Determination of the Fe−CO Bond Energy in Myoglobin Using Heterodyne-Detected Transient Thermal Phase Grating Spectroscopy

Role of Ionic Strength and pH in Modulating Thermodynamic Profiles Associated with CO Escape from Rice Nonsymbiotic Hemoglobin 1

Type 1 nonsymbiotic hemoglobins are found in a wide variety of land plants and exhibit very high affinities for exogenous gaseous ligands. These proteins are presumed to have a role in protecting plant cells from oxidative stress under etiolated/hypoxic conditions through NO dioxygenase activity. In this study we have employed photoacoustic calorimetry, time-resolved absorption spectroscopy, and classical molecular dynamics simulations in order to elucidate thermodynamics, kinetics, and ligand migration pathways upon CO photodissociation from WT and a H73L mutant of type 1 nonsymbiotic hemoglobin from Oryza sativa (rice). We observe a temperature dependence of the resolved thermodynamic parameters for CO photodissociation from CO-rHb1 which we attribute to temperature dependent formation of a network of electrostatic interactions in the vicinity of the heme propionate groups. We also observe slower ligand escape from the protein matrix under mildly acidic conditions in both the WT and H73L mutant (τ = 134 ± 19 and 90 ± 15 ns). Visualization of transient hydrophobic channels within our classical molecular dynamics trajectories allows us to attribute this phenomenon to a change in the ligand migration pathway which occurs upon protonation of the distal His73, His117, and His152. Protonation of these residues may be relevant to the functioning of the protein in vivo given that etiolation/hypoxia can cause a decrease in intracellular pH in plant cells.

A high-repetition rate scheme for synchrotron-based picosecond laser pump/x-ray probe experiments on chemical and biological systems in solution

We present the extension of time-resolved optical pump/x-ray absorption spectroscopy (XAS) probe experiments towards data collection at MHz repetition rates. The use of a high-power picosecond laser operating at an integer fraction of the repetition rate of the storage ring allows exploitation of up to two orders of magnitude more x-ray photons than in previous schemes based on the use of kHz lasers. Consequently, we demonstrate an order of magnitude increase in the signal-to-noise of time-resolved XAS of molecular systems in solution. This makes it possible to investigate highly dilute samples at concentrations approaching physiological conditions for biological systems. The simplicity and compactness of the scheme allows for straightforward implementation at any synchrotron beamline and for a wide range of x-ray probe techniques, such as time-resolved diffraction or x-ray emission studies.

`Making the molecular movie': first frames

Recent advances in high-intensity electron and X-ray pulsed sources now make it possible to directly observe atomic motions as they occur in barrier-crossing processes. These rare events require the structural dynamics to be triggered by femtosecond excitation pulses that prepare the system above the barrier or access new potential energy surfaces that drive the structural changes. In general, the sampling process modifies the system such that the structural probes should ideally have sufficient intensity to fully resolve structures near the single-shot limit for a given time point. New developments in both source intensity and temporal characterization of the pulsed sampling mode have made it possible to make so-called `molecular movies',i.e.measure relative atomic motions faster than collisions can blur information on correlations. Strongly driven phase transitions from thermally propagated melting to optically modified potential energy surfaces leading to ballistic phase transitions and bond stiffening are given as examples of the new insights that can be gained from an atomic level perspective of structural dynamics. The most important impact will likely be made in the fields of chemistry and biology where the central unifying concept of the transition state will come under direct observation and enable a reduction of high-dimensional complex reaction surfaces to the key reactive modes, as long mastered by Mother Nature.

Diffractive optics based four-wave, six-wave, ..., nu-wave nonlinear spectroscopy

A detailed understanding of chemical processes requires information about both structure and dynamics. By definition, a reaction involves nonstationary states and is a dynamic process. Structure describes the atomic positions at global minima in the nuclear potential energy surface. Dynamics are related to the anharmonicities in this potential that couple different minima and lead to changes in atomic positions (reactions) and correlations. Studies of molecular dynamics can be configured to directly access information on the anharmonic interactions that lead to chemical reactions and are as central to chemistry as structural information. In this regard, nonlinear spectroscopies have distinct advantages over more conventional linear spectroscopies. Because of this potential, nonlinear spectroscopies could eventually attain a comparable level of importance for studying dynamics on the relevant time scales to barrier crossings and reactive processes as NMR has for determining structure. Despite this potential, nonlinear spectroscopy has not attained the same degree of utility as linear spectroscopy largely because nonlinear studies are more technically challenging. For example, unlike the linear spectrometers that exist in almost all chemistry departments, there are no "black box" four-wave mixing spectrometers. This Account describes recent advances in the application of diffractive optics (DOs) to nonlinear spectroscopy, which reduces the complexity level of this technology to be closer to that of linear spectroscopy. The combination of recent advances in femtosecond laser technology and this single optic approach could bring this form of spectroscopy out of the exclusive realm of specialists and into the general user community. However, the real driving force for this research is the pursuit of higher sensitivity limits, which would enable new forms of nonlinear spectroscopy. This Account chronicles the research that has now extended nonlinear spectroscopy to six-wave processes and to a completely generalized "nu-wave" mixing form to fully control state preparation and coherences. For example, direct observation of global protein motions and energetics has led to the collective mode coupling model to understand structure-function correlations in biological systems. Direct studies of the hydrogen bond network of liquid H(2)O have recently shown that both intramolecular and intermolecular degrees of freedom are strongly coupled so that the primary excitations of water have an excitonic-like character. This fundamentally different view of liquid water has now resolved a 100-year-old problem of homogeneous versus inhomogeneous broadening of the vibrational line shapes. By adding programmable pulse shaping, we can access new information about the many-body interactions directly relevant to chemical reaction dynamics. We can also steer the course of the reaction along multidimensional surfaces to provide information about fluctuations far from the equilibrium, which are most relevant to chemical reactivity.

Ultrafast dynamics of ligands within heme proteins

Physiological bond formation and bond breaking events between proteins and ligands and their immediate consequences are difficult to synchronize and study in general. However, diatomic ligands can be photodissociated from heme, and thus in heme proteins ligand release and rebinding dynamics and trajectories have been studied on timescales of the internal vibrations of the protein that drive many biochemical reactions, and longer. The rapidly expanding number of characterized heme proteins involved in a large variety of functions allows comparative dynamics-structure-function studies. In this review, an overview is given of recent progress in this field, and in particular on initial sensing processes in signaling proteins, and on ligand and electron transfer dynamics in oxidases and cytochromes.