Ok, unfolding....the core process

[TallTravel]

I have spent more than a few moments on the main F@H web site, and I cannot get a true sense of whether the folding of the proteins simulated in the F@H software occurs as the proteins are being built from the amino acids, or whether the software is simulating what would happen to finished protein chains if they were to be broken down from their finished form.

Anyone understand enough about what I am asking to lead me to an answer on the F@H site for the core biological process and explanation? Is there a forum for this type of question associated with the F&H web site?

My understanding of the folding, or building, of proteins from base amino acids within our bodies or those of other living organisms is dependent on the availability of essential amino acids. If the protein building plan, the DNA, is lacking basic building blocks, that in itself is a cause of another protein folding, right?

EDITED TO ADD:

OK, I found this Forum for more biologically oriented questions:

http://forum.folding-community.org/viewforum.php?f=4

Here is a touch of biology to explain part of this:

Proteins are necklaces of amino acids --- long chain molecules. Proteins are the basis of how biology gets things done. As enzymes, they are the driving force behind all of the biochemical reactions which make biology work. As structural elements, they are the main constituent of our bones, muscles, hair, skin and blood vessels. As antibodies, they recognize invading elements and allow the immune system to get rid of the unwanted invaders. For these reasons, scientists have sequenced the human genome -- the blueprint for all of the proteins in biology -- but how can we understand what these proteins do and how they work?

However, only knowing this sequence tells us little about what the protein does and how it does it. In order to carry out their function (e.g. as enzymes or antibodies), they must take on a particular shape, also known as a "fold." Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called "folding."

[enhanced08]

Sorry but I honestly have no idea! I am pretty good when it comes to science, except when it comes to the building blocks of life such as amino acids and proteins.

Might just post a thread at the folding forums and ask them.

http://forum.folding-community.org/

[mojo]

Here's the answer in a nutshell. I have an undergraduate degree in Biology so I understand it pretty well. Proteins are made of many many amino acids. The only thing that DNA specifies is the order in which these amino acids are chained together. As you know, the order of the amino acids is only a small part of the overall functionality of the proteins, and the shape is also a very important part of how the proteins work.

The way that the proteins attain their shape is spontaneous and occurs because of the natural interactions between the different types of amino acids in the protein, and the water-based environment of the cell. The amino acids have several properties that determine their behavior in folding. Some of them like water, some of them do not like water, some of them are quite large, some are pretty small, and many other properties. These different properties make them react in a certain way and "fold" into their final state. Think of it like a room at a party full of cliques of people. People who like each other tend to stick together, and avoid groups of people that they do not like.

As you can imagine, this process of spontaneously attaining a shape based on all these small interactions is quite complex, and this is the very process that we are trying to understand more completely with the folding@home project. The point in time that the project is simulating is after all the amino acids are linked together in order, but before they attain their functional shape.

[mojo]

What happened to this thread?