Hydration of hydrophobic biological porphyrins

Cuya, Teobaldo; Louro, Sônia R.W.; Anteneodo, Celia

doi:10.1063/1.3544376

Cited by 11 publications

(6 citation statements)

References 19 publications

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“…At 310 K and within simulation time, only the second barrier could be overcome, meaning that the substituents had restricted rotation ability. The SDF of water molecules revealed a moderate hydration of the central porphyrin ring, especially of the nitrogen atoms, in agreement with the trends reported by Guizado et al − Hydration was more pronounced for the Mpyr+ as compared to the Phe groups. In fact, experimental measurements of n -butanol/water partition coefficients (see Table ) demonstrate that the affinity of the different photosensitizers for water is improved as the number of strongly hydrated Mpyr+ groups increases in relation to the number of Phe groups. , …”

Section: Resultssupporting

confidence: 90%

Photodynamic Efficiency of Cationicmeso-Porphyrins at Lipid Bilayers: Insights from Molecular Dynamics Simulations

2012

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Porphyrin derivatives have applications as photoactive drugs in photodynamic therapy. However, little is known about their interactions with phospholipid membranes at the molecular level. We employed molecular dynamics simulations to model the binding between a series of cationic meso-(N-methyl-4-pyridinium)phenylporphyrins and anionic phosphatidylglycerol lipid bilayers. This was done in the presence of molecular oxygen within the membrane. The ability of various porphyrins to cause photodamage was quantified in terms of their immersion depth and degree of exposition to a higher oxygen concentration inside the membrane. Simulations showed that the photodynamic efficiency could be improved as the number of hydrophobic phenyl substituents attached to the porphyrinic ring increased. In the specific case of porphyrins containing two hydrophobic and two charged substituents, the cis isomer was significantly more efficient than the trans. These results correlate well with previous experimental observations. They highlight the importance of both the total charge and amphiphilicity of the photosensitizer for its performance in photodynamic therapy.

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Section: Resultssupporting

confidence: 90%

Photodynamic Efficiency of Cationicmeso-Porphyrins at Lipid Bilayers: Insights from Molecular Dynamics Simulations

2012

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“…Aqueous solvation of ferriheme species was investigated using SDFs as previously described for other metal complexes. , Owing to the flexibility of the propionate side-chains, solvation of only the porphyrin ring is described. Monomeric ferriheme species displayed three main regions with high probabilities of hydration by water O atoms (see Figure and Supporting Information Figure S8), similar to that reported for ferrous heme by Cuya Guizado and co-workers . Highly solvated areas included the axial water and hydroxide ligands, H meso on the porphyrin ring, and the unligated face.…”

Section: Resultssupporting

confidence: 75%

“…Monomeric ferriheme species displayed three main regions with high probabilities of hydration by water O atoms (see Figure 2 and Supporting Information Figure S8), similar to that reported for ferrous heme by Cuya Guizado and co-workers. 57 Highly solvated areas included the axial water and hydroxide ligands, H meso on the porphyrin ring, and the unligated face. Strong solvation of the axial ligands is expected given the propensity of water and hydroxide molecules to hydrogen bond.…”

Section: Inorganic Chemistrymentioning

confidence: 99%

Molecular Structures and Solvation of Free Monomeric and Dimeric Ferriheme in Aqueous Solution: Insights from Molecular Dynamics Simulations and Extended X-ray Absorption Fine Structure Spectroscopy

Kuter¹,

Streltsov

Davydova

et al. 2014

Inorg. Chem.

