Prediction of the Three-dimensional Structure of Proteins in the Lipid Monolayer on the Basis of a-helix Bundling : The Apolipoprotein B-100 Structure

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Protein structures profoundly affect their functions. However, strategies for the prediction of protein structures, especially those with complicate intrinsic and extrinsic interactions, remain unsatisfactory. Our present study thus aimed to develop an algorithm to predict the three dimensional structure of membrane proteins on the basis of a-helix bundling. For this purpose, we have taken apolipoprotein B-100 (apoB-100) as an example. Apolipoprotein B-100 is the largest monometric molecule of human plasma proteins, plays an important role in the specific binding of low density lipoprotein (LDL) to the cellsurface receptor, and is strongly correlated with the prevalence of atherosclerosis. Because of its extraordinary size and insoluble nature, its three dimensional structure has been difficult to deduce. In this study, an algorithm was developed based on the consideration that sites of a-helices with higher hydrophilicity are more likely to combine with each other and form bundles in the nonpolar environment. Two cylinder models were established and the interactive force (F) between them was calculated according to hydrophobicity and the charge on the ammo acids. Consequently, a series of values of F ranging from 383 to 7315 was obtained. Extremely high F values, representing areas prone to form bundles, were chosen and analyzed. When regions in close proximity to each other were combined, 5 candidates for a-helix bundles were identified. These regions matched well with the lipid-binding motifs of apoB-100 as reported by others. Multiple helix structures in apolipoprotein A-I were also successfully identified by this program. Thus, the established algorithm is useful in predicting the higher-order structure of apolipoproteins.
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Prediction of the Three-dimensional Structure of Proteins in the Lipid Monolayer on the Basis of a-helix Bundling : The Apolipoprotein B-100 Structure

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