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Full-Text Articles in Physical Sciences and Mathematics
Class A Sortases: Structures And Alternative Substrate Binding And Cleavage, Brandon Vogel
Class A Sortases: Structures And Alternative Substrate Binding And Cleavage, Brandon Vogel
WWU Graduate School Collection
Sortases, consisting of classes A-F, are cysteine transpeptidases found in the cell wall of Gram-positive bacteria. They play a crucial role in ligating proteins to the cell wall that are responsible for cell adhesion, immune evasion, host cell invasion, and nutrient acquisition through a transpeptidation reaction. Consequently, they are an attractive therapeutic target. Class A sortases are also utilized in protein engineering applications such as sortase-mediated ligations and sortagging. Despite extensive research in the past two decades, gaps persist in understanding how class A sortases recognize their substrates, primarily due to a lack of structural information on sortases non-covalently bound …
Exploring Biochemical Mechanisms With Hybrid Quantum Mechanics/Molecular Mechanics And Enhanced Sampling Methods, Edwin Enciso
Exploring Biochemical Mechanisms With Hybrid Quantum Mechanics/Molecular Mechanics And Enhanced Sampling Methods, Edwin Enciso
WWU Graduate School Collection
In the field of molecular dynamics (MD), a long-standing issue is the time frame required in order to fully observe a chemical reaction. Enhanced sampling methods have been the primary way of overcoming this issue for the past 40 years. In this experiment our goal was to combine new and existing sampling methods in order to create an efficient and accurate way of retrieving kinetics data from simulations. In order to do this, we examined two test cases: the enzymes chorismate mutase and cytosine deaminase. We did this using hybrid quantum mechanics/molecular mechanics simulations coupled with enhanced sampling methods. The …
Progress Towards The Substrate-Bound Structure Of Streptococcus Pneumoniae Sortase A, Nicholas M. Horvath
Progress Towards The Substrate-Bound Structure Of Streptococcus Pneumoniae Sortase A, Nicholas M. Horvath
WWU Graduate School Collection
Sortases are cysteine transpeptidases found primarily on the cell surface of Gram-positive bacteria. Sortase-mediated ligations have become an attractive option for protein modification chemistry, enabling the synthesis of a wide range of non-natural polypeptide derivatives. Attempts at understanding how these enzymes recognize and bind substrates are integral to furthering their usefulness in protein engineering and, potentially, treatment of bacterial diseases. However, the variable substrate specificity and activity between homologs of these enzymes is not yet fully understood. Of specific interest to us is sortase A from Streptococcus pneumoniae (SrtApneu), as it demonstrates a broad substrate tolerance not …