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Computational Analysis of the Mechanism of the Ubiquitin Conjugating Enzyme Ubc13

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case we examined the sodiumdependent glucose co-transporter of Vibrio parahaemolyticus (vSGLT) which mediates galactose transport into the cytoplasm of vibrio parahaemolyticus bacteria. According literature, kinetic of cotransporter has between 5… Click to show full abstract

case we examined the sodiumdependent glucose co-transporter of Vibrio parahaemolyticus (vSGLT) which mediates galactose transport into the cytoplasm of vibrio parahaemolyticus bacteria. According literature, kinetic of cotransporter has between 5 and 6 states or conformations, but in this case the unbinding of substrates is studied by inward-facing conformation, also known as state release model of co-transporter. We performed a computational study to analyze the global movements of a vSGLT transporter, and we compared our computational results with those found in previous experimental reports. Normal modes analysis with an Elastic Network Model (ENM) was used to explore the changes in global movements between vSGLT in the presence or absence of the ions they transport (NaĆ¾, galactose). ENM has been shown to be a useful computational tool for predicting the dynamics of membrane proteins in many applications. The lowest normal modes generated by the ENM provide valuable insight into the global dynamics of biomolecules that are relevant to their function.

Keywords: analysis mechanism; conjugating enzyme; analysis; computational analysis; ubiquitin conjugating; mechanism ubiquitin

Journal Title: Biophysical Journal
Year Published: 2017

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