Biomedical subjects

Mazdak Khajehpour

Publications and source records attributed to Mazdak Khajehpour.

6 recordsLinked to original sources

PubMed2005

Infrared spectroscopy used to evaluate glycosylation of proteins.

Infrared (IR) spectroscopy is used for studying the carbohydrate moieties of glycosylated proteins. IR spectra of mono- and disaccharides in the fingerprint region are specific to each sugar and to the environment of the sugar molecules (i.e., aqueous solution or anhydrous glass phase). The IR spectra of glycosylated proteins (mucin, soybean peroxidase, collagen IV, and avidin) were compared with those of the constituent sugars and cytochrome c (a protein with no glycosylation). Our results demonstrate that the IR absorption spectra of glycosylated proteins show distinct absorption bands for the sugar moiety, the protein amide group, and water. Therefore, IR can be used to detect glycosylation.

Absorption↗

PubMed2004

Melittin as model system for probing interactions between proteins and cyclodextrins.

Cylcodextrin sugars are cyclic sugars that have a hydrophilic exterior and a hydrophobic center. This enables cyclodextrins to solubilize hydrophobic molecules in aqueous media. Cyclodextrins may inhibit aggregation by intercalating surface aromatic residues and competing with interprotein aromatic clusters (pi-pi interactions). In order to investigate this concept, the interaction of hydroxypropyl-beta-cyclodextrin (HPBCD) with melittin is studied with steady-state and time-resolved fluorescence, fluorescence polarization, circular dichroism, and IR spectroscopy. HPBCD inhibits the aggregation of melittin. This inhibition and the spectroscopic results are consistent with the lone aromatic tryptophan of the peptide being intercalated within HPBCD.

2-Hydroxypropyl-beta-cyclodextrin↗

PubMed2003

Accessibility of oxygen with respect to the heme pocket in horseradish peroxidase.

Oxygen and other molecules of similar size take part in a variety of protein reactions. Therefore, it is critical to understand how these small molecules penetrate the protein matrix. The protein system studied in this case is horseradish peroxidase (HRP). We have converted the native HRP into a phosphorescent analog by replacing the heme prosthetic group by Pd-mesoporphyrin. Oxygen readily quenches the phosphorescence of Pd porphyrins, and this can be used to characterize oxygen diffusion through the protein matrix. Our measurements indicate that solvent viscosity and pH modulate the accessibility of the heme pocket relative to small molecules. The binding of the substrate benzohydroxamic acid (BHA) to the protein drastically impedes oxygen access to the heme pocket. These results indicate that, first, the penetration of small molecules through the protein matrix is a function of protein dynamics, and second, there are specific pathways for the diffusion of these molecules. The effect of substrate and pH on protein dynamics has been investigated with the use of molecular dynamics calculations. We demonstrate that the model of a "fluctuating entry point," as suggested by Zwanzig (J Chem Phys 1992;97:3587-3589), properly describes the diffusion of oxygen through the protein matrix.

Binding Sites↗

PubMed2003

Luminescent Zn and Pd tetranaphthaloporphyrins.

Zn and Pd complexes of meso-tetraphenyltetranaphthaloporphyrins (Ph(4)TNP) exhibit strong infrared absorption bands and luminesce in solutions at room temperature. S1 --> S0 fluorescence (lambda(max) = 732 nm, phi = 5.3%) is the predominant emission in the case of ZnPh(4)TNP (1). This emission is in part due to the delayed fluorescence (phi = 1.1%). Phosphorescence (T1 --> S0) of 1 (lambda(max) = 973 nm) is very weak (phi = 0.04%) and occurs with lifetime of about 440 micros in deoxygenated DMF. In the case of PdPh(4)TNP (2), almost no S1 --> S0 fluorescence could be observed, while the main emission detected was T1 --> S0 phosphorescence (lambda(max) = 938 nm). The phosphorescence of 2 occurs with lifetime of about 65 micros and (phi=6.5%) in deoxygenated DMF solution. Metalloporphyrins 1 and 2 are promising near infrared dyes biomedical applications.

Fluorescent Dyes↗

PubMed2003

Effect of protein dynamics upon reactions that occur in the heme pocket of horseradish peroxidase.

Free base and Pd porphyrin derivatives of horseradish peroxidase show long-lived excited states that are quenched by the presence of the peroxidase inhibitor, benzhydroxamic acid. The relaxation times of the excited-state luminescence and the rates of the quenching reaction for these derivatives of peroxidase were monitored as a function of pH, temperature, and viscosity with the view of examining how protein dynamics affect the quenching reaction. As solvent viscosity increases, the rate decreases, but at the limit of very high viscosity (i.e., high glycerol or sugar glass) the quenching still occurs. A model is presented that is consistent with the known structure of the enzyme-inhibitor complex. It is considered that the inhibitor is held at an established position but that solvent-dependent and independent motions allow a limited diffusion of the two reactants. Since there is a steep dependence upon distance and orientation, the diffusion toward the favorable position for reaction enhances the reaction rate. The solvent viscosity dependent and independent effects were separated and analyzed. The importance of internal reaction dynamics is demonstrated in the observation that rigidity of solvent imposed by incorporating the protein into glass at room temperature allows the reaction to occur, while the reaction is inhibited at low temperature. The results emphasize that protein dynamics plays a role in determining reaction rates.

Binding Sites↗

PubMedDate not supplied

Probing the active site of trypsin with rose bengal: insights into the photodynamic inactivation of the enzyme.

In this work the active site of trypsin has been probed with the dye rose bengal. The dye binds competitively to the enzyme, and it can be used as a probe of the active site of the enzyme. On the basis of the emission wavelength, the binding site of trypsin is relatively polar and is similar to that of acetone in its polarity. The triplet state of rose bengal is quenched by trypsin. This quenching may be caused by the tryptophan and tyrosine residues that are in the near vicinity of the trypsin active site. This quenching can compete with the formation of singlet oxygen from the excited triplet state of rose bengal. We demonstrate that the singlet oxygen involved in the photoinactivation of trypsin is produced by the free rose bengal in solution and the bound dye is incapable of producing singlet oxygen. This explains the lack of correlation between photoinactivation efficiency and sensitizer binding capability previously reported by Wade and Spikes.

Binding Sites↗