolved electron density that depicts motion as a color gradient across the atom or group of atoms that move. A sequence of these time-resolved images have been stitched together into a movie, which allows one to literally "watch" the protein as it executes its function.

Amino Acid Substitution↗

PubMed2004

Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein.

We use time-resolved crystallography to observe the structural progression of a bacterial blue light photoreceptor throughout its photocycle. Data were collected from 10 ns to 100 ms after photoactivation of the E46Q mutant of photoactive yellow protein. Refinement of transient chromophore conformations shows that the spectroscopically distinct intermediates are formed via progressive disruption of the hydrogen bond network to the chromophore. Although structural change occurs within a few nanoseconds on and around the chromophore, it takes milliseconds for a distinct pattern of tertiary structural change to fully progress through the entire molecule, thus generating the putative signaling state. Remarkably, the coupling between the chromophore conformation and the tertiary structure of this small protein is not tight: there are leads and lags between changes in the conformation of the chromophore and the protein tertiary structure.

Bacterial Proteins↗

PubMed2003

Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography.

Although conformational changes are essential for the function of proteins, little is known about their structural dynamics at atomic level resolution. Myoglobin (Mb) is the paradigm to investigate conformational dynamics because it is a simple globular heme protein displaying a photosensitivity of the iron-ligand bond. Upon laser photodissociation of carboxymyoglobin Mb a nonequilibrium population of protein structures is generated that relaxes over a broad time range extending from picoseconds to milliseconds. This process is associated with migration of the ligand to cavities in the matrix and with a reduction in the geminate rebinding rate by several orders of magnitude. Here we report nanosecond time-resolved Laue diffraction data to 1.55-A resolution on a Mb mutant, which depicts the sequence of structural events associated with this extended relaxation. Motions of the distal E-helix, including the mutated residue Gln-64(E7), and of the CD-turn are found to lag significantly (100-300 ns) behind local rearrangements around the heme such as heme tilting, iron motion out of the heme plane, and swinging of the mutated residue Tyr-29(B10), all of which occur promptly (< or =3 ns). Over the same delayed time range, CO is observed to migrate from a cavity distal to the heme known to bind xenon (called Xe4) to another such cavity proximal to the heme (Xe1). We propose that the extended relaxation of the globin moiety reflects reequilibration among conformational substates known to play an essential role in controlling protein function.

Amino Acid Substitution↗

PubMed2003

The performance of a cryogenically cooled monochromator for an in-vacuum undulator beamline.

The channel-cut silicon monochromator on beamline ID09 at the European Synchrotron Radiation Facility is indirectly cooled from the sides by liquid nitrogen. The thermal slope error of the diffracting surface is calculated by finite-element analysis and the results are compared with experiments. The slope error is studied as a function of cooling coefficients, beam size, position of the footprint and power distribution. It is found that the slope error versus power curve can be divided into three regions: (i). The linear region: the thermal slope error is linearly proportional to the power. (ii). The transition region: the temperature of the Si crystal is close to 125 K; the thermal slope error is below the straight line extrapolated from the linear curve described above. (iii). The non-linear region: the temperature of the Si crystal is higher than 125 K and the thermal slope error increases much faster than the power. Heat-load tests were also performed and the measured rocking-curve widths are compared with those calculated by finite-element modeling. When the broadening from the intrinsic rocking-curve width and mounting strain are included, the calculated rocking-curve width versus heat load is in excellent agreement with experiment.

Journal Article↗

PubMed2003

Watching a protein as it functions with 150-ps time-resolved x-ray crystallography.

We report picosecond time-resolved x-ray diffraction from the myoglobin (Mb) mutant in which Leu29 is replaced by Phe (L29Fmutant). The frame-by-frame structural evolution, resolved to 1.8 angstroms, allows one to literally "watch" the protein as it executes its function. Time-resolved mid-infrared spectroscopy of flash-photolyzed L29F MbCO revealed a short-lived CO intermediate whose 140-ps lifetime is shorter than that found in wild-type protein by a factor of 1000. The electron density maps of the protein unveil transient conformational changes far more dramatic than the structural differences between the carboxy and deoxy states and depict the correlated side-chain motion responsible for rapidly sweeping CO away from its primary docking site.

Amino Acid Substitution↗

PubMed2003

Laser-induced ferroelectric structural order in an organic charge-transfer crystal.

We report the direct observation by x-ray diffraction of a photoinduced paraelectric-to-ferroelectric structural phase transition using monochromatic 100-picosecond synchrotron pulses. It occurs in tetrathiafulvalene-p-chloranil, a charge-transfer molecular material in which electronic and structural changes are strongly coupled. An optical 300-femtosecond laser pulse switches the material from a neutral to an ionic state on a 500-picosecond time scale and, by virtue of intrinsic cooperativity, generates self-organized long-range structural order. The x-ray data indicate a macroscopic ferroelectric reorganization after the laser irradiation. Refinement of the structures before and after laser irradiation indicates structural changes at the molecular level.

