Computational chemistry draws for the first time the “interactive cartographic map" of enzymes during chemical reactions

Enzyme map

Researchers in Spain have used computational chemistry to plot for the first time a "cartographic map" of enzyme behavior during the catalytic process. Features include the moment when a given enzyme is at the point of maximum energy on the way from taking reactants to final product, which all happens within a femtosecond. The study conducted by researchers at the Universitat Jaume I and the University of Valencia was published in Nature Chemistry. "We can [now] make a quantitative estimate of the flexibility of the protein, how much it deforms itself, how much energy you need to deform that protein to generate the reaction that you want," explains UJI's Vicent Moliner.
Computational chemistry draws for the first time the "interactive cartographic map" of enzymes during chemical reactions
http://www.uji.es/UK/ocit/noticies/detall&id_a=33312503

Enzymes Make the World Go 'Round

We often talk about reactions and the molecules that change in those reactions. Those changes don't happen on their own. If you leave a blob of protein in a Petri dish, will it just break down to the amino acids? No. What will do it? Enzymes! Enzymes are the biological substances (proteins) that act as catalysts and help complex reactions occur everywhere in life.

Assembly Line Robots

You all know about cars and the assembly lines where they are made. There are giant robots helping people do specific tasks. Some lift the whole cars, some lift doors, and some just put bolts on. Enzymes are like those giant robots. They grab one or two pieces, do something to them, and then release them. Once their job is done, they move to the next piece and do the same thing again. They are little protein robots inside your cells.

Enzymes complete very, very specific jobs and do nothing else. The robot that was designed to move a car door can't put brakes on the car. The specialized robot arms just can't do the job. Enzymes are the same. They can only work with specific molecules and only do specific tasks. For example, you might have a protein in a cell. Even with hundreds of amino acids in the chain, the overall shape changes if one amino acid is different. That tiny shape change could stop the enzyme from doing its job. Some herbicides are used to block enzyme activity. Plants have adapted by changing one or two amino acids in the enzymes. They can continue to work with the correct proteins and there is no bonding to the herbicides. In the same way that there are specialized robots for different types of cars, there are enzymes for neural cells, intestinal cells, and your saliva.

There are four steps in the process of an enzyme at work:
1. An enzyme and a substrate are in the same area. The substrate is the biological molecule that the enzyme will work on.
2. The enzyme grabs on to the substrate at a special area called the active site. Enzymes are very, very specific and don't just grab on to any molecule. The active site is a specially shaped area of the enzyme that fits around the substrate. The active site is like the grasping handle of the robot on the assembly line. It can only pick up one part.
3. A process called catalysis happens. Catalysis is when the substrate is changed. It could be broken down or combined with another molecule to make something new.
4. The enzyme lets go. This is a big deal. When the enzyme lets go, it returns to normal, ready to work on another molecule of substrate. The first molecule is no longer the same. It is now called the product.

Enzymes

At any given moment, all of the work being done inside any cell is being done by enzymes. If you understand enzymes, you understand cells. A bacterium like E. coli has about 1,000 different types of enzymes floating around in the cytoplasm at any given time.
Enzymes have extremely interesting properties that make them little chemical-reaction machines. The purpose of an enzyme in a cell is to allow the cell to carry out chemical reactions very quickly. These reactions allow the cell to build things or take things apart as needed. This is how a cell grows and reproduces. At the most basic level, a cell is really a little bag full of chemical reactions that are made possible by enzymes!
Enzymes are made from amino acids, and they are proteins. When an enzyme is formed, it is made by stringing together between 100 and 1,000 amino acids in a very specific and unique order. The chain of amino acids then folds into a unique shape. That shape allows the enzyme to carry out specific chemical reactions -- an enzyme acts as a very efficient catalyst for a specific chemical reaction. The enzyme speeds that reaction up tremendously.
For example, the sugar maltose is made from two glucose molecules bonded together. The enzyme maltase is shaped in such a way that it can break the bond and free the two glucose pieces. The only thing maltase can do is break maltose molecules, but it can do that very rapidly and efficiently. Other types of enzymes can put atoms and molecules together. Breaking molecules apart and putting molecules together is what enzymes do, and there is a specific enzyme for each chemical reaction needed to make the cell work properly.

Maltose is made of two glucose molecules bonded together (1). The maltase enzyme is a protein that is perfectly shaped to accept a maltose molecule and break the bond (2). The two glucose molecules are released (3). A single maltase enzyme can break in excess of 1,000 maltose bonds per second, and will only accept maltose molecules.

You can see in the diagram above the basic action of an enzyme. A maltose molecule floats near and is captured at a specific site on the maltase enzyme. The active site on the enzyme breaks the bond, and then the two glucose molecules float away.
You may have heard of people who are lactose intolerant, or you may suffer from this problem yourself. The problem arises because the sugar in milk -- lactose -- does not get broken into its glucose components. Therefore, it cannot be digested. The intestinal cells of lactose-intolerant people do not produce lactase, the enzyme needed to break down lactose. This problem shows how the lack of just one enzyme in the human body can lead to problems. A person who is lactose intolerant can swallow a drop of lactase prior to drinking milk and the problem is solved. Many enzyme deficiencies are not nearly so easy to fix.
Inside a bacterium there are about 1,000 types of enzymes (lactase being one of them). All of the enzymes float freely in the cytoplasm waiting for the chemical they recognize to float by. There are hundreds or millions of copies of each different type of enzyme, depending on how important a reaction is to a cell and how often the reaction is needed. These enzymes do everything from breaking glucose down for energy to building cell walls, constructing new enzymes and allowing the cell to reproduce. Enzymes do all of the work inside cells.