Combination of Resonance Raman Spectroscopy and Docking Simulations to Study the Nonspecific Binding of a Free-Base Porphyrin to a Globular Protein

Water-Soluble Star Polymer as a Potential Photoactivated Nanotool for Lysozyme Degradation

The development of nanotools for chemical sensing and macromolecular modifications is a new challenge in the biomedical field, with emphasis on artificial peptidases designed to cleave peptide bonds at specific sites. In this landscape, metal porphyrins are attractive due to their ability to form stable complexes with amino acids and to generate reactive oxygen species when irradiated by light of appropriate wavelengths. The issues of hydrophobic behavior and aggregation in aqueous environments of porphyrins can be solved by using its PEGylated derivatives. This work proposes the design of an artificial photo-protease agent based on a PEGylated mercury porphyrin, able to form a stable complex with l-Tryptophan, an amino acid present also in the lysozyme structure (a well-known protein model). The sensing and photodegradation features of PEGylated mercury porphyrin were exploited to detect and degrade both l-Trp and lysozyme using ROS, generated under green (532 nm) and red (650 nm) light lasers. The obtained system (Star3600_Hg) and its behavior as a photo-protease agent were studied by means of several spectroscopies (UV-Vis, fluorescence and circular dichroism), and MALDI-TOF mass spectrometry, showing the cleavage of lysozyme and the appearance of several short-chain residues. The approach of this study paves the way for potential applications in theranostics and targeted bio-medical therapies.

Characterization of the interaction of metal-protoporphyrins photosensitizers with β- lactoglobulin

We investigated the interaction of a series of metal-protoporphyrins (PPIXs) with bovine β- lactoglobulin (BLG) using a combination of optical spectroscopy and computational simulations. Unlike other studies, the simulations were not merely used to rationalize the experimental data but were employed to refine the experimental data itself. The study was carried out at two pH values, 5 and 9, where BLG is known to have different conformation dictated by the so-called Tanford transition which occurs near pH 7.5. The transition is postulated to regulate access to the interior binding cavity of the protein, thus the pH variation was used as a parameter to investigate whether PPIXs access the central cavity of BLG. The results of our study show that indeed binding increases significantly at alkaline pH, however, the increased affinity is not due to the accessibility of the central cavity. Instead, binding appears to be determined by the tendency of PPIXs to form large inhomogeneous aggregates at acidic pH which hinders interactions with proteins. The binding site determined through a combination of experimental and computational methods is located at the interface between two BLG monomers where the long α-helix segment of the protein face each other. This region is rich in positively charged Lys residues that interact with the propionic acid chains of the protoporphyrins. Establishing the modality of binding between protoporphyrins and BLG would have important consequences for the use of BLG:PPIX complexes in applications such as artificial photoreceptors, artificial metallo-enzymes, delivery of photosensitizers for phototherapy and even solar energy conversion.

Comparative study of binding interactions between porphyrin systems and aromatic compounds of biological importance by multiple spectroscopic techniques: A review

The specific spectroscopic and redox properties of porphyrins predestine them to fulfill the role of sensors during interacting with different biologically active substances. Monitoring of binding interactions in the systems porphyrin-biologically active compound is a key question not only in the field of physiological functions of living organisms, but also in environmental protection, notably in the light of the rapidly growing drug consumption and concurrently the production of drug effluents. Not always beneficial action of drugs on natural porphyrin systems induces to further studies, with commercially available porphyrins as the model systems. Therefore the binding process between several water-soluble porphyrins and a series of biologically active compounds (e.g. caffeine, guanine, theophylline, theobromine, xanthine, uric acid) has been studied in different aqueous solutions analyzing their absorption and steady-state fluorescence spectra, the porphyrin fluorescence lifetimes and their quantum yields. The magnitude of the binding and fluorescence quenching constants values for particular quenchers decreases in a series: uric acid > guanine > caffeine > theophylline > theobromine > xanthine. In all the systems studied there are characters of static quenching, as a consequence of the π-π-stacked non-covalent and non-fluorescent complexes formation between porphyrins and interacting compounds, accompanied simultaneously by the additional specific binding interactions. The porphyrin fluorescence quenching can be explain by the photoinduced intermolecular electron transfer from aromatic compound to the center of the porphyrin molecule, playing the role of the binding site. Presented results can be valuable for designing of new fluorescent porphyrin chemosensors or monitoring of drug traces in aqueous solutions. The obtained outcomes have also the toxicological and medical importance, providing insight into the interactions of the water-soluble porphyrins with biologically active substances.

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.

Effects of Visible-Light Irradiation of Protoporphyrin IX on the Self-Assembly of Tubulin Heterodimers

The formation and the effects of laser irradiation of the complex formed by protoporphyrin IX (PPIX) and tubulin was investigated. We have used tubulin as a model protein to investigate whether docked photoactive ligands can affect the structure and function of polypeptides upon exposure to visible light. We observed that laser irradiation in the Soret band prompts bleaching of the PPIX, which is accompanied by a sharp decrease in the intensity and average fluorescence lifetime of the protein (dominated by the four tryptophan residues of the tubulin monomer). The kinetics indicate non-trivial effects and suggest that the photosensitization of the PPIX bound to tubulin prompts structural alterations of the protein. These modifications were also observed through changes in the energy transfer between Trp residues and PPIX. The results suggest that laser irradiation produces localized partial unfolding of tubulin and that the changes prompt modification of the formation of microtubules in vitro. Measurements of singlet oxygen formation were inconclusive in determining whether the changes are prompted by reactive oxygen species or other excited state mechanisms.

