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Using Molecular Dynamics Simulations to Evaluate Ligand Binding of L, L‐diaminopimelate Aminotransferase, an Enzyme Involved in Protein and Peptidoglycan Biosynthesis
Author(s) -
Adams Lily,
Babbitt Gregory,
Hudson André
Publication year - 2019
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2019.33.1_supplement.642.1
Subject(s) - peptidoglycan , enzyme , biochemistry , mutagenesis , computational biology , alanine scanning , gene , biology , chemistry , mutation
A common protocol, Site Directed Mutagenesis (SDM) experiments facilitate the alterations to a gene sequence to study downstream effects on its product. In addition, inhibitor/antagonistic studies investigate the potential of common ligands to inhibit or inactivate enzymes. Both approaches have seen minor updates in recent years, but methods to streamline these processes are highly desired. For example, a rate‐limiting step in SDM lies in choosing key nucleotides that will subsequently affect enzymatic activity. To facilitate SDM studies and subsequent analyses to save time and resources, a comprehensive and comparative molecular dynamics (MD) software package – DROIDS ( D etecting R elative O utlier I mpacts in D ynamic S imulations) 2.0 – has been applied. Here, we use a novel aminotransferase, L, L‐diaminopimelate aminotransferase (DapL) as a test to propose a method of augmenting SDM and related experiments using MD simulations. DapL is involved in peptidoglycan and protein metabolism. As such, the essentiality of the dapL gene in eubacteria is currently a key question yet to be answered. Information to supplement knowledge of this enzyme will aid in evaluating its potential as a narrow spectrum antibiotic target. We have used DROIDS 2.0 to investigate the impact of different point mutations and putative antagonistic ligands on the activity of the DapL enzyme, identifying those that most significantly impact its dynamic behavior. In addition, the DROIDS 2.0 protocol was taken further to predict mutations that lessen binding affinity to chosen inhibitors, which may have the potential to guide the rational design of inhibitory ligands. Comparative dynamics in DROIDS 2.0 can be visualized (Figure 1) in a variety of statistical plots, colored structures, and colored movies of protein movement, enhancing interpretation and communication to a broad audience. Support or Funding Information National Institutes of Health (NIH) award (R15GM120653) This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .