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Cooperativity is essential for the proper functioning of numerous proteins by allosteric interactions. Hemoglobin from Scapharca inaequivalvis (HbI) is a homodimeric protein that can serve as a minimal unit for studying cooperativity. We investigated the structural changes in HbI after carbon monoxide dissociation using time-resolved resonance Raman spectroscopy and observed structural rearrangements in the Fe–proximal histidine bond, the position of the heme in the pocket, and the hydrogen bonds between heme and interfacial water upon ligand dissociation. Some of the spectral changes were different from those observed for human adult hemoglobin due to differences in subunit assembly and quaternary changes. The structural rearrangements were similar for the singly and doubly dissociated species but occurred at different rates. The rates of the observed rearrangements indicated that they occurred synchronously with subunit rotation and are influenced by intersubunit coupling, which underlies the positive cooperativity of HbI. [ABSTRACT FROM AUTHOR]

Vibrational energy exchange between various degrees of freedom is critical to barrier-crossing processes in proteins. Hemeproteins are well suited for studying vibrational energy exchange in proteins because the heme group is an efficient photothermal converter. The released energy by heme following photoexcitation shows migration in a protein moiety on a picosecond timescale, which is observed using time-resolved ultraviolet resonance Raman spectroscopy. The anti-Stokes ultraviolet resonance Raman intensity of a tryptophan residue is an excellent probe for the vibrational energy in proteins, allowing the mapping of energy flow with the spatial resolution of a single amino acid residue. This Perspective provides an overview of studies on vibrational energy flow in proteins, including future perspectives for both methodologies and applications. [ABSTRACT FROM AUTHOR]

Vibrational energy flow in the many degrees of freedom in proteins governs energy-barrier-crossing processes, such as conformational exchanges and thermal reactions. The intensity of anti-Stokes Raman bands arises from vibrationally excited populations and can thus function as a selective probe for the excess energy. Time-resolved observations of the anti-Stokes ultraviolet resonance Raman (UVRR) intensity of amino acid residues provide information about the flow of excess energy in proteins, with the spatial resolution of an amino acid residue. The answer to the question of whether the extent of vibrational excitation in any given vibrational modes reflects the extent of excitation in the whole molecule under nonequilibrium conditions is not straightforward. Here, we calculated the occupation probabilities of vibrational states for model compounds of amino acids under equilibrium and nonequilibrium conditions. At a given temperature, the occupation probability of the model compound of tryptophan under nonequilibrium conditions was nearly identical to that under equilibrium conditions at high temperature. Thus, the anti-Stokes band intensities of Trp residues in the nonequilibrium condition indicate the temperature of the molecules with equivalent energy in the equilibrium condition. In addition, we showed that the temperatures calculated on the basis of two UVRR bands of tryptophan in a time-resolved spectrum agreed with each other within the experimental uncertainty. The present results demonstrate that anti-Stokes UVRR bands of Trp residues serve as an excellent spectroscopic thermometer for determining the local temperature in proteins under nonequilibrium conditions. [ABSTRACT FROM AUTHOR]

Picosecond protein dynamics of myoglobin in response to structural changes in heme upon Carbon Monoxide (CO) dissociation were observed in a site-specific fashion for the first time using time-resolved UV resonance Raman spectroscopy. The spectral changes suggest that the change in heme structure impulsively drives concerted movement of the EF helical section and that rearrangement toward a deoxy structure occur in the heme vicinity and in he a helix within a time frame of nanoseconds.

Identification of histidine 77 as the axial heme ligand of carbonmonoxy CooA has been carried out using picosecond time-resolved resonance Raman spectroscopy. It has been shown that His77 is the axial ligand of Co-bound CooA and CO displaces the axial ligand trans to His77 with ligated His77 to activate CooA as the transcriptional activator retained.

It has been possible to use 1,2-phenylene-bridged (ortho) Zn(II)-porphyrin dimers and 1,3-phenylene-bridged (meta) Zn(II)-porphyrin dimers to investigate the links between geometric and electronic structures in the excited state. Particular attention was given to the properties of the S1 stat of Zn(II)-porphyrin dimers.