Protein Dynamics

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I have interests in several areas of protein dynamics, particularly with respect to the interpretation of X-ray diffraction data.


TLS refinement
Normal modes
Analysis of anisotropic U factors

TLS refinement

See developing pages on TLS refinement.

TLS parameters describe the translation, libration and screw-rotation of a rigid body, and represent the simplest collective motion of groups of atoms. This motion is anisotropic, but is described by far fewer parameters than treating individual atoms anisotropically. Thus, refining TLS parameters against X-ray data rather than individual anisotropic displacement parameters (U's) requires fewer refinement parameters, and is feasible at intermediate resolutions.

Refinement of TLS parameters has been implemented in the refinement program REFMAC, and is available in the current release. REFMAC documentation can be found here. There is also some background information on TLS.

Normal modes

Normal modes represent another type of collective motion. Refinement of parameters modelling such collective motions is planned.

Analysis of anisotropic U factors

At high enough resolution, individual anisotropic displacement parameters (U's) can be refined. The result of such refinement is typically a large quantity of numbers plus some ORTEP figures! The CCP4 program ANISOANL provides a number of utilities for interpreting the results of individual U factor refinement:
Attempt to fit TLS parameters to refined U values, for given rigid groups, as is done routinely for small molecules.
Assess Rosenfield's rigid-body postulate, which states that for two atoms belonging to the same rigid-body (not necessarily bonded), the projections of the anisotropic displacement parameters along the interatomic vector should be equal.
Produce plots of equivalent isotropic B values, anisotropy, and radial and tangential projections of U.

The following references give examples of the use of ANISOANL:
Last modified: Fri May 26 16:17:00 BST 2000