IBM and NeSC workshop on Protein Science
National e-Science Centre, Edinburgh, March
15-16 2002
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Effect of ion binding on the conformational dynamics
of calmodulin Yuk Yin Sham, Ruhong Zhou, Frank Suits, and Robert Germain. IBM Research, TJ Watson Research Center, Yorktown Heights, NY 10598 Nanoseconds molecular dynamics simulation were carried out to study the effect of binding on the conformation dynamics of calmodulin. It was found the removal of calcium ions results in the enhance flexibility of the calcium binding region. The flexibility of the commonly known flexible region (res 76-78) within the central helical linker between the N and C domain remains mostly unchanged between the apo and holo form. Removal of calcium ions also results in the collapse of the N-domain to a structure very similar to the experimentally observed “closed” conformation. These observations suggest a) the activation of calmodulin to bind to its target substrates involve stabilization of the “open” conformation and b) calcium binding does not affect the unfolding of the flexible region of the central helical linker, an essential requirement for calmodulin to attain a folded conformation. |
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