The N-terminal domain of apolipoprotein B-100: structural characterization by homology modeling.
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.


CONCLUSIONS
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.
Al-Ali
Hassan
H
Computational Sciences and Bioinformatics Laboratory, American University of Beirut, Beirut, Lebanon. bioinfo@aub.edu.lb <bioinfo@aub.edu.lb>
Khachfe
Hassan M
HM
D000595:Amino Acid Sequence; D053299:Apolipoprotein B-100 / Q000737:chemistry* / Q000235:genetics; D001055:Apolipoproteins B / Q000737:chemistry / Q000235:genetics; D003198:Computer Simulation; D004220:Disulfides / Q000737:chemistry; D004527:Egg Proteins / Q000737:chemistry; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D040681:Structural Homology, Protein
D053299:Apolipoprotein B-100; D001055:Apolipoproteins B; D004220:Disulfides; D004527:Egg Proteins; C416027:apolipoprotein b-17; C001549:lipovitellin