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CHARMM force field parameters have been developed to model nonprotein bound five-coordinate ferriheme (ferriprotoporphyrin IX) species in aqueous solution. Structures and solvation were determined from molecular dynamics (MD) simulations at 298 K of monomeric [HO-ferriheme](2-), [H2O-ferriheme](-), and [H2O-ferriheme](0); π-π dimeric [(HO-ferriheme)2](4-), [(H2O-ferriheme)(HO-ferriheme)](3-), [(H2O-ferriheme)2](2-), and [(H2O-ferriheme)2](0); and μ-oxo dimeric [μ-(ferriheme)2O](4-). Solvation of monomeric species predominated around the axial ligand, meso-hydrogen atoms of the porphyrin ring (Hmeso), and the unligated face. Existence of π-π ferriheme dimers in aqueous solution was supported by MD calculations where such dimers remained associated over the course of the simulation. Porphyrin rings were essentially coplanar. In these dimers major and minor solvation was observed around the axial ligand and Hmeso positions, respectively. In μ-oxo ferriheme, strong solvation of the unligated face and bridging oxide ligand was observed. The solution structure of the μ-oxo dimer was investigated using extended X-ray absorption fine structure (EXAFS) spectroscopy. The EXAFS spectrum obtained from frozen solution was markedly different from that recorded on dried μ-oxo ferriheme solid. Inclusion of five solvent molecules obtained from spatial distribution functions in the structure generated from MD simulation was required to produce acceptable fits to the EXAFS spectra of the dimer in solution, while the solid was suitably fitted using the crystal structure of μ-oxo ferriheme dimethyl ester which included no solvent molecules.

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“…On the other hand such effects have not been focus of previous, purely classical simulation studies. Therefore, an ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) 19,20 study of dianionic porphyrin (POR) and magnesium-porphyrin (Mg-POR) in aqueous solution was performed which is expected to serve as a biomimetic model for PPIX and CHl molecules in aqueous environments whereas the computational effort required to treat the entire PPIX and CHl molecules in water 15,21 at a quantum mechanical level is beyond the capabilities of present computational facilities. Fig.…”

Section: Introductionmentioning

confidence: 99%

Hydration of porphyrin and Mg–porphyrin: ab initio quantum mechanical charge field molecular dynamics simulations

Moin

Hofer

2014

Mol. BioSyst.

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Ab initio QMCF-MD simulations were performed for porphyrin (POR) and magnesium-porphyrin (Mg-POR) immersed in water to study their structural and dynamical properties. The observed hydration behaviour of these solutes representing biomimetic models is in fair agreement with structural and dynamical features of their biological analogues, protoporphyrin IX (PPIX) and chlorophyll (CHl). Structural data obtained from the radial, angular and spatial distribution functions as well as the angular-radial distributions have a consensus on possessing a contrasting hydration behaviour of POR and Mg-POR. Flexibility of the ring in both solutes described by the improper torsional distribution and root mean square fluctuation showed an influence on H-bond interactions between the nitrogen atoms and water molecules that are also reflected in the respective dynamics. An axial water molecule coordinated to the Mg(ii) ion indicates the penta-coordinated Mg-POR to be stable along the simulation. It was also shown that complexation of the Mg(ii) ion to the porphyrin influences the hydration patterns significantly compared to the porphyrin itself, which is further supported by the vibrational power spectra evaluated for both solutes. Free energy of binding and solvent accessible surface area calculations also confirmed that these two solutes have distinct hydration behaviour. Detailed knowledge of the individual hydration patterns is expected to be of particular benefit.

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Hydration of hydrophobic biological porphyrins

Cited by 11 publications

References 19 publications

Photodynamic Efficiency of Cationicmeso-Porphyrins at Lipid Bilayers: Insights from Molecular Dynamics Simulations

Photodynamic Efficiency of Cationicmeso-Porphyrins at Lipid Bilayers: Insights from Molecular Dynamics Simulations

Molecular Structures and Solvation of Free Monomeric and Dimeric Ferriheme in Aqueous Solution: Insights from Molecular Dynamics Simulations and Extended X-ray Absorption Fine Structure Spectroscopy

Hydration of porphyrin and Mg–porphyrin: ab initio quantum mechanical charge field molecular dynamics simulations

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