Stories tagged enzymes

Apr
11
2009

Amazing nano factories known as proteins

Protein structure: three representations of the protein triose phosphate isomerase.
Protein structure: three representations of the protein triose phosphate isomerase.Courtesy Opabinia regalis
Understanding proteins and how they work is very useful. One type of protein called an enzyme is like a nano sized factory that can take apart molecules or build new molecules out of smaller parts.

Plant cellulose can be turned into ethanol fuel. Oil slicks could be digested into non-pollutants. Custom designed proteins will soon allow "living" factories that can manufacture almost anything we can imagine. Protein "hackers" are creating synthetic antibodies — proteins designed to bind tightly to specific targets, such as tumor cells, which can then be destroyed.

The Defense Advanced Research Projects Agency

To accomplish this goal, DARPA is investing in the development of new tools in diverse areas such as topology, optimization, the calculation of ab initio potentials, synthetic chemistry, and informatics leading to the ability to design proteins to order. At the conclusion of this program, researchers expect to be able to design a new complex protein, within 24 hours, that will inactivate a pathogenic organism. Protein Design Processes (DARPA)

The Protein Data Bank and Rosetta@Home

Proteins are made from a complex chain of amino acids. Several resources are helping to illuminate the complex relationship between the sequence of a chain of amino acids, the shape into which that chain will ultimately fold, and the function executed by the resulting protein.

The Protein Data Bank is an ever growing data bank of detailed schematic protein information. Another program that is helping to understand how proteins are shaped is the Rosetta@Home project which allows thousands of home computers to determine the 3-dimensional shapes of proteins being designed by researchers.

Try protein folding

"Would you like to play a new computer game and help scientists analyze protein chemistry -- at the same time? Here is a fun and interesting computer puzzle game that is designed to fold proteins -- the objective is to correctly fold a protein into the smallest possible space." Grrlscientist

Watch this video to learn how to "fold-it"

Jul
23
2007

Blood donation.: Image courtesy size8jeans.
Blood donation.: Image courtesy size8jeans.
I am a blood donor – and if you are not, and are able to, I would encourage you to be a donor too. The process of blood donation is relatively simple, and sort of painless. And although all blood looks the same, and is made of the same basic elements, there are actually eight different common blood types: A(+/-), B(+/-), AB(+/-), and O(+/-). The letters A and B stand for two antigens that can be present on the surface of a red blood cell. Someone with the A antigen can’t donate to someone with the B antigen, and vice versa. For example, I have type A blood, meaning the A antigen is present on my blood cells. My blood can be donated to persons who have types A or AB blood and I can get blood from donors who are also type A or who are type O. If I received type B blood I would suffer a serious, possibly fatal, hemolytic reaction. It is therefore very important that the blood type of a donor and a recipient be properly identified.

To further complicate matters, blood types are also either positive or negative for the presence of another antigen, Rh. If you have the Rh antigen on the surface of your red blood cells you have Rh+ blood, if you do not have the Rh antigen, you are Rh-. So, if you have Rh- blood you can only receive blood from others of the same blood type (A, B, AB, or O) who also have Rh- blood. But, if you are Rh+ you can receive from both Rh+ and Rh- blood types.

Now, type O blood (called type zero in some countries) has neither the A or B antigen and therefore, type O negative blood can be given to anyone. Persons with type O negative blood are referred to as “universal donors”. If everyone had type O negative, blood transfusions would be less risky – unfortunately, only about 7% of Americans have type O negative blood.

Recently a company called ZymeQuest in Massachusetts announced that it had discovered two enzymes, called glycosidases and derived from bacteria, that could be used to strip A or B antigens from the surface of the red blood cells, essentially enzyme-converting them to type O cells. By converting all A-negative, B-negative and AB-negative blood into O-negative blood would increase the availability of “universal donor blood” from 7% to 16%. While we’re likely far away from this blood conversion being used in patients, it is currently being tested in the U.S. and in Europe.

Learn more about donating blood here and here.

Play a game to see if you can match the right blood donor to the right recipient here.