Conformation of myelin basic protein bound to phosphatidylinositol membrane characterized by vacuum‐ultraviolet circular‐dichroism spectroscopy and molecular‐dynamics simulations

Abstract

The 18.5‐kDa isoform of myelin basic protein (MBP) interacts with the membrane surface of the myelin sheath to construct its compact multilamellar structure. This study characterized the conformation of MBP in the membrane by measuring the vacuum‐ultraviolet circular‐dichroism (VUVCD) spectra of MBP in the bilayer liposome comprising the following essential lipid constituents of the myelin sheath: phosphatidylinositol (PI), phosphatidylinositol‐4‐phosphate (PIP), and phosphatidylinositol‐4,5‐bisphosphate (PIP2). The spectra of MBP exhibited the characteristic peaks of the helix structure in the presence of PI liposome, and the intensity increased markedly in the presence of PIP and PIP2 liposomes to show an isodichroic point. This suggests that the amount of the membrane‐bound conformation of MBP enhanced due to the increased number of negative net charges on the liposome surfaces. Secondary‐structure analysis revealed that MBP in the membrane comprised approximately 40% helix contents and eight helix segments. Molecular‐dynamics (MD) simulations of the eight segments were conducted for 250 ns in the presence of PI membrane, which predicted two amphiphilic and three nonamphiphilic helices as the membrane‐interaction sites. Further analysis of the distances of the amino‐acid residues in each segment from the phosphate group suggested that the nonamphiphilic helices interact with the membrane surface electrostatically, while the amphiphilic ones invade the inside of the membrane to produce electrostatic and hydrophobic interactions. These results show that MBP can interact with the PI membrane via amphiphilic and nonamphiphilic helices under the control of a delicate balance between electrostatic and hydrophobic interactions.

Characterization of membrane‐interaction mechanisms of proteins using vacuum‐ultraviolet circular dichroism spectroscopy

“…This figure is a modified version of the reference. 21 contrast, the hydrophobic V85, F88, and F89 (D-helix), L149, and F153 (G-helix) residues were inside the PI membranes. These simulations indicate that the A-, B-, and F-helical regions interact electrostatically with the surface of PI membranes.…”

“…This figure is a modified version of the reference. 21 L/P = 0 to 26, as shown in Figure 7. The M2 spectrum, in the absence of liposomes, exhibited the characteristic peaks of an unordered structure.…”

“…The accuracy of this prediction method was 74.9% for 30 reference soluble proteins and 73% for 15 integral membrane proteins. 21 As shown in Figure 2, six helical regions were predicted in the PI state and were denoted as the A-, B-, C-, D-, E-, and F-helices. For comparison, the positions of α-helices and β-strands in the native state predicted by the VUVCD-NN method and those estimated from the X-ray data (PDBID:3kq0) 30 were also described.…”

“…This figure is a modified version of the reference. 21 F I G U R E 3 Mean hydrophobic moments and net charges of A-, B-, C-, D-, E-, and F-helices of AGP in the PI state. is shown in Figure 5.…”

A novel gyrase inhibitor from toxin–antitoxin system expressed by Staphylococcus aureus

“…Hence, although there are some limitations on the predictive accuracy compared to the current sequence-based predictions, the position of the a-helical and b-strand segments were estimated again by combining the secondary structure data from VUVCD with neural network algorithm (VUVCD-NN method), in which the experimental parameters can be input into the prediction process of NN to regulate the number of a-helix and b-strand amino acid residues and the number of a-helix and bstrand segments that identify with the experimental data [27]. This combination method has been used for the structural analysis of several unknown proteins in native and other states [28][29][30]. This analysis showed that the 22nd-32nd residues and the 18th-20th residues of TsbT formed an a-helix and a b-strand structure respectively (Fig.…”