Amino Acids Thesis

SLC38A9 reconstituted in proteoliposomes transports arginine, an abundant amino acid in the lysosome and necessary for m TORC1 pathway activity.

These results place SLC38A9 between amino acids and the Rag GTPases and are consistent with the notion that amino acids are sensed at the lysosome.

Our aim is to quantify this measure of similarity to improve peptide: MHC binding prediction methods.

This should help compensate for holes and bias in the sequence space coverage of existing peptide binding datasets.

However, PMBEC differs markedly from existing matrices in cases where residue substitution involves a reversal of electrostatic charge.

To demonstrate its usefulness, we have developed a new peptide: MHC class I binding prediction method, using the matrix as a Bayesian prior.We show that the new method can compensate for missing information on specific residues in the training data.We also carried out a large-scale benchmark, and its results indicate that prediction performance of the new method is comparable to that of the best neural network based approaches for peptide: MHC class I binding.A software implementation of the method is available at: Amino acid similarity matrices define a quantitative measure of likeness between each of the 20 canonical amino acids. The Rags are unusual GTPases in that they function as obligate heterodimers, which consist of Rag A or B bound to Rag C or D. The Rag GTPases interact with m TORC1 and signal amino acid sufficiency by promoting the translocation of m TORC1 to the lysosomal surface, its site of activation.They are utilized throughout computational biology in areas such as phylogenetics, protein structure modeling, and prediction of protein ligand interactions.Depending on the application, different measures of similarity are appropriate.We show that Rag C/D is a key regulator of the interaction of m TORC1 with the Rag heterodimer and that, unexpectedly, Rag C/D must be GDP-bound for the interaction to occur.We identify FLCN and its binding partners, FNIP1/2, as Rag-interacting proteins with GTPase activating activity for Rag C/D, but not Rag A/B.

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