Advances in Grating-Based Photoacoustic Spectroscopy for the Study of Protein Dynamics

Automated transient grating spectroscopy mapping and signal control for large samples

We present developments for the mapping of large areas using transient grating spectroscopy (TGS) that allow for smoother, larger, autonomous measurements of material samples. The addition of a precise linear stage in the direction parallel to laser sampling coupled with signal optimizing control allows for hands free, self-correcting measurements. In addition, the simplification of the sample holding design to a form that is small enough to mount directly to the linear stage exhibits a straightforward, low-cost solution for automated TGS applications. This capability is demonstrated by taking large uninterrupted maps of gradient wafers, and the results are validated on calibrated tungsten samples and control TGS samples from gradient wafers.

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

The bond energies at active sites of proteins are intimately coupled to the structure-function relationship in biological systems. Due to the unknown nature of the protein relaxation along a reaction coordinate, it has not been possible to directly determine bond energies relevant to protein function. By embedding proteins in trehalose glasses, it is possible to freeze out protein relaxation on short time scales and determine the bond energies of photolabile ligands using photothermal spectroscopies. As a prototypical example, the photodissociation dynamics and energetics of carboxy-myoglobin (MbCO) in a trehalose glass matrix at room temperature were studied by transient absorption (or pump-probe) and transient thermal phase grating spectroscopy to determine the CO recombination dynamics and associated energetics, respectively. Both the initial energetics of the bond breaking and the energy released upon bond reformation could be used, on a time scale faster than significant protein relaxation, to determine the Fe-CO bond energy as 34 +/- 4 kcal/mol. This bond energy is significantly larger than that typically cited (25 kcal/mol) on the basis of indirect measurements but is in good agreement with recent theoretical predictions (35 kcal/mol) (Rovira, C.; Parrinello, M. Int. J. Quantum Chem. 2000, 80, 1172). This result in combination with the theoretical study suggests that protein structure plays a significant role in the bond energies at active sites which in turn provides a tuning element of the effective barrier heights independent to the transition state region.

Nonlinear optical studies of heme protein dynamics: Implications for proteins as hybrid states of matter

Protein structure is fundamentally related to function. However, static structures alone are insufficient to understand how a protein works. Dynamics play an equally important role. Given that proteins are highly associated aperiodic systems, it may be expected that protein dynamics would follow glass-like dynamics. However, protein functions occur on time scales orders of magnitude faster than the time scales typically associated with glassy systems. It is becoming clear that the reaction forces driving functions do not sample entirely the large number of configurations available to a protein but are highly directed along an optimized pathway. Could there be any correlation between specific topological features in protein structures and dynamics that leads to strongly correlated atomic displacements in the dynamical response to a perturbation? This review will try to provide an answer by focusing upon recent nonlinear optical studies with the aim of directly observing functionally important protein motions over the entire dynamic range of the protein response function. The specific system chosen is photoinduced dynamics of ligand dissociation at the active site in heme proteins, with myoglobin serving as the simplest model system. The energetics and nuclear motions from the very earliest events involved in bond breaking on the femtosecond time scale all the way out to ligand escape and bimolecular rebinding on the microsecond and millisecond time scale have been mapped out. The picture that is emerging is that the system consists of strongly coupled motions from the very instant the bond breaks at the active site that cascade into low frequency collective modes specific to the protein structure. It is this coupling that imparts the ability of a protein to function on time scales more commensurate with liquids while simultaneously conserving structural integrity akin to solids.

Time-resolved photothermal methods: accessing time-resolved thermodynamics of photoinduced processes in chemistry and biology

Photothermal methods are currently being employed in a variety of research areas, ranging from materials science to environmental monitoring. Despite the common term which they are collected under, the implementations of these techniques are as diverse as the fields of application. In this review, we concentrate on the recent applications of time-resolved methods in photochemistry and photobiology.

Observation of the cascaded atomic-to-global length scales driving protein motion

Model studies of the ligand photodissociation process of carboxymyoglobin have been conducted by using amplified few-cycle laser pulses short enough in duration (<10 fs) to capture the phase of the induced nuclear motions. The reaction-driven modes are observed directly in real time and depict the pathway by which energy liberated in the localized reaction site is efficiently channeled to functionally relevant mesoscale motions of the protein.

