Hydrophobic Cavity Of Protein Research Articles

Change in the Microviscosity of Erythrocyte Membranes and Proteins in Blood Plasma after Graphene Oxide Addition: The ESR Spectroscopy Study

The change in the microviscosity of erythrocyte membranes and the proteins in blood plasma after graphene oxide addition is studied by the ESR spectroscopy exploiting two spin probes with different lipophilic components in the structures. Experiments with charged spin probe 2 embedded into the erythrocyte membrane showed that the introduction of graphene oxide in small concentrations (∼70 μg/ml) into a suspension of erythrocytes did not lead to significant changes in the microviscosity of their membranes. Correlation times of hydrophobic spin probe 1 adsorbed to hydrophobic pockets of plasma proteins demonstrate a gradual slowdown at the graphene oxide injection into blood plasma that indicates a small deformation of the hydrophobic cavity of protein at the adsorption. However, this protein binding with graphene oxide does not cause the displacement of the spin probe from their hydrophobic cavities, which is evidence about small changes in the protein secondary structure. The obtained results indicate the insignificant cytotoxicity effect of small concentrations of graphene oxide for erythrocytes and blood plasma.

Anticancer Activity of Iridium(III) Complexes Based on a Pyrazole-Appended Quinoline-Based BODIPY.

A pyrazole-appended quinoline-based 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (L1, BODIPY) has been synthesized and used as a ligand for the preparation of iridium(III) complexes [Ir(phpy)2(L1)]PF6 (1; phpy = 2-phenylpyridine) and [(η5-C5Me5)Ir(L1)Cl]PF6 (2). The ligand L1 and complexes 1 and 2 have been meticulously characterized by elemental analyses and spectral studies (IR, electrospray ionization mass spectrometry, 1H and 13C NMR, UV/vis, fluorescence) and their structures explicitly authenticated by single-crystal X-ray analyses. UV/vis, fluorescence, and circular dichroism studies showed that complexes strongly bind with calf-thymus DNA and bovine serum albumin. Molecular docking studies clearly illustrated binding through DNA minor grooves via van der Waals forces and their electrostatic interaction and occurrence in the hydrophobic cavity of protein (subdomain IIA). Cytotoxicity, morphological changes, and apoptosis have been explored by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and Hoechst 33342 staining. IC50 values for complexes (1, 30 μM; 2, 50 μM) at 24 h toward the human cervical cancer cell line (HeLa) are as good as that of cisplatin (21.6 μM) under analogous conditions, and their ability to kill cancer cells lies in the order 1 > 2. Because of the inherent emissive nature of the BODIPY moiety, these are apt for intracellular visualization at low concentration and may find potential applications in cellular imaging and behave as a theranostic agent.

Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity

This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine β-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)⁷⁻ ions, compared with that of the (Lg + PA)⁷⁻ ion, it is concluded that the –OH groups of the X-OHPA ligands participate in strong (5-11 kcal mol⁻¹) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the –OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the –OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 ± 0.2) × 10⁵ M⁻¹] is similar to the value for the PA [(3.8 ± 0.1) × 10⁵ M⁻¹]; Ka for 3-OHPA [(1.1 ± 0.3) × 10⁶ M⁻¹] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 ± 0.2) × 10⁴ M⁻¹] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand –OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.

Energetics of Lipid Binding in a Hydrophobic Protein Cavity

Hydrophobic bonding is central to many biochemical processes, such as protein folding and association. However, a complete description of the forces underlying hydrophobic interactions is lacking. The goal of this study was to evaluate the intrinsic energetic contributions of -CH(3), >CH(2), and -HC═CH- groups to protein-lipid binding. To this end, Arrhenius parameters were measured for dissociation of gaseous deprotonated ions (at the -7 charge state) of complexes of bovine β-lactoglobulin (Lg), a model lipid-binding protein, and a series of saturated, unsaturated, and branched fatty acids (FA). In the gas phase, the (Lg + FA)(7-) ions adopt one of two noninterconverting structures, which we refer to as the fast and slow dissociating components. The dissociation activation energies measured for the fast components of the (Lg + FA)(7-) ions were found to correlate linearly with the association free energies measured in aqueous solution, suggesting that the specific protein-lipid interactions are preserved in the gas phase. The average contributions that the -CH(3), >CH(2), and -HC═CH- groups make to the dissociation activation energies measured for the fast components of the (Lg + FA)(7-) ions were compared with enthalpies for the transfer of hydrocarbons from the gas phase to organic solvents. For >CH(2) groups, the interior of the cavity was found to most closely resemble the relatively polar solvents acetone and N,N-dimethylformamide, which have dielectric constants (ε) of 21 and 39, respectively. For -CH(3) groups, the solvent environment most closely resembles 1-butanol (ε = 17), although the energetic contribution is dependent on the location of the methyl group in the FA. In contrast, the solvation of -HC═CH- groups is similar to that afforded by the nonpolar solvent cyclohexane (ε = 2).

