Hassan Al-Ali Merheby1, Diana Azzam2, Sawsan Khuri3 and Hassan Khachfe1,2
1Computational Sciences and Bioinformatics Unit and 2Department of Physiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon. 3The Dr. John T. Macdonald Foundation Center for Medical Genetics, University of Miami School of Medicine, Florida, USA.

Atherosclerosis is a condition of the arteries caused by the build up of fatty substances, cholesterol, and other deposits along the artery walls. The accumulation of this plaque can cause a variety of heart problems and strokes. Systemic inflammatory mechanisms may underlie the pathogenesis of atherosclerosis. However, no structural study has yet linked any of the various risk factors with these inflammatory mechanisms. Background: Small low-density lipoprotein (LDL) is a major risk factor for atherosclerosis. Apolipoprotein B-100 (apoB) is the sole protein component of LDL, but its large size (4536 amino acids) and the limitation of current experimental techniques require that it be studied in pieces corresponding to its structural domains. Low-resolution biophysical techniques showed that the N-terminal region of apoB corresponds to a particular lipid-free domain of LDL. This work reports the computational structural analysis of B17, the N-terminal 17% of the apoB sequence (residues 1-782).
Methods and Results: The structure of B17 was modeled using HOMOLOGY in Insight II, based on the crystal structure of lipovitellin (LV), a fish homologue. The original model had six “free” cysteine pairs, which form six S-S bridges in the native structure. In our model, four cystein residues had their sulfur atoms < 5 Å apart, forming 4 S-S bridges, and the sulfurs of the remaining 2 pairs were < 10 Å apart. A constrained energy minimization (using DISCOVER with CVFF ForceField) was carried out to bring the sulfurs within 5 Å of distance, allowing for two more disulfide bridges to form. Residues 705-782 align with a region in LV that has no electron density in the crystal structure. This part was therefore modeled separately, whereby the structure was predicted using the Chou-Fasman algorithm integrated within the GCG Wisconsin Package. The structure was then attached to the parent molecule keeping the energy of the model at an overall minimum. The backbone of the structure was fixed during a short dynamics simulation, then the molecule was subjected to a final energy minimization in order to optimize interactions between side chains.
All structural motifs in this model correlate well with reported data from other biophysical probes. The C-terminus of B17 shows considerable homology with a conserved region in the constant domain of the T-cell receptor – a protein that is necessarily present during inflammation. It also contains several residues that are essential in the interfacial connectivity with the variable domain, which binds to the different antigens specific to each inflammatory pathway. This therefore establishes a potential link between LDL and the inflammatory state correlated with atherosclerosis.