Computers and Proteins: Using Molecular Dynamics to probe the Catalytic Mechanisms of Streptococcus Pyogenes and Listeria Monocytogenes Class A Sortases
Research Mentor(s)
Jeanine Amacher
Description
Sortases are an enzyme family found in gram-positive bacteria that are responsible for ligating proteins responsible for cell adhesion, immune evasion, host cell invasion, and nutrient acquisition to the cell wall through a trans peptide reaction. Class A sortases accomplish this task by recognizing cell wall sorting signal, LPXTG, and cleaving the amide bond between the Thr and Gly residues at which point a glycine nucleophile will bind to the cleaved LPXT- side of the reaction. This mechanism is the subject of considerable interest as a target for therapeutic intervention and as a tool for protein engineering, where sortases have enabled sortase‑mediated ligation or sortagging strategies. Our work solved the first structure of crystalized Streptococcus pyogenes class A sortases with a non-covalent peptide bound including one with a biologically relevant lipid II peptidoglycan precursor. Here we present that work and molecular dynamics simulations ran in an NVT ensemble using those structures and previously known crystal structures in order to glean information about binding site interactions and the interactions of the enzyme with lipid II. We also present preliminary results of MD simulations that were run on the Listeria monocytogenes class A sortases based on a previously made crystal structure.
Document Type
Event
Start Date
May 2022
End Date
May 2022
Location
Carver Gym (Bellingham, Wash.)
Department
CSE - Chemistry
Genre/Form
student projects; posters
Type
Image
Rights
Copying of this document in whole or in part is allowable only for scholarly purposes. It is understood, however, that any copying or publication of this document for commercial purposes, or for financial gain, shall not be allowed without the author’s written permission.
Language
English
Format
application/pdf
Computers and Proteins: Using Molecular Dynamics to probe the Catalytic Mechanisms of Streptococcus Pyogenes and Listeria Monocytogenes Class A Sortases
Carver Gym (Bellingham, Wash.)
Sortases are an enzyme family found in gram-positive bacteria that are responsible for ligating proteins responsible for cell adhesion, immune evasion, host cell invasion, and nutrient acquisition to the cell wall through a trans peptide reaction. Class A sortases accomplish this task by recognizing cell wall sorting signal, LPXTG, and cleaving the amide bond between the Thr and Gly residues at which point a glycine nucleophile will bind to the cleaved LPXT- side of the reaction. This mechanism is the subject of considerable interest as a target for therapeutic intervention and as a tool for protein engineering, where sortases have enabled sortase‑mediated ligation or sortagging strategies. Our work solved the first structure of crystalized Streptococcus pyogenes class A sortases with a non-covalent peptide bound including one with a biologically relevant lipid II peptidoglycan precursor. Here we present that work and molecular dynamics simulations ran in an NVT ensemble using those structures and previously known crystal structures in order to glean information about binding site interactions and the interactions of the enzyme with lipid II. We also present preliminary results of MD simulations that were run on the Listeria monocytogenes class A sortases based on a previously made crystal structure.