Characteristic Fluorescence Behavior of Dialkynylpyrene Derivatives in Hydrophobic Cavity of Protein

Abstract Water-soluble fluorescent molecules consisting of dialkynylpyrene skeleton with an oxyethylene unit were designed and synthesized for interacting with hydrophobic cavities of proteins. In the presence of serum albumin, the fluorescent spectra of dialkynylpyrene derivatives were remarkably changed. These behavior can be explained by monomer–excimer emission switching and twisted intramolecular charge-transfer mechanism.

Characterization of monoclonal antibodies to human protein 1/Clara cell 10 kilodalton protein.

Human protein 1/Clara cell Mr 10,000 protein consists of two identical subunits of seventy amino acid residues each. In the present study, eight clones of monoclonal antibodies against native protein 1 were prepared and their respective epitopes were immunochemically and immunohistochemically characterized using native protein 1, truncated recombinant protein 1 and synthesized peptides. Among the clones, three designated as TY-5, TY-7 and TY-8 recognized amino acid residues 7-16, residues 19-28, and residues 39-46, respectively, all of which comprise the hydrophobic cavity of protein 1, possibly associated with chemical binding function. With the exception of TY-4, the remaining clones recognized residues 61-68 which are exposed to solvent. The epitope of TY-4 remains undetermined. Proper selection and combination of clones and recombinant protein 1 may be useful for fundamental and clinical studies of protein 1.

Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography.

Water in the hydrophobic cavity of human interleukin 1beta, which was detected by NMR spectroscopy but was invisible by high resolution x-ray crystallography, has been mapped quantitatively by measurement and phasing of all of the low resolution x-ray diffraction data from a single crystal. Phases for the low resolution data were refined by iterative density modification of an initial flat solvent model outside the envelope of the atomic model. The refinement was restrained by the condition that the map of the difference between the electron density distribution in the full unit cell and that of the atomic model be flat within the envelope of the well ordered protein structure. Care was taken to avoid overfitting the diffraction data by maintaining phases for the high resolution data from the atomic model and by a resolution-dependent damping of the structure factor differences between data and model. The cavity region in the protein could accommodate up to four water molecules. The refined solvent difference map indicates that there are about two water molecules in the cavity region. This map is compatible with an atomic model of the water distribution refined by using XPLOR. About 70% of the time, there appears to be a water dimer in the central hydrophobic cavity, which is connected to the outside by two constricted channels occupied by single water molecules approximately 40% of the time on one side and approximately 10% on the other.

Directional preferences of intermolecular contacts to hydrophobic groups.

Analysis of data from the IsoStar library shows that many hydrophobic groups exhibit strikingly strong directional preferences in their intermolecular interactions. Specific directional interactions may occur because of the large quadrupole moments of many aromatic ring systems, the residual electropositive charge on most carbon-bound H atoms and the effects of polarization on soft hetero-ring atoms such as sulfur. In consequence, the binding of a hydrophobic group to a hydrophobic protein cavity is not simply a matter of matching complementary shapes. Directional preferences of nonbonded contacts to hydrophobic groups may need to be taken into account in parameterizing the next generation of protein-ligand docking programs.

Structural Volume Changes upon Photoisomerization of the Bilirubin‐Albumin Complex: A Laser‐Induced Optoacoustic Study‡

The Z-->E photoisomerization of the 1:1 complexes of human serum albumin (HSA) and several bilirubins (BR-IX alpha, -III alpha, meso-IX alpha and a mixture of -IX alpha, -III alpha and XIII alpha) affords in every case an almost negligible structural volume change (delta VR approximately 0) within detection limits (i.e. less than 2-4 cm3/mol for this isomerization with very low quantum yield) as determined by laser-induced optoacoustic spectroscopy. Based on previous model studies of photoisomerizations in aqueous environment, this negligible small change is interpreted as indicating that the part of the molecule undergoing photoisomerization is not exposed to water but is located in a hydrophobic protein cavity that shields the molecule from the aqueous medium. The BR-protein interaction within this cavity seems to be very loose in view of the small structural volume change observed. The energy difference between the Z and E isomers of the BR-HSA complexes was estimated to be less than 4 kJ/mol, probably close to zero (delta H approximately 0).

Conformational change due to reduction of cytochrome-c oxidase in lauryl maltoside: picosecond time-resolved tryptophan fluorescence studies on the native and heat modified enzyme

Detailed fluorescence studies on bovine heart cytochrome-c oxidase (CcO) has been carried out in lauryl maltoside solution. Steady-state fluorescence of the tryptophan residues of the enzyme showed that the fluorophores are embedded deep inside the hydrophobic protein cavity. Time resolved studies of tryptophan fluorescence of native and heat treated CcO have been carried out in both reduced and oxidised forms using synchronously pumped pulsed picosecond dye laser and single photon counting technique. Decay of the tryptophan fluorescence have been fitted using discrete four exponential model. Amplitude distribution of lifetimes also showed four distinct regions in the analysis of the decay profiles by maximum entropy method (MEM). The results indicate that controlled heat treatment of CcO affects the conformation of the enzyme near the active centers which makes it incapable of active proton pumping while the electron transfer property is still conserved. Reduction of the native CcO is associated with a large conformation change in lauryl maltoside near the active centers which is not observed in case of CcO encapsulated in vesicles. Reduction of the heat treated enzyme was found to have a conformation different from the reduced native CcO.