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Protein Interaction Graphs

Graphs are discrete structures consisting of vertices and edges that connect these vertices. There are different kinds of graphs, depending on whether edges have directions, whether multiple edges can connect the same pair of vertices, and whether loops are allowed. Problems in almost every conceivable discipline can be solved using graph models.

A protein interaction in a living cell occurs when two or more proteins in that cell bind to perform a biological function. Because protein interactions are crucial for most biological functions, many scientists work on discovering new proteins and understanding interactions between proteins. Protein interactions within a cell can be modeled using a protein interaction graph (also called a protein–protein interaction network), an undirected graph in which each protein is represented by a vertex, with an edge connecting the vertices representing each pair of proteins that interact. It is a challenging problem to determine genuine protein interactions in a cell, as experiments often produce false positives, which conclude that two proteins interact when they really do not. Protein interaction graphs can be used to deduce important biological information, such as by identifying the most important proteins for various functions and the functionality of newly discovered proteins.

Because there are thousands of different proteins in a typical cell, the protein interaction graph of a cell is extremely large and complex. For example, yeast cells have more than 6,000 proteins, and more than 80,000 interactions between them are known, and human cells have more than 100,000 proteins, with perhaps as many as 1,000,000 interactions between them. Additional vertices and edges are added to a protein interaction graph when new proteins and interactions between proteins are discovered. Because of the complexity of protein interaction graphs, they are often split into smaller graphs called modules that represent groups of proteins that are involved in a particular function of a cell. The Figure illustrates a module of the protein interaction graph, comprising the complex of proteins that degrade RNA in human cells.

WHO EATS THE GRAIN?

Do we harvest our fields to feed livestock/poultry or should we use the grain we grow directly for human consumption? Understanding the complexities of this question is important as we face the challenge of feeding an increasingly hungry world.

 

Protein is an essential component of the diet. However, protein once eaten are not used directly to perform a biological funtion, even if the dietary protein functions in the same way as a protein we require. Instead, the priteins in the diet are digested into individual amino acids before they are absorbed from the intestine into the blood. The individual amino acids are then transported to the cells, where they are synthesized into whatever protein the cell needs at that moment.

If our diet does not contain a sufficient supply of certain amino acids, others can be altered into the needed structures. Other amino acids can be synthesized from nonprotein sources in the diet. However, human beings have lost the ability to synthesize some amino acids in any fashion. These essential amino acids must be present in our diet in adequate supply. What appears to be critical in the diet is not a specific total amount of protein. Rather it is a sufficient supply of each of the essential amino acids. The lack of the single essential amino acid, even in the presence of more than adequate total supply of protein, leads to a state of malnutrition. Furthermore, we do not store amino acids in the sense that we store body fat. Our ability to utilize a particular day's supply of amino acids for synthesis of new proteins is restricted to the quantity of the least adequately supplied essential amino acids. Beyond this, the amino acids are metabolized for energy, even the essential amino acids that might be limiting at the next meal. If there is a continued shortage of an essential amino acid, body proteins beginning with liver and muscle protein are broken down to supply the scarce amino acid. Obviously this situation leads to serious problems if allowed to continue.

Recently, concern has been expressed about the increase in the earth's population and the ability of human beings to continue to feed themselves. Frequently, the wastefulness of feeding grain to animals, then consuming the animals, is pointed out. Without question we lose a large percentage of the total calories of the grain in this way. Fewer acres of land would be required to provide the minimum diet if consumed the grain ourselves (See Figures above). The equation is not as simple as it is often presented to be, however. First many of the grasslands upon which grazing animals are raised are of borderline value for the planting of grain. More importantly, vegetable protein does not provide as satisfactory a distribution of amino acids as does animal protein, such as meat, eggs, fish, and milk. A person who meet his or her amino acids requirement with about 20 g of meat or egg would require about 70 g of whole wheat bread to supply the same level of amino acid nutrition.

Maintenance of an adequate protein nutrition is most important in children. Perhaps the greatest nutritional problem in the world is the disease often termed kwashiorkor.  Problem occurs when infants are prematurely weaned onto a low-protein cereal diet. This diet has less than half the protein per calorie as mother's milk. It is often particularly short of lysine. As the child runs short of essential amino acids, tissue protein is sacrificed. In extreme cases, the production of digestive enzymes is halted, destroying the ability to digest what proteinis present in the diet. High mortality also results from infection or dehydration because of diarrhoa. Addition of lysine to the diet or the introduction of new strains of corn very high in lysine are employed to combat kwashiorkor.