Amino Acids Thesis

Amino Acids Thesis-41
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.

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.

Our group has been interested in amino acid similarity in the context of peptides binding to proteins.

Given binding data for several peptide ligands, the challenge is to predict the affinity of any peptide of arbitrary sequence.

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.

For example, the commonly used PAM and BLOSUM matrices [1, 2] have been built based on the frequencies of amino acid substitutions observed in aligned protein sequences.

This measure, routinely used in programs such as BLAST [3], represents both evolutionary and functional similarity between amino acids.

Our specific interest is in peptide binding to proteins involved in antigen processing and presentation, such as the TAP transporter [4, 5] and MHC molecules.

In recent large-scale benchmark studies, the best performing prediction method for peptide: MHC class I binding is the Net MHC artificial neural network, outperforming linear methods such as SMM [6, 7].

Given that many proteins known to signal amino acid sufficiency to m TORC1, including the Rag GTPases, localize to the lysosome and that intralysosomal amino acid accumulation is necessary for m TORC1 activation, we began our search for potential direct amino acid sensors at the lysosomal membrane.

We identify SLC38A9, an uncharacterized protein with homology to amino acid transporters, as a lysosomal transmembrane protein.

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