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A protein is a long link of amino acids. In its natural (folded) state each protein forms a
well-defined globular cluster. The shape of this cluster is one of the main factors that determine
how the protein functions; hence understanding the folding mechanism is an important question. In
our joint work with Burak Erman, we use the Gaussian model where the protein is modeled as a chain
of beads (representing the amino acids) and the underlying forces as springs joining certain pairs
of beads. Quadratic forces allowing us to do explicit calculations, we have considered the following
two questions: (1) How accurate is such a representation; in other words is it possible to
approximate the shape of a protein this way by choosing appropriate spring constants? More
important, can we find universal spring constants for pairs of amino acids that will work for all
(or for a large group) of proteins ? (2) How does the Gaussian model explain the dynamics of the
protein ?
Albert Erkip (Sabanci University)
General Seminar,
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