Paper Citing NAMD - Abstract
Lin, Ying-Wu; Ying, Tian-Lei; Liao, Li-Fu
Molecular modeling and dynamics simulation of a histidine-tagged cytochrome b (5)
JOURNAL OF MOLECULAR MODELING, 17:971-978, MAY 2011
Although an affinity tag such as six consecutive histidines, (His)(6)-tag, has been widely used to obtain high quantity of recombinant proteins, little is known about its influences on heme proteins for lack of structural information. When (His)(6)-tag was introduced to the N-terminus of a small heme protein, cytochrome b (5), experimental results showed the resultant protein, (His)(6)-cyt b (5), has similar property and function to that of isolated cyt b (5). To provide structural information for this observation, we herein performed a structural prediction of (His)(6)-cyt b (5) by molecular modeling in combination with molecular dynamics simulation. The predicted structure, as assessed by a series of criteria with good quality, reveals that the (His)(6)-tag adopts a helical conformation and packs against the hydrophobic core 2 of cyt b (5) through salt bridges, hydrogen bonding and hydrophobic interactions. The heme group, with the axial His ligands slightly rotated, was found to have similar conformation as in isolated cyt b (5), which indicates that the N-terminal (His)(6)-tag does not alter the heme active site, resulting in similar dynamics properties for core 1. This study provides valuable information of interactions between (His)(6)-tag and the rest of the protein, aiding in rational design and application of functional His-tagged proteins.
