Molecular dynamics of polypeptides and proteins

Motion in a protein may be modeled by computer using Isaac Newton s equation of motion, / = ma. This modeling requires the three-dimensional coordinates from an X-ray structure analysis as a starting point and some knowledge of interatomic potentials, so that only reasonable interatomic distances will be employed at all stages.Such molecular dynamics calculations lead to a prediction of where atoms will move in a short period of time, and result in the calculation of a time-dependent trajectory of all atoms. Initially each atom is moved in the direction of the force on it from other atoms and then, as each atom moves, its trajectory may change to accommodate this. In addition, this method aids in protein structure refinement,as was described in Chapter 10, although it is important to ensure that the model so refined still fits the electron density map. 

The intensities of Bragg reflections at high scattering angles are decreased as a result of the vibration of atoms. This causes an exponential decreeise in the scattering factor. 

A similar effect is found if there is slight disorder from unit cell to unit cell in the crystal (static disorder). 

In order to determine whether a decrease in scattering at high angles is due to vibration effects or to disorder, the data should be measured at a series of temperatures. Only the vibration effects should show a strong temperature dependence. Displacements of atoms from their equilibrium positions can be anisotropic and are represented by anisotropic displacement parameters which, are refined by least-squares techniques together with the atomic coordinates (see Chapter 10). A further analysis of these anisotropic displacement parameters in terms of translation T, libration L, and screw S motions can give information on the nature of the molecular motion. 

Molecular motion will affect the apparent molecular geometry and must be corrected for. 

---