Deconvolution of X-ray diffraction profile by using the regularization technique

Abstract

Refining an initial protein model to its final structure is usually composed of rounds of refinement performed by programs such as CNS and REFMAC, and manual model modification that includes linking and extending fragments, and fitting the ill matched residues of model by using the computer graphics program such as O. The manual model modification requires expertise of crystallography to recognize structural conformation based on electron density, and it is a time consuming process.For the purpose of reducing the time and manual intervention of refinement, we developed a software named LAFIRE (Localcorrelation-coefficient-based Automatic FItting for REfinement) to automate the whole refinement process. Four function modules are designed: building the missing parts in the current model, fitting the model to the electron density map, monitor program and an interface for combining the first two modules and the refinement programs CNS and REFMAC5.The LAFIRE is already in the state that builds the whole model from fragments by iterative approach, and performs structural refinement process without manual intervention in a few hours or days.LAFIRE A novel refinement method called HipHop refinement is described. Although HipHop refinement seems to be similar to simulated annealing refinement it is based on a different philosophynamely that it is in principle impossible to determine a complete structure at a limited resolution. Thus, the limited resolution and the inaccuracy of the underlying X-ray data cause not only errors in the refined structural parameters but principal structural errors in the single model, which is usually used to explain the data.HipHop refinement is performed in several steps. In the first step, a proper number of pseudo waters corresponding to maxima in the difference Fourier map is added to the model (HIP step, H 2 O input). In the next step, the model is refined and waters not fulfilling density, shape or position criteria are removed from the model (steps HOP, H 2 O output). The process is in fact jumping between local minimaHipHop. During HipHop cycles not only the water arrangement but also side/main chain orientation is changed. The best presentation of HipHop refinement is a multi conformer PDB file.The method was tested on several different protein structures with excellent results [1,2] The programs are available on http://www.img.cas.cz/hiphop/.[1] Ondrá ek J., Weiss M.S., Mesters J.R., Acta Cryst., manuscript in preparation.[2] Ondrá ek J., Weiss M.S., Brynda J., Fiala J., Jursík F., ezá ová P., Jenner L.B., Sedlá ek J., Acta Crys., submitted for publication.Keywords The deconvolution of the instrumental function in X-Ray diffraction profile analysis is a basic step in order to obtain reliable results on the microstructure (crystallite size, lattice microstrain, etc.) and is a typical example of ill-posed inverse problems. The implementation of an eigen function method with different regularization techniques is investigated and a simple regularization algorithm is proposed.A simulat...