The ability of proteins to fold into their native state is essential for cell function; misfolded proteins not only lose their function, but can also cause neurodegenerative diseases, including Alzheimer and Huntington. Study of protein folding can aid in preventing protein misfolding diseases and in designing proteins with novel functions. Although most cellular proteins fold on timescales of milliseconds to seconds, several small proteins have been designed and characterized experimentally to fold on a timescale of less than 20 µs. The project will employ Center-developed long-time MD simulation with NAMD to investigate: (1) the folding pathway of λ-repressor and (2) the effect of mutations on folding of the λ-repressor.

Spotlight: Large Protein Folded Computationally (Jul 2012)

lambda folding

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Proteins are the biological workhorses in living cells. For example, they respond to external signals arriving at the cell surface or transport cargo, much larger than themselves, from one place to another in the cell. However, before a protein can carry out his job, it must first assume the proper shape. Proteins are long polymers of twenty different amino acids linked in a linear sequence; the latter is particular for each protein. It is still a mystery how a protein folds into the proper shape based on its sequence. Scientists hope that one day they can "watch" this folding process for any given protein. The dream has been realized, at least partially, through the use of computer simulation. After tackling the protein-folding problem already computationally for two small proteins (see May 2008 highlight and Nov 2009 highlight), researchers have now successfully visualized the complete folding process of a relatively large protein, the so-called λ-repessor (see movie, 7.8 MB). In fact, it is one of the largest proteins folded to date using a computer. As reported recently, simulations carried out with the program NAMD, as well as simulations carried out on a special purpose supercomputer, Anton, achieved to follow λ-repessor's folding movement for more than 0.0001 seconds, long enough to observe the protein assume its proper shape. More information is available on our protein folding website.

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  • Funded by a grant from
    the National Institute of
    General Medical Sciences
    of the National Institutes
    of Health