Detecting the saddling deformations in nickel meso-phenyl substituted porphyrins using low-frequency Raman characteristic peaks

The out-of-plane (OOP) deformations of metalloporphyrins macrocycle are closely related to their biological functions, and Raman spectroscopy is a powerful tool for investigating OOP deformations. However, due to the interplay of electronic structure, substituents, porphyrin macrocycle in-plane (IP) and OOP deformations, it is challenging to measure the OOP deformations directly, or, establish a confirmative correlation between the frequency shifts of characteristic peaks and specific OOP deformation changes. In this work, we first selected the model porphyrin Ni-P and employed DFT calculations to explore the relationship between the ruffling and saddling deformation changes and their corresponding Raman spectral differences. Subsequently, we focused on nickel meso-tetraphenyl porphyrin (NiTPP), nickel meso-tetrachlorophenylporphyrin (NiTClP), and nickel meso-tetramethoxyphenyl porphyrin (NiTMeOP), which are structurally similar in nature, and investigated the relationship between their OOP deformations and Raman spectra bands based on both experiments and DFT calculations. The results indicate that the ruffling deformation magnitudes of the three nickel porphyrins are almost identical, while the saddling deformation magnitudes differ remarkably. The frequency change of the characteristic peak γ18 in relation to saddling deformation of the three porphyrins is 7.7cm-1/Å, which is close to that of the model porphyrin Ni-P 10.6cm-1/Å. Therefore, the characteristic peak γ18 can be used as a "reporter" for the change in saddling deformation. As such, this work demonstrates how to utilize the frequency shifts of low-frequency Raman characteristic peaks to identify the OOP deformation changes of the porphyrin macrocycle caused by variations in the external environment, thereby providing a theoretically assisted tool for revealing the reasons for their biological function variations.

Heme-Protein Interactions and Functional Relevant Heme Deformations: The Cytochrome c Case

Heme proteins are known to perform a plethora of biologically important functions. This article reviews work that has been conducted on various class I cytochrome c proteins over a period of nearly 50 years. The article focuses on the relevance of symmetry-lowering heme-protein interactions that affect the function of the electron transfer protein cytochrome c. The article provides an overview of various, mostly spectroscopic studies that explored the electronic structure of the heme group in these proteins and how it is affected by symmetry-lowering deformations. In addition to discussing a large variety of spectroscopic studies, the article provides a theoretical framework that should enable a comprehensive understanding of the physical chemistry that underlies the function not only of cytochrome c but of all heme proteins.

Heme-Edge Residues Modulate Signal Transduction within a Bifunctional Homo-Dimeric Sensor Protein

Bifunctional enzymes, which contain two domains with opposing enzymatic activities, are widely distributed in bacteria, but the regulatory mechanism(s) that prevent futile cycling are still poorly understood. The recently described bifunctional enzyme, DcpG, exhibits unusual heme properties and is surprisingly able to differentially regulate its two cyclic dimeric guanosine monophosphate (c-di-GMP) metabolic domains in response to heme gaseous ligands. Mutagenesis of heme-edge residues was used to probe the heme pocket and resulted in decreased O₂ dissociation kinetics, identifying roles for these residues in modulating DcpG gas sensing. In addition, the resonance Raman spectra of the DcpG wild type and heme-edge mutants revealed that the mutations alter the heme electrostatic environment, vinyl group conformations, and spin state population. Using small-angle X-ray scattering and negative stain electron microscopy, the heme-edge mutations were demonstrated to cause changes to the protein conformation, which resulted in altered signaling transduction and enzyme kinetics. These findings provide insights into molecular interactions that regulate DcpG gas sensing as well as mechanisms that have evolved to control multidomain bacterial signaling proteins.

Impact of binding to the multidrug resistance regulator protein LmrR on the photo-physics and -chemistry of photosensitizers

Light activated photosensitizers generate reactive oxygen species (ROS) that interfere with cellular components and can induce cell death, e.g., in photodynamic therapy (PDT). The effect of cellular components and especially proteins on the photochemistry and photophysics of the sensitizers is a key aspect in drug design and the correlating cellular response with the generation of specific ROS species. Here, we show the complex range of effects of binding of photosensitizer to a multidrug resistance protein, produced by bacteria, on the formers reactivity. We show that recruitment of drug like molecules by LmrR (Lactococcal multidrug resistance Regulator) modifies their photophysical properties and their capacity to induce oxidative stress especially in 1O2 generation, including rose bengal (RB), protoporphyrin IX (PpIX), bodipy, eosin Y (EY), riboflavin (RBF), and rhodamine 6G (Rh6G). The range of neutral and charged dyes with different exited redox potentials, are broadly representative of the dyes used in PDT.