Journal Article↗

PubMed2003

Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase.

The enzyme hydroxymethylbilane synthase (HMBS, EC 4.3.1.8), 313 amino acid residues and MW 34 kDa, also known as porphobilinogen deaminase (PBGD), catalyses the stepwise polymerization of four molecules of porphobilinogen (PBG) to the linear tetrapyrrole 1-hydroxymethylbilane. Several crystallographic structures of HMBS have been previously determined, most recently including by time-resolved Laue protein crystallography of the Lys59Gln mutant form with reaction initiation undertaken by use of a flow cell carrying the substrate PBG. In this paper we review these structures and add new molecular graphics representations and analyses. Moreover we present a new structure refined at 1.66 A resolution using diffraction data recorded at cryo-temperature (100 K) in an attempt at trapping the polypeptide loop (residues 47 to 58) in the vicinity of the enzyme active site, missing in all previous structure determinations. This loop still has not appeared in the electron density maps, in spite of the advantage of cryo-temperature, but nevertheless the 1.66 A cryo-structure extends the ensemble of known HMBS structures. The cryomodel of protein, cofactor and 320 bound water molecules has been refined to a final R-factor and R-free of 0.198 and 0.247 respectively; the PDB deposition codes, coordinates and structure factors are 1GTK and R1GTKSF respectively. Finally a protein comparison study is presented of the Mycobacterium tuberculosis (MTb) HMBS, with the E. coli HMBS. This has been done as preparation for future structural studies on the MTb HMBS from this important disease bearing organism. The overall amino acid sequence identity is 41%. Most interestingly there is a two-residue reduction in length of the loop referred to above (Asp 50 and Gly 58 being missing in the MTb form). This gives the hope that this loop will be less flexible and thus might become visible to crystallographic analysis.

Crystallography, X-Ray↗

PubMed2003

Nanosecond time-resolved crystallography of photo-induced species: case study and instrument development for high-resolution excited-state single-crystal structure determination.

This work describes one of the first stages in the development of time-resolved photo-induced small-molecule single-crystal diffraction, whereby transient electron density perturbations, with lifetimes down to the nanosecond level, can be resolved at the atomic level. Knowledge of such ephemeral electronic effects is likely to yield key information regarding the origins of certain important physical properties, e.g. luminescent and non-linear optical effects, since it will allow the dynamics of electron density to be identified and quantified, and it is this that underpins such phenomena in a given molecule. The experimental methodology employs phase-locking pump-probe techniques such that the inherent time-structure of a synchrotron X-ray beam (nanoseconds) is harnessed and time-gated in-phase with a femtosecond laser. The resultant beams, made coincident on the crystal in a periodic manner, and a diffraction pattern are recorded as a function of the Bragg angle, theta. Such technology is based upon the pioneering work carried out in sub-nanosecond time-resolved crystallography of macromolecular biological moieties (non-atomic resolution) at the ESRF, although one crucial difference here is the use of monochromatic irradiation and oscillatory motion rather than Laue 'snapshot' methodology, so that atomic resolution is possible. The experimental details of a case study conducted on ID9 at the ESRF, France, are described, whereby the feasibility of the excited-state structure determination of a luminescent rhenium carbene complex, [HNCH2CH2NHCRe(2,2'-bipyridine)(CO)3]Br, is realised. Key experimental parameters that are required for the success of such an experiment are discussed in the light of this study, together with other feasibility work conducted at the SRS, UK, and in the laboratory. Plans, designs and tests for the implementation of this technique in the UK, first at the SRS, and then at DIAMOND, the forthcoming UK synchrotron, are described, in particular with reference to the world-leading potential that DIAMOND could lend toward the development of this technique.

Journal Article↗

PubMed2003

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.

Bacterial Proteins↗

PubMed2002

Diffuse scattering from liquid solutions with white-beam undulator radiation for photoexcitation studies.

Scattering from molecules in solution is a natural way to study fast reactions in solution with X-ray probes. With the availability of reliable femtosecond laser systems and pulsed synchrotron sources with high brilliance, it has become possible to study picosecond time-resolved photoexcitation in condensed matter. Owing to the low scattering cross section and the high background from the non-excited solvent, high flux and long exposure times are required to obtain information about isolated molecules in the conventional monochromatic scattering scheme. It is proposed that the full spectrum of a single-line undulator be used to obtain the diffuse scattering distribution. The bandwidth of 2-5% of the first harmonic, which is easily achievable in current insertion devices, is sufficient to allow the derivation of molecular form factors even in diluted systems. The relaxed bandwidth augments the usable flux drastically.

Journal Article↗