Pavel Afonine | bioRxiv Science

bioRxiv2015

From deep TLS validation to ensembles of atomic models built from elemental motions

The widely used Translation Libration Screw (TLS) approximation describes concerted motions of atomic groups in X-ray refinement. TLS refinement often provides a better interpretation of diffraction data and the resulting rigid body motions may subsequently be assigned biochemical significance. In TLS refinement, three matrices (T, L and S) describe harmonic vibration, libration and their correlation. Because these matrices describe specific motions, they impose a number of conditions on their elements. Ignoring these conditions while refining the matrix elements may result in matrices that cannot be interpreted in terms of physically realistic motions. We describe a mathematical framework and the computational tools to analyze refined TLS matrices through their decomposition into descriptors of underlying motions. This allows for straightforward validation and identification of implausible TLS parameters. An algorithm for the generation of structural ensembles that are consistent with given TLS parameters, implemented as a part of the Phenix project, is also described.\n\nSynopsisProcedures for the decomposition of TLS matrices into elementary vibrations and librations indicates possible errors in the definition of these matrices and corrects them when possible. The program outputs the corresponding vibration-libration parameters and generates structural ensembles.

Biophysics↗

bioRxiv2015

Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. While Bragg diffraction describes the average positional distribution of crystalline atoms, many different models can fit this distribution equally well. Diffuse X-ray scattering can reduce this degeneracy by directly reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guiniers equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to Translation-Libration-Screw (TLS) refinement, which models rigid body displacement for segments of the macromolecule. To enable calculation of diffuse scattering from TLS refined structures, phenix.tls_models builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how X-ray diffuse scattering can extend macromolecular structural refinement, validation, and analysis.\n\nSynopsisA method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different Translation-Libration-Screw refinement strategies produce unique diffuse intensity patterns.

Biophysics↗