Time-resolved infrared spectroscopic studies of ligand dynamics in the active site from cytochrome c oxidase

Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography

Cytochrome c oxidase (CcO) is a large membrane-bound hemeprotein that catalyzes the reduction of dioxygen to water. Unlike classical dioxygen binding hemeproteins with a heme b group in their active sites, CcO has a unique binuclear center (BNC) composed of a copper atom (CuB) and a heme a3 iron, where O2 binds and is reduced to water. CO is a versatile O2 surrogate in ligand binding and escape reactions. Previous time-resolved spectroscopic studies of the CO complexes of bovine CcO (bCcO) revealed that photolyzing CO from the heme a3 iron leads to a metastable intermediate (CuB-CO), where CO is bound to CuB, before it escapes out of the BNC. Here, with a pump-probe based time-resolved serial femtosecond X-ray crystallography, we detected a geminate photoproduct of the bCcO-CO complex, where CO is dissociated from the heme a3 iron and moved to a temporary binding site midway between the CuB and the heme a3 iron, while the locations of the two metal centers and the conformation of Helix-X, housing the proximal histidine ligand of the heme a3 iron, remain in the CO complex state. This new structure, combined with other reported structures of bCcO, allows for a clearer definition of the ligand dissociation trajectory as well as the associated protein dynamics.

High-throughput single-cell live imaging of photobiomodulation with multispectral near-infrared lasers in cultured T cells

SIGNIFICANCE

Photobiomodulation is a well-established therapeutic modality. However, the mechanism of action is poorly understood, due to lack of research in the causal relationship between the near-infrared (NIR) light irradiation and its specific biological effects, hindering broader applications of this technology.

AIM

Since biological chromophores typically show several absorption peaks, we determined whether specific effects of photobiomodulation are induced with a combination of two wavelengths at a certain range of irradiance only, rather than a single wavelength of NIR light.

APPROACH

In order to analyze a wide array of combinations of multispectral NIR light at various irradiances efficiently, we developed a new optical platform equipped with two distinct wavelengths of NIR lasers by high-throughput multiple dosing for single-cell live imaging. Two wavelengths of 1064 and 1270 nm were selected based on their photobiomodulatory effects reported in the literature.

RESULTS

A specific combination of wavelengths at low irradiances (250 to 400  mW  /  cm2 for 1064 nm and 55 to 65  mW  /  cm2 for 1270 nm) modulates mitochondrial retrograde signaling, including intracellular calcium and reactive oxygen species in T cells. The time-dependent density functional theory computation of binding of nitric oxide (NO) to cytochrome c oxidase indicates that the illumination with NIR light could result in the NO release, which might be involved in these changes.

CONCLUSIONS

This optical platform is a powerful tool to study causal relationship between a specific parameter of NIR light and its biological effects. Such a platform is useful for a further mechanistic study on not only photobiomodulation but also other modalities in photomedicine.

Ultrafast Dynamics and Vibrational Relaxation in Six-Coordinate Heme Proteins Revealed by Femtosecond Stimulated Raman Spectroscopy

Identifying the structural rearrangements during photoinduced reactions is a fundamental challenge for understanding from a microscopic perspective the dynamics underlying the functional mechanisms of heme proteins. Here, femtosecond stimulated Raman spectroscopy is applied to follow the ultrafast evolution of two different proteins, each bearing a six-coordinate heme with two amino acid axial ligands. By exploiting the sensitivity of Raman spectra to the structural configuration, we investigate the effects of photolysis and the binding of amino acid residues in cytochrome c and neuroglobin. By comparing the system response for different time delays and Raman pump resonances, we show how detailed properties of atomic motions and energy redistribution can be unveiled. In particular, we demonstrate substantially faster energy flow from the dissociated heme to the protein moiety in cytochrome c, which we assign to the presence of covalent heme–protein bonds.

Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions

To understand functions of biomolecules such as proteins, not only structures but their conformational change and kinetics need to be characterized, but its atomistic details are hard to obtain both experimentally and computationally. Here, we review our recent computational studies using novel enhanced sampling techniques for conformational sampling of biomolecules and calculations of their kinetics. For efficiently characterizing the free energy landscape of a biomolecule, we introduce the multiscale enhanced sampling method, which uses a combined system of atomistic and coarse-grained models. Based on the idea of Hamiltonian replica exchange, we can recover the statistical properties of the atomistic model without any biases. We next introduce the string method as a path search method to calculate the minimum free energy pathways along a multidimensional curve in high dimensional space. Finally we introduce novel methods to calculate kinetics of biomolecules based on the ideas of path sampling: one is the Onsager⁻Machlup action method, and the other is the weighted ensemble method. Some applications of the above methods to biomolecular systems are also discussed and illustrated.

Gasotransmitter Heterocellular Signaling

SIGNIFICANCE

The family of gasotransmitter molecules, nitric oxide (NO), carbon monoxide (CO), and hydrogen sulfide (H₂S), has emerged as an important mediator of numerous cellular signal transduction and pathophysiological responses. As such, these molecules have been reported to influence a diverse array of biochemical, molecular, and cell biology events often impacting one another. Recent Advances: Discrete regulation of gasotransmitter molecule formation, movement, and reaction is critical to their biological function. Due to the chemical nature of these molecules, they can move rapidly throughout cells and tissues acting on targets through reactions with metal groups, reactive chemical species, and protein amino acids.

CRITICAL ISSUES

Given the breadth and complexity of gasotransmitter reactions, this field of research is expanding into exciting, yet sometimes confusing, areas of study with significant promise for understanding health and disease. The precise amounts of tissue and cellular gasotransmitter levels and where they are formed, as well as how they react with molecular targets or themselves, all remain poorly understood.

FUTURE DIRECTIONS

Elucidation of specific molecular targets, characteristics of gasotransmitter molecule heterotypic interactions, and spatiotemporal formation and metabolism are all important to better understand their true pathophysiological importance in various organ systems. Antioxid. Redox Signal. 26, 936-960.

Isocyanide or nitrosyl complexation to hemes with varying tethered axial base ligand donors: synthesis and characterization

A series of ferrous-heme 2,6-dimethylphenyl isocyanide (DIMPI) and ferrous-heme mononitrosyl complexes have been synthesized and characterized. The heme portion of the complexes studied is varied with respect to the nature of the axial ligand, including complexes, where it is covalently tethered to the porphyrinate periphery. Reduced heme complexes, [(F8)Fe(II)], [(P(Py))Fe(II)], [(P(Im))Fe(II)], and [(P(ImH))Fe(II)], where F8 = tetrakis(2,6-difluorophenyl)-porphyrinate and P(Py), P(Im), and P(ImH) are partially fluorinated tetraaryl porphyrinates with covalently appended axial base pyridyl/imidazolyl or histamine moieties, were employed; P(ImH) is a new construct. Room temperature addition of DIMPI to these iron(II) complexes affords the bis-isocyanide species [(F8)Fe(II)-(DIMPI)2] in the case of [(F8)Fe(II)], while for the other hemes, mono-DIMPI compounds are obtained, [(P(Py))Fe(II)-(DIMPI)] [(2)-DIMPI], [(P(Im))Fe(II)-(DIMPI)] [(3)-DIMPI], and [(P(ImH))Fe(II)-(DIMPI)] [(4)-DIMPI]. The structures of complexes (3)-DIMPI and (4)-DIMPI have been determined by single crystal X-ray crystallography, where interesting H…F(porphryinate aryl group) interactions are observed. (19)F-NMR spectra determined for these complexes suggest that H…F(porphyrinate aryl groups) attractions also occur in solution, the H atom coming either from the DIMPI methyl groups or from a porphyinate axial base imidazole or porphyrinate pyrrole. Similarly, we have used nitrogen monoxide to generate ferrous-nitrosyl complexes, a five-coordinate species for F8, [(F8)Fe(II)-(NO)], or low-spin six-coordinate compounds [(P(Py))Fe(II)-(NO)], [(P(Im))Fe(II)-(NO)], and [(P(ImH))Fe(II)-(NO)]. The DIMPI and mononitrosyl complexes have also been characterized using UV-Vis, IR, (1)H-NMR, and EPR spectroscopies.