Examination of abiotic cofactor assembly in photosynthetic biomimetics: site-specific stereoselectivity in the conjugation of a ruthenium(II) tris(bipyridine) photosensitizer to a multi-heme protein

To understand design principles for assembling photosynthetic biohybrids that incorporate precisely-controlled sites for electron injection into redox enzyme cofactor arrays, we investigated the influence of chirality in assembly of the photosensitizer ruthenium(II)bis(2,2'-bipyridine)(4-bromomethyl-4'-methyl-2,2'-bipyridine), Ru(bpy)2(Br-bpy), when covalently conjugated to cysteine residues introduced by site-directed mutagenesis in the triheme periplasmic cytochrome A (PpcA) as a model biohybrid system. For two investigated conjugates that show ultrafast electron transfer, A23C-Ru and K29C-Ru, analysis by circular dichroism spectroscopy, CD, demonstrated site-specific chiral discrimination as a factor emerging from the close association between [Ru(bpy)3]2+ and heme cofactors. CD analysis showed the A23C-Ru and K29C-Ru conjugates to have distinct, but opposite, stereoselectivity for the Λ and Δ-Ru(bpy)2(Br-bpy) enantiomers, with enantiomeric excesses of 33.1% and 65.6%, respectively. In contrast, Ru(bpy)2(Br-bpy) conjugation to a protein site with high flexibility, represented by the E39C-Ru construct, exhibited a nearly negligible chiral selectivity, measured by an enantiomeric excess of 4.2% for the Λ enantiomer. Molecular dynamics simulations showed that site-specific stereoselectivity reflects steric constraints at the conjugating sites and that a high degree of chiral selectivity correlates to reduced structural disorder for [Ru(bpy)3]2+ in the linked assembly. This work identifies chiral discrimination as means to achieve site-specific, precise geometric positioning of introduced photosensitizers relative to the heme cofactors in manner that mimics the tuning of cofactors in photosynthesis.

Diboron Porphyrins: The Raman Signature of the In-Plane Tetragonal Elongation of the Macrocycle

We describe an unusual in-plane type of porphyrin core distortion, tetragonal elongation (TE), observed experimentally in diboron porphyrins. The vibrational spectra of several of these complexes exhibit shifts that we have assigned to this TE distortion by comparing experimental spectra with DFT computational findings. The influence of TE in porphyrin systems was isolated using DFT analysis of the well-known model compounds Ni(II)porphine and Zn(II)porphine, with the macrocycle ring constrained to eliminate the influence of out-of-plane (OOP) distortions. A significant down-shift in frequencies was observed for porphyrin normal vibrational modes, particularly the in-plane A_1g/B_1g modes that are dominated by contributions from stretching and bending of C_α-C_m coordinates. In contrast, TE had little effect on the v(Pyr_halfring) and δ(Pyr_def) modes, though the lowered symmetry of the system resulted in significant splitting of the B_2u and B_3u modes. The impact of the TE distortion upon the diboron porphyrin vibrational spectrum was probed experimentally using Raman spectroscopy of B₂O₂(BCl₃)₂(TTP), B₂OF₂(TTP), and B₂OPhOH₂(TTP) (TTP = 5,10,15,20-(tetra- p-tolyl)porphyrin). Comparing the experimentally obtained spectral signatures to the computational findings allowed us to assign the large shifts observed for the v₂ and v₃ modes to the TE distortion in diboron porphyrins.

Photophysical properties of porphyrin derivatives: Influence of the alkyl chains in homogeneous and micro-heterogeneous systems

This work is focused on the evaluation of the photophysical properties of protoporphyrin-IX derivatives with different alkyl chains. The goal of this work is to understand the physicochemical properties and select prototypes of photosensitizers for photodynamic therapy. Solvents with different dielectric constants were used to obtain relevant data on different physical and chemical processes, such as fluorescence quantum yield and emission level of aggregation in nonpolar media. In addition, studies were conducted in micro-heterogeneous systems through the interaction of porphyrin derivatives with different surfactants, such as cetyltrimethylammonium bromide, sodium dodecyl sulfate and octyl phenol ethoxylate. The compounds were characterized by electronic absorption spectroscopy in the ultraviolet-visible region and fluorescence emission spectroscopy. The comparative study between the different chemical environments evaluated in the present study represents a relevant contribution to the comprehension of the properties acquired by the porphyrins in different micro-heterogeneous systems, which allows us to understand various interactions that these compounds are subject in biological medium, such as the influence of the polarity of the medium in the reactivity of porphyrins with nonpolar substituents. These results show the decisive physicochemical influence of the alkyl chains on the properties of the tetraazomacrocycle porphyrin.