Millisecond Timescale, Atomistic Protein Folding Simulations Yield a Network Theory for Protein Folding
نویسندگان
چکیده
منابع مشابه
Native contacts determine protein folding mechanisms in atomistic simulations.
The recent availability of long equilibrium simulations of protein folding in atomistic detail for more than 10 proteins allows us to identify the key interactions driving folding. We find that the collective fraction of native amino acid contacts, Q, captures remarkably well the transition states for all the proteins with a folding free energy barrier. Going beyond this global picture, we devi...
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Determining protein folding kinetics and thermodynamics from all-atom molecular dynamics (MD) simulations without using experimental data represents a formidable scientific challenge because simulations can easily get trapped in local minima on rough free energy landscapes. This necessitates the computation of multiple simulation trajectories, which can be independent from each other or coupled...
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A protein is a linear chain of amino acids. The proteins of natural living organisms are composed of 20 different types of amino acids. A typical protein is a polymer of 300 amino acids, of which there are 20 = 2× 10 different possibilities. The human body uses about 80,000 different proteins for most of its functionality, including structure, communication, transport, and catalysis. The order ...
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Proteins are involved in virtually every biological process and in order to function, it is necessary for these polypeptide chains to fold into the unique, native conformation. This folding process can take place rapidly. NMR line shape analyses and transverse relaxation measurements allow protein folding studies on a microsecond-to-millisecond time scale. Together with an overview of current a...
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Protein folding should be complex. Proteins organize themselves into specific three-dimensional structures, through a myriad of conformational changes. The classical view of protein folding describes this process as a nearly sequential series of discrete intermediates. In contrast, the energy landscape theory of folding considers folding as the progressive organization of an ensemble of partial...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2010
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2009.12.3352