2000 John C. Polanyi Award LectureMother Nature and the molecular Big Bang

Biological molecules are mesoscopic systems that bridge the quantum and classical worlds. At the single molecule level, there are often more than 1 × 104 degrees of freedom that are involved in protein-mediated processes. These molecules are sufficiently large that the bath coordinate convolved to the reaction at an active site is defined by the surrounding protein tertiary structure. In this context, the very interatomic forces that determine the active protein structures create a strongly associated system. Thus, the bath fluctuations leading to reactive crossings involve highly hindered motions within a myriad of local minima that would act to cast the reaction dynamics into the high viscosity limit appropriate to glasses. However, the time scales observed for biological events are orders of magnitude too fast to meet this anticipated categorization. In this context, the apparent deterministic nature of biological processes represents an enormous challenge to our understanding of chemical processes. Somehow Nature has discovered a molecular scaffolding that enables minute amounts of energy to be efficiently channeled to perform biological functions without becoming entrapped in local minima. Clearly, energy derived from chemical processes is highly directed in biological systems. To understand this problem, we must first understand how energy is redistributed among the different degrees of freedom and fully characterize the protein relaxation processes along representative reaction coordinates in relation to these dissipative processes. This paper discusses the development of new nonlinear spectroscopic methods that have enabled interferometric sensitivity to protein motions on femtosecond time scales appropriate to the very fastest motions (i.e., bond breaking or the molecular "Big Bang") out to the slowest relaxation steps. This work has led to the Collective Mode Coupling Model as an explanation of the required reduced dimensionality in biological systems. Within this model, the largest coupling coefficients of the reaction coordinate are to the damped inertial collective modes of the protein defined by the strongly correlated secondary structures. These modes act to guide the reaction along the correct seam(s) in an otherwise highly complex potential energy surface. The mechanism by which biological molecules have been able to harness chemical energy over meso-length scales represents the first step towards higher levels of organization. The new insight afforded by the collective mode mechanism may prove important in understanding this larger issue of scaling in biological systems.Key words: biodynamics, energy transduction, ultrafast spectroscopy, nonlinear spectroscopy, primary processes in biology.

Diffractive optics-based heterodyne-detected four-wave mixing signals of protein motion: from "protein quakes" to ligand escape for myoglobin

Ligand transport through myoglobin (Mb) has been observed by using optically heterodyne-detected transient grating spectroscopy. Experimental implementation using diffractive optics has provided unprecedented sensitivity for the study of protein motions by enabling the passive phase locking of the four beams that constitute the experiment, and an unambiguous separation of the Real and Imaginary parts of the signal. Ligand photodissociation of carboxymyoglobin (MbCO) induces a sequence of events involving the relaxation of the protein structure to accommodate ligand escape. These motions show up in the Real part of the signal. The ligand (CO) transport process involves an initial, small amplitude, change in volume, reflecting the transit time of the ligand through the protein, followed by a significantly larger volume change with ligand escape to the surrounding water. The latter process is well described by a single exponential process of 725 +/- 15 ns. at room temperature. The overall dynamics provide a distinctive signature that can be understood in the context of segmental protein fluctuations that aid ligand escape via a few specific cavities, and they suggest the existence of discrete escape pathways.

Dynamics of structure and energy of horse carboxymyoglobin after photodissociation of carbon monoxide

The energetics and structural volume changes after photodissociation of carboxymyoglobin are quantitatively investigated by laser-induced transient grating (TG) and photoacoustic calorimetric techniques. Various origins of the TG signal are distinguished: the phase grating signals due to temperature change, due to absorption spectrum change, and due to volume change. We found a new kinetics of approximately 700 ns (at room temperature), which was not observed by the flash photolysis technique. This kinetics should be attributed to the intermediate between the geminate pair and the fully dissociated state. The enthalpy of an intermediate species is determined to be 61 +/- 10 kJ/mol, which is smaller than the expected Fe-CO bond energy. The volume of MbCO slightly contracts (5 +/- 3 cm(3)/mol) during this process. CO is fully released from the protein by an exponential kinetics from 25 to -2 degrees C. During this escaping process, the volume expands by 14.7 +/- 2 cm(3)/mol at room temperature and 14 +/- 10 kJ/mol is released, which should represent the protein relaxation and the solvation of the CO (the enthalpy of this final state is 47 +/- 10 kJ/mol). A potential barrier between the intermediate and the fully dissociated state is DeltaH(*) = 41.3 kJ/mol and DeltaS(*) = 13.6 J mol(-1) K(-1). The TG experiment under a high wavenumber reveals that the volume expansion depends on the temperature from 25 to -2 degrees C. The volume changes and the energies of the intermediate species are discussed.

Diffractive optics implementation of six-wave mixing

Diffractive optics are applied to six-wave mixing processes to provide a single optic approach to attaining the required, relatively complex, phase-matching geometry to discriminate against lower-order nonlinear responses. The diffractive optics were designed specifically for broad-bandwidth operation and passive phase locking of the appropriate pulse pairs for use in femtosecond two-dimensional Raman studies of the dynamic structure of liquids. The fifth-order signal was studied in liquid CS>(2); two different colors were used for the excitation and the probe to reduce background scatter, as were two different phase-matching geometries with different degrees of suppression of cascaded third-order processes.