Combined use of optical spectroscopy and computational methods to study the binding and the photoinduced conformational modification of proteins when NMR and X-ray structural determinations are not an option

The functions of proteins depend on their interactions with various ligands and these interactions are controlled by the structure of the polypeptides. If one can manipulate the structure of proteins, their functions can in principle be modulated. The issue of protein structure-function relationship is not only a central problem in biophysics, but is becoming clear that the ability to "artificially" modify the structure of proteins could be relevant in fields beyond the biomedical area to provide, for instance, light responses in proteins which would not possess such properties in their native state. This chapter presents an overview of the combination of optical electronic and vibrational spectroscopy with various computational methods to investigate the binding between photoactive ligands and proteins.

Partial Unfolding of Tubulin Heterodimers Induced by Two-Photon Excitation of Bound meso-Tetrakis(sulfonatophenyl)porphyrin

The water-soluble porphyrin meso-tetrakis(p-sulfonatophenyl)porphyrin (TSPP) can be noncovalently bound to tubulin and used as a photosensitizer, which upon irradiation triggers photochemical reactions that lead to conformational changes of the protein. These conformational changes in turn inhibit tubulin's primary function of polymerizing into microtubules. We explored the possibility of using two-photon excitation of the bound porphyrin to induce photosensitized protein unfolding. Although TSPP has a relatively low cross section (∼30 GM) our results did find that two-photon excitation of the ligand causes partial unfolding of the tubulin host and the inhibition of the in vitro formation of microtubules. Conversely, irradiating tubulin alone caused no such effects despite the large irradiance per pulse (97-190 GW/cm(2)). The conformational changes were characterized using spectroscopic studies and provide a promising protocol for the future application of non-native photosensitization of proteins.

Resonance Raman and vibrational mode analysis used to predict ligand geometry for docking simulations of a water soluble porphyrin and tubulin

The ability to modify the conformation of a protein by controlled partial unfolding may have practical applications such as inhibiting its function or providing non-native photosensitive properties. A water-soluble porphyrin, meso-tetrakis (p-sulfonatophenyl) porphyrin (TSPP), non-covalently bound to tubulin can be used as a photosensitizer, which upon irradiation can lead to conformational changes of the protein. To fully understand the mechanism responsible for this partial unfolding and determine the amino acid residues and atoms involved, it is essential to find the most likely binding location and the configuration of the ligand and protein. Techniques typically used to analyze atomic position details, such as nuclear magnetic resonance and X-ray crystallography, require large concentrations, which are incompatible with the dilute conditions required in experiments for photoinduced mechanisms. Instead, we develop an atomistic description of the TSPP-tubulin complex using vibrational mode analysis from density functional theory calculations correlated to resonance Raman spectra of the porphyrin paired with docking simulations. Changes in the Raman peaks of the porphyrin molecule correlate with changes in its structural vibrational modes when bound to tubulin. The data allow us to construct the relative geometry of the porphyrin when bound to protein, which are then used with docking simulations to find the most likely configuration of the TSPP-tubulin complex.

Photoinduced partial unfolding of tubulin bound to meso-tetrakis(sulfonatophenyl) porphyrin leads to inhibition of microtubule formation in vitro

The irradiation of the complex formed by meso-tetrakis (sulfonatophenyl) porphyrin (TSPP) and tubulin was investigated as well as its effects on the structure and function of the protein. We have used tubulin as a model target to investigate whether photoactive ligands docked to the protein can affect the structure and function of the protein upon exposure to visible light. We observed that laser irradiation prompts bleaching of the porphyrin which is accompanied by a sharp decrease (∼2 ns) in the average fluorescence lifetime of the protein and a change in the dichroic spectrum consistent with a decrease of helical structure. The result indicated the photoinduced partial unfolding of tubulin. We also observed that such partial conformational change inhibits the formation of microtubules in vitro. We investigated whether photosensitization of reactive oxygen species was responsible for these effects. Even upon removal of O2 the protein still undergoes conformational changes indicating that irradiation of the bound porphyrin does not require the presence of O2 to prompt conformational and functional effects opening the possibility that other mechanisms (e.g., charge transfer) are responsible for the photoinduced mechanism.

Interaction of human serum albumin with novel 3,9-disubstituted perylenes

Human serum albumin (HSA) has been used as a model for the binding of a number of different ligands, including polyaromatic hydrocarbons, to proteins. In this case we have investigated the interaction of HSA with a novel set of perylene derivatives. Di-substituted perylene analogues have been synthesized as potentially useful organic photovoltaic materials. Their photophysical properties may make them viable for fuel cell applications too. However, these molecules are poorly soluble especially in aqueous solvents. Binding to water-soluble proteins may provide a way to solubilize them. At the same time one can study whether the photophysical processes initiated by the irradiation of a perylene ligand can cause conformational changes to the host protein. With the present study we demonstrated that of the three perylene derivatives investigated only one, the dimethoxy analogue, has a significant affinity for HSA at a binding site near the bottom of the central cleft (in proximity of the Trp214 residue). The small affinity prevents any significant photoinduced changes to occur in the protein.