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Background: Apolipoprotein B-100 (apo B-100) stands as one of the largest proteins in humans. Its large size of 4536 amino acids hampers the production of X-ray diffraction quality crystals and hinders in-solution NMR analysis, and thus necessitates a domain-based approach for the structural characterization of the multi-domain full-length apo B. Results: The structure of apo B-17 (the N-terminal 17% of apolipoprotein B-100) was predicted by homology modeling based on the structure of the N-terminal domain of lipovitellin (LV), a protein that shares not only sequence similarity with B17, but also a functional aspect of lipid binding and transport. The model structure was first induced to accommodate the six disulfide bonds found in that region, and then optimized using simulated annealing. Conclusion: The content of secondary structural elements in this model structure correlates well with the reported data from other biophysical probes. The overall topology of the model conforms with the structural outline corresponding to the apo B-17 domain as seen in the EM representation of the complete LDL structure. Background Atherosclerosis is a complex disease that has been linked to many risk factors, including hyperlipidemia, dyslipidemia, high blood pressure, and endothelial dysfunction [1]. Oxidative modification to the small low-density lipoprotein (LDL) has been dubbed the central event that initiates and propagates coronary artery diseases [2,3], and therefore, LDL is considered a major risk factor for atherosclerosis [4]. It was also shown that systemic inflammatory mechanisms may underlie the pathogenesis of atherosclerosis [5-7]. However, the specific structural interactions implicated in these mechanisms have not yet been elucidated. Apolipoprotein B-100 (apo B) is the sole protein component of LDL [8]; however, its large size (4536 a.a.) and the limitation of current experimental techniques require that the structures of its multiple domains be analyzed separately [9,10]. Biochemical [10], calorimetric [11], computational [12-15], and spectroscopic [16] approaches were used to probe the domain arrangement and characterization of the protein, but no molecular structure has ever been assigned to any of the different domains. These techniques, however, helped in the understanding of the overall arrangement of apo B on the LDL particle and the interactions that the various secondary structures have with both the lipid and aqueous phases, and in the ability Published: 22 July 2007 BMC Biochemistry 2007, 8:12 doi:10.1186/1471-2091-8-12 Received: 9 October 2006 Accepted: 22 July 2007 This article is available from: http://www.biomedcentral.com/1471-2091/8/12 © 2007 Al-Ali and Khachfe; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.