From Protein Structure to Function with Bioinformatics.pdf

9 Protein Dynamics: From Structure to Function 223Fig. 9.3 Hinge-bending motion in bacteriophage T4-lysozyme. Domain fluctuations (domainsare coloured differently) are essential for enzyme function, allowing the substrate to enter and theproducts to leave the active siteThe wealth of experimental data also provides the opportunity to assess the reliabilityand sampling performance of simulation methods. Two MD simulationshave been carried out using a closed (simulation 1) and an open conformation(simulation 2) as starting points, respectively. In order to assess the sampling efficiencya principal components analysis (PCA, see Section 9.2 below) has been carriedout on the ensemble of experimentally determined structures and the X-rayensemble and the two MD trajectories have been projected onto the first two eigenvectors.The first eigenvector represents the hinge-bending motion, whereas thesecond eigenvector represents a twist of the two domains of T4L. The projectionsare shown in Fig. 9.4. The X-ray ensemble is represented by dots, each dot representinga single conformation. Movement along the first eigenvector (x-axis)describes a collective motion from the closed to the open state. It can be seen thatneither of the individual the MD trajectories, represented by lines, fully samples theentire conformational space covered by the X-ray ensemble, although the simulationtimes (184 ns for simulation 1 and 117 ns for simulation 2) are one order ofmagnitude larger than in the previously discussed Cse1p simulation. From thephase space density one can assume that an energy barrier exists between the closedand the open state and neither simulation achieves a full transition, from the closedto the open state, or vice versa.