Included Sequence Files

The sequence files included with Bio2Midi consist of a marked set of proteins ready for loading into the Bio2Midi program. The set includes 12 proteins, which can be divided into four groups: oxygen binding globins (beta-globin and myoglobin), lysozymes (human and bovine lysozyme, lactalbumin) , digestive enzymes (trypsin, snake venom, thrombin and fibrinogen, not an enzyme itself, but activated by thrombin), and light-sensitive proteins (bacteriorhodopsin, human rhodopsin, and human red cone opsin). These proteins demonstrate both the variability available to proteins and the fact that proteins form families of related molecules.

Human beta-globin (betaglob.txt)

Hemoglobin, the oxygen-carrying protein of red blood cells, is composed of four protein chains, 2 alpha chains and two beta chains. Each of the four chains of hemoglobin binds an oxygen molecule. The beta chain is altered in sickle-cell anemia, with the glutamic acid (E) at position 6 being replaced by valine (V). This substitution causes the entire hemoglobin complex to refold into a form that deforms the blood cell at low oxygen concentrations.

Sperm whale myoglobin (whalemyo.txt)

Myoglobin is also an oxygen binding protein, but is found as an oxygen reservoir in muscle tissue. Sperm whales are deep divers and their ability to store large quantities of oxygen in their muscles contributes to this ability.

Human lysozyme (humnlyso.txt)

Lysozyme is an enzyme that digests the cell walls of some types of bacteria and is in many human glandular secretions, including tears and milk. The bacteria-digesting activity of this enzyme is a defense against infection.

Bovine lysozyme (bovlyso.txt)

Many ruminant herbivores, like cows or sheep, have a modified lysozyme in their stomachs. Cud-chewing animals use a rich mixture of bacteria and protozoans to help them digest cellulose; the acid-resistant enzyme in their stomachs digests these helping bacteria, and obtains additional nutrients from them.

Alpha lactalbumin (lactalb.txt)

Alpha lactalbumin is a relative of lysozyme, which is also secreted in milk. Lactalbumin is a milk protein that functions as one subunit of a carbohydrate synthesizing enzyme.

Human trypsin (trypsin.txt)

The protein sequence in this package is that of trypsinogen, the precursor to the pancreatic enzyme trypsin, which breaks down protein in the intestine. Many protein-digesting enzymes are first synthesized as inactive precursor molecules, which are converted into their active forms when part of the protein is removed. Trypsin attacks proteins at the positions of the amino acids lysine (K) and arginine ( R ).

Human thrombin (thrombin.txt)

Thrombin is a protein-digesting enzyme similar to trypsin, and also synthesized in its inactive form prothrombin. However the function of this protein is to remove part of another protein, fibrinogen. The removal of this piece converts fibrinogen to the insoluble protein fibrin, which forms the meshwork of a blood clot. Prothrombin itself is converted to the active enzyme thrombin by the action of another protein-digesting enzyme.

Human alpha-fibrinogen (fibrinogen.txt)

This protein is one of several that contributes to the formation of blood clots. In the case of alpha-fibrinogen, a string of about 35 amino acids is removed from the beginning of the protein, which allows the protein to refold into its insoluble form. The protein is interesting because it contains a long 39-unit segment that is repeated twice; this segment in turn is made up of modifications of a 13-unit motif. You can hear this reiterated motif in music derived from the protein sequence.

Fer-de-lance venom (snakvenm.txt)

Most snake venoms are derived from digestive enzymes, and in addition to immobilizing or killing prey, also help to predigest it – a tenderizing mechanism important for an animal that cannot chew its food. This fer-de-lance venom is related to both trypsin and to thrombin.

Bacteriorhodopsin (bactrhod.txt)

The opsins are components of membrane-embedded proteins that are activated by visible light. This bacteriorhodopsin from a bacterium that lives in salt water uses light energy to pump hydrogen ions across its membrane. This hydrogen pump is part of a major energy storing mechanism for the organism.

Human rhodopsin (rhodopin.txt)

Rhodopsin, in combination with a type of vitamin A, forms part of a light sensing pigment in many species from protozoans to mammals. When the pigment is activated by the absorption of light, it produces a signal that in higher animals is transmitted through optic nerves to visual centers in the brain. Various opsin make the vitamin A unit receptive to light at various wavelengths. Rhodopsin is the primary pigment of the rod cells of the retina, and is important for night vision.

Red cone opsin (redcone.txt)

Color vision in humans and some other animals comes from three proteins found in the cone cells of the retina. In humans, there are red, green, and blue cones and the colors we sense come from various combinations of red, green and blue cone activation. The red and green cone opsins are very similar molecules, but the differences in the proteins are responsible for the different wave lengths of light absorbed by the opsin-vitamin A complex. The red/ green opsins are in turn related to the blue opsins, and all three seem to be related to rhodopsin.

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