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Thread: What is Protein Folding?

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    Thumbs up What is Protein Folding?

    The Folding@home project (FAH) is dedicated to understanding protein folding, the diseases that result from protein misfolding and aggregation, and novel computational ways to develop new drugs in general.



    What is protein folding and how is it related to disease?

    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 that 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."

    For several decades, understanding how proteins self-assemble (or "fold") has been a challenging problem in physical chemistry with important ramifications for structural biology and nanotechnology. Moreover, understanding protein folding is an important paradigm for many other difficult problems in structural biology and physical chemistry. Our goals have been to develop novel computational methods for greatly pushing the envelope in folding simulation, with a goal of directly and quantitatively predicting all possible experimental observables. Using novel algorithms and the power of Folding@home, we have been able to, for the first time, simulate folding dynamics directly from the sequence.

    What happens if proteins don't fold correctly?

    Diseases such as Alzheimer's disease, Huntington's disease, cystic fibrosis, BSE (Mad Cow disease), an inherited form of emphysema, and even many cancers are believed to result from protein misfolding. When proteins misfold, they can clump together ("aggregate"). These clumps can often gather in the brain, where they are believed to cause the symptoms of Mad Cow or Alzheimer's disease.

    Which diseases or biomedical problems are you currently studying?

    Alzheimer's Disease (AD)

    AD is caused by the aggregation of relatively small (42 amino acid) proteins, called Abeta peptides. These proteins form aggregates which even in small clumps appear to be toxic to neurons and cause neuronal cell death involved in Alzheimer's Disease and the horrible neurodegenerative consequences.

    Huntington's Disease (HD)

    HD is caused by the aggregation of a different type of proteins. Some proteins have a repeat of a single amino acid (glutamine, often abbreviated as "Q"). These poly-Q repeats, if long enough, form aggregates which cause HD. We are studying the structure of poly-Q aggregates as well as predicting the pathway by which they form. Similar to AD, these HD studies, if successful, would be useful for rational drug design approaches as well as further insight into how HD aggregates form kinetically (hopefully paving the way for a method to stop the HD aggregate formation).

    Cancer and P53

    Half of all known cancers involve some mutation in p53, the so-called guardian of the cell. P53 is a tumor suppressor which signals for cell death if their DNA gets damaged. If these cells didn't die, their damaged DNA would lead to the strange and unusual growths found in cancer tumors and this growth would continue unchecked, until death. When p53 breaks down and does not fold correctly (or even perhaps if it doesn't fold quickly enough), then DNA damage goes unchecked and one can get cancer. We have been studying specific domains of p53 in order to predict mutations relevant in cancer and to study known cancer related mutants.

    Chagas Disease

    In 2010, a pilot project started on Chagas Disease, a major disease in Latin America. 2010 FAH/Pande Group researcher Paul Novick has applied ligand-based methods to Chagas disease and in collaboration with the SPARK project (UCSF) and the McKerrow Lab (UCSF) has started to test the results. The early results are looking promising, but it is very early to tell.

    Antibiotics

    The Ribosome is an amazing molecular machine and plays a critical role in biology, as it is the machine that synthesizes proteins. Because of this critical role, and some small but fundamental differences in the ribosomes of mammals and bacteria, the ribosome is the target for about half of all known antibiotics. These antibiotics typically work by preventing bacterial ribosomes from making new proteins, thus killing them. We have several projects on going to study the ribosome. Since the ribosome is so huge, these WUs are big WUs and have required us to push the state of the art of FAH calculations. However, with these new bigWUs, FAH is set up to study more and more complex problems, and if successful, with greater and greater biomedical impact.

    Viral diseases

    Viruses such as influenza and HIV pose major threats to human health and can be exceptionally difficult to treat. Most treatments concentrate on preventing viral replication, but another strategy is to keep the virus out in the first place.

    In order to infect human cells, viruses must pass through the cell membrane. They have established special machinery to accomplish this process, which usually requires an activation signal, a protein conformational change, and then protein-membrane interactions to achieve cell entry. Prof. Kasson's group studies this process to better understand and prevent viral diseases. We have focused on influenza both because it has a repeated history of causing widespread global disease (such as in 1918) and because advances in influenza treatment should be applicable to other similar viruses. Based on advances Dr. Kasson made while at Stanford in collaboration with Dr. Pande, we have made good initial progress in understanding the basic reactions influenza employs to enter cells. We are now well positioned to start studying the details of how the virus works.

    Why Study, Simulate and Use Folding@Home?





    What is RNA Folding?

    RNA folding presents many additional challenges in understanding molecular self-assembly, when compared with protein folding. In particular, RNA molecules are considerably larger, electrostatics plays a much more dominant and complex role and the nature of tertiary interactions is considerably more subtle. By combining a tight coupling with experimental collaborators, we are examining RNA folding on many scales, from atomistic simulations of small RNA motifs to simulations of the entire Tetrahymena ribozyme.
    Last edited by JamesLT3; 19-09-2012 at 01:10.

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