Paper Citing NAMD - Abstract
Chumningan, Sansai; Pornputtapong, Natapol; Laoteng, Kobkul; Cheevadhanarak, Supapon; Thammarongtham, Chinae
3D Structure Modeling of a Transmembrane Protein, Fatty Acid Elongase
COMPUTATIONAL SYSTEMS-BIOLOGY AND BIOINFORMATICS, 115:36-45, 2010
Fatty acid elongase is an enzyme responsible for fatty acid chain elongation, a key step in synthesis of long chain fatty acids, including polyunsaturated fatty acids (PUFAs). Currently, the increasing demand has raised the interest in obtaining these PUFAs from alternative sources, e.g. filamentous fungi that are more economical and sustainable. To date, many research on primary structures of fatty acid elongases ELO family, including fugal elongases, revealed several conserved motifs. However, molecular mechanism for their functions is still unclear. In addition to experimental study, computational analysis of elongase structures may provide more insight into their substrate specificities and mechanisms of fatty acid chain elongation. Thus, this work proposes a 3D structural model of elongase of Mortierella alpina (BAF97073). This fungal elongase has been reported to be a PUFA-specific elongation enzyme. The model was built by an ab initio membrane-modeling application using ROSETTA 3.1, and was then refined by molecular dynamic simulation. The 7-transmembrane helices of the constructed model folds into an anti-parallel configuration and embeds in the lipid bilayer. The model reveals that all four conserved signature motifs of fatty acid elongase enzymes are located within the juxta-cytosolic transmembrane helix regions. This work also suggests a modeling strategy of this elongase structural model that can be applied to model other transmembrane proteins.
