I am working with Annette Nti on this project and this is what we are working on: Glucosyltransferases is an enzyme like protein that aids in transferring glucose within the body. Amino acids are the building blocks of proteins; they are organic molecules containing an amino group as well as a carboxyl group. The amino acids that serve as building blocks of proteins are alpha amino acids, which have both the amino and carboxyl group linked to the same carbon atom (Alberts G-2). All 20 amino acids have the same amino and carboxyl group and differ only in their side chains or residuals (or R-group). Proteins are the working molecules of the cell; they catalyze a wide variety of chemical reactions, supplies structural rigidity, regulate membrane permeability, and perform a wide range of other tasks (Darnell 44). Proteins are also called polypeptide chains because the amino acids are held together by peptide bonds. Each type of protein has a three- dimensional structure, which is a result of the order of the amino acids in its chain. The final folded structure is called a conformation. The conformation of a polypeptide chain is usually the one in which the free energy is minimized (Darnell 134). Protein folding in a living cell is usually assisted by special proteins called molecular chaperones. Molecular chaperones bind to incompletely folded polypeptide chains and help them progress in the most energy efficient folding pathway. Although the 3-D structure of all proteins are unique, two standard folding patterns are found in parts of them. The first folding pattern that was discovered is the alpha helix and the second folding pattern is known as the beta sheet. These two patterns are common because they result from the hydrogen bonding between the carboxyl and amino groups in the polypeptide "backbone" (Not including the R-group). An alpha helix is formed when a polypeptide chain twists around itself to form a cylinder. Beta sheets are formed when polypeptide chains are parallel to one another or when a single polypeptide chain folds back and forth on itself (Darnell 136).
Some work in the area of UDP binding has been done including: work in multivariate analysis, the production of dendrograms using descriptors of the amino acid sequences that make up proteins. The descriptors are based on the characteristics of glucosyltransferases. Glucosyltransferases are proteins that act as enzymes and transfer sugar throughout cell. Graph theory has been used to model thirteen glucosyltransferases, eleven of which work on flavonoids and two which do not. Flavonoids are a large group of chemicals which are found in vascular plants. Glucosyltransferases accept UDP glucose from flavonoids at a particular site on protein called the PSPG (Post Secondary Product Glucosyltransferase) box. The graphs used in previous work are based on output from an online protein structure predictor. The goal of the project was to use an artificial neural network to find a pattern in the graphical invariants that distinguishes the glucosyltransferases that work on flavonoids from the ones that do not work on flavonoids.
In the future we would like to be able to characterize some properties of proteins using graph theory and graphical invariants. More work still needs to be done concerning the neural network and also with being better able to characterize protein with graphical invariants and descriptors.
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