MOLECULAR DYNAMICS STUDY OF CYTOCHROME C – LIPID COMPLEXES

The interactions between a mitochondrial hemoprotein cytochrome c (cyt c) and the model lipid membranes composed of zwitterionic lipid phosphatidylcholine (PC) and anionic lipids phosphatidylglycerol (PG), phosphatidylserine (PS) or cardiolipin (CL) were studied using the method of molecular dynamics. It was found that cyt c structure remains virtually unchanged in the protein complexes with PC/PG or PC/PS bilayers. In turn, protein binding to PC/CL bilayer is followed by the rise in cyt c radius of gyration and root-mean-square fluctuations. The magnitude of these changes was demonstrated to increase with the anionic lipid content. The revealed effect was interpreted in terms of the partial unfolding of polypeptide chain in the region Ala15-Leu32, widening of the heme crevice and enhancement of the conformational fluctuations in the region Pro76-Asp93 upon increasing the CL molar fraction from 5 to 25%. The results obtained seem to be of utmost importance in the context of amyloidogenic propensity of cyt c

SPECTRAL BEHAVIOR OF INDICATOR DYES IN THE MODEL PROTEIN – LIPID SYSTEMS

The protolytic and partition equilibria of the indicator dyes in the model lipid and protein-lipid systems have been analyzed. A methodological approach has been developed allowing the partition coefficients of the protonated and deprotonated dye forms to be derived from the spectrophotometric measurements. The partitioning of the indicator dye bromothymol blue into the model bilayer membranes composed of phosphatidylcholine and cardiolipin (9:1, mol:mol) has been examined. The partition coefficient of the protonated dye species into a lipid phase has been found to be 5 orders of magnitude higher than that of the deprotonated dye form. This effect has been interpreted in terms of the differences in the charge distribution over the protonated and deprotonated dye ions, preventing the hydrophobic dye-lipid interactions in the latter case. The reduction of the bromothymol blue partitioning into lipid bilayer in the presence of hemoglobin has been attributed to the protein-induced changes in the structure and physicochemical characteristics of the interfacial membrane region. In the practical aspect, the obtained findings may prove of significance in the design of hemosome-based blood substitutes and elucidating the role of hemoglobin in the molecular etiology of the amyloid disorders, particularly, Alzheimer's disease

AURAMINE O AS POTENTIAL AMYLOID MARKER: FLUORESCENCE AND MOLECULAR DOCKING STUDIES

The applicability of Auramine O to the detection and characterization of lysozyme and serum albumin amyloid fibrils has been assessed using the fluorimetric titration and molecular docking. The parameters of the dye binding to native and fibrillar proteins were estimated in terms of the Langmuir adsorption model. It was found that Auramine O displays the high affinity for amyloid fibrils, being of the same order of magnitude as that of the classical amyloid markers. The dye also showed greater fluorescence response to lysozyme fibrils and lower sensitivity to the native protein, than Thioflavin T. Furthermore, unlike Thioflavin T, Auramine O was able to detect the morphological differences between lysozyme and albumin fibrils due to the shifts in the position of the emission maxima of the fibril-incorporated fluorophore. The molecular docking studies revealed that Auramine O and Thioflavin T form the most stable complexes with the G54_L56/S60_W62 groove of lysozyme fibrils, running parallel to the fibril axis. The results obtained suggest the contribution of both hydrophobic and electrostatic interactions to the stabilization of the dye complexes with amyloid fibrils

THIOFLAVIN T BINDING TO THE MODEL FIBRILS OF LYSOZYME: THE EFFECTS OF FIBRIL TWISTING

Amyloid fibrils are highly ordered insoluble protein aggregates that are involved in molecular etiology of a number of severe disorders, including Alzheimer's, Parkinson’s and prion’s diseases, some types of systemic amyloidosis, etc. One of the most effective approaches to detecting the amyloid fibrils is based on monitoring the spectral behavior of specific fluorescent dye Thioflavin T (ThT). Using the molecular docking and molecular dynamics tools, such as PatchDock, FireDock, CreateFibril and GROMACS, the model of twisted K-peptide fibril that supposedly represent the core region of lysozyme amyloid fibrils, has been constructed and analyzed. The effect of fibril twisting angle on the binding characteristics of ThT has been evaluated. The results obtained strongly suggest that ThT specificity for the twisted ribbon fibril polymorphs is primarily determined by the curvature effects rather than amino acid composition of fibril grooveswhich accomodate ThT molecule

EFFECT OF AMYLOID FIBRILS ON ELECTROKINETIC PROPERTIES OF LIPID VESICLES

The influence of the lysozyme and serum albumin in their native and amyloid forms on the electrokinetic behavior of the negatively charged uni- and multilamellar liposomes from the zwitterionic lipid phosphatidylcholine and anionic lipid cardiolipin has been investigated using the microelectrophoresis technique. The zeta - potential, the surface electrostatic potential and surface charge density of the lipid vesicles have been determined upon varying the lipid-to-protein molar ratio. The complex dependencies of the electrophoretic mobility on the protein concentration and reversal of the surface charge observed for the multilamellar vesicles have been explained by the multilayer protein adsorption on the liposomal surface. It has been found that the native and fibrillar proteins differ in their ability to modify the charge state of the model membranes

NOVEL CYANINE DYES AS POTENTIAL AMYLOID PROBES: A FLUORESCENCE STUDY

The applicability of the novel heptamethine cyanine dyes AK7-5 and AK7-6 to the detection and characterization of one-dimensional protein aggregates (amyloid fibrils) associated with numerous pathologies has been evaluated using the method of fluorescence spectroscopy. It was found that both the monomeric and aggregated forms of these dyes can bind to amyloidogenic protein lysozyme, but the concomitant changes in the electronic structure of H-aggregates render them capable of fluorescing. The growth of the hypsochromic bands with negligible changes of the monomeric peaks induced by the native protein and the opposite effects induced by the lysozyme fibrils suggest that the native lysozyme has more binding sites for the dye aggregates than fibrillar protein, while the fibril grooves represent specific binding site for the dyes monomers. The observed spectral behavior of the cyanine dyes, viz. significant distinctions in the fluorescence responses produced by the monomeric and fibrillar forms of lysozyme, suggest the possibility of recruiting these compounds as fluorescent amyloid markers along with the classical amyloid marker Thioflavin T

A novel phosphonium dye for amyloid fibril detection

Молекулярная биофизик

A novel phosphonium dye for amyloid fibril detection

Молекулярная биофизик