Chandra, NR and Muirhead, Hilary and Holbrook, John J and Bernstein, Bradley E and Hol, Wim GJ and Sessions, Richard B (1998) A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme. In: Protien Structure, Function, and Genetics, 30 (4). pp. 372-380.
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The occurrence of large domain motions associated with the mechanism of action of many proteins is well established. We present a general method of predicting domain closure applicable to proteins containing domains separated by an apparent hinge, The method attempts to allow far natural directional bias within the closing protein by repeatedly applying a weak pulling force over a short distance between pairs of atoms chosen at random in the two domains in question. Appropriate parameters governing the pulling function were determined empirically. The method was applied to the bi-lobal protein PGR anti a closed-form activated ternary complex generated for Bacillus stearothermophilus PGK. This model was compared with the recently determined crystal structure of closed-form Trypanosoma brucei PGK. The model predicts the correct hinge regions, although the magnitude of movement at one hinge point was overestimated, and provides a reasonable representation of the closed-form ternary complex.
|Item Type:||Journal Article|
|Additional Information:||Copyright of this article belongs to John Wiley and Sons.|
|Keywords:||protein modeling; crystal structure; conformation change; prediction; mechanism.|
|Department/Centre:||Division of Biological Sciences > Molecular Biophysics Unit|
|Date Deposited:||22 Jul 2009 12:13|
|Last Modified:||19 Sep 2010 04:59|
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