Paper Citing NAMD - Abstract
Joshi, Manali; Ebalunode, Jerry Osagie; Briggs, James M.
Computational insights into the interaction of the anthrax lethal factor with the N-terminal region of its substrates
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:323-335, MAY 1 2009
The anthrax lethal factor is a zinc metalloprotease toxin secreted by Bacillus anthracis which cleaves at the N-terminal region of six mitogen activated protein kinase kinases (MEKs) in the cell. Additionally, it is known to cleave a nine residue peptide "LF10," 50-fold more efficiently than nine residues of MEK1. There is very little sequence similarity between the MEK N-termini, thus, it is unclear how the lethal factor can accommodate and cleave the diverse N-termini of the MEKs and whether there is a hierarchy in this interaction, as there is between LF10 and MEK1. To investigate this problem, we carried out multiple molecular dynamics simulations of the lethal factor with nine residues of each of the substrates. Our simulations reveal that like LF10, certain MEK substrates have residue compositions that favor beta-sheet formation with the lethal factor over others. The formation of this secondary structure maintains a catalytic conformation. Binding energetics using the MM-PBSA method was used to rank-order the substrates for their affinity to LF (K(M)). On the basis of the results, we conclude that the LF does not equally accommodate the MEK substrates and further predict that there will be differences between rates of cleavage among the nine residue MEK N-termini.
