Computational insights into the interaction of the anthrax lethal factor with the N-terminal region of its substrates
Manali Joshi1, Jerry Osagie Ebalunode, James M Briggs
1Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA.
Abstract:
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.
Insights
Anthrax lethal factor (LF) cleaves specific protein targets. Molecular dynamics simulations reveal substrate-dependent interactions, suggesting varied cleavage rates for mitogen-activated protein kinase kinases (MEKs).
Area of Science:
- Biochemistry
- Molecular Biology
- Toxicology
Background:
- Bacillus anthracis secretes anthrax lethal factor (LF), a zinc metalloprotease.
- LF cleaves mitogen-activated protein kinase kinases (MEKs) at their N-terminal regions.
- LF exhibits higher cleavage efficiency for the peptide LF10 compared to MEK1 N-termini.
Purpose of the Study:
- To investigate how LF accommodates and cleaves diverse MEK N-termini.
- To determine if a hierarchy exists in LF's interaction with MEK substrates.
- To explore the structural basis for differential substrate recognition by LF.
Main Methods:
- Multiple molecular dynamics simulations were performed.
- Simulations involved LF and nine-residue peptides of each MEK substrate.
- Binding energetics were calculated using the MM-PBSA method to determine substrate affinity (K(M)).
Main Results:
- Simulations showed that MEK substrates, similar to LF10, form beta-sheet structures with LF.
- Substrate residue composition influences the favorability of beta-sheet formation, maintaining catalytic conformation.
- MM-PBSA analysis allowed for the ranking of MEK substrates based on their affinity to LF.
Conclusions:
- LF does not equally accommodate all MEK substrates.
- Differences in binding affinity and structural interactions are predicted.
- Varied cleavage rates among the nine-residue MEK N-termini are anticipated.
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