Computational Assignment of Chemical Shifts for Protein Residues (1311.3186v1)

Abstract: Fast and accurate protein structure prediction is one of the major challenges in structural biology, biotechnology and molecular biomedicine. These fields require 3D protein structures for rational design of proteins with improved or novel properties. X-ray crystallography is the most common approach even with its low success rate, but lately NMR based approaches have gained popularity. The general approach involves a set of distance restraints used to guide a structure prediction, but simple NMR triple-resonance experiments often provide enough structural information to predict the structure of small proteins. Previous protein folding simulations that have utilised experimental data have weighted the experimental data and physical force field terms more or less arbitrarily, and the method is thus not generally applicable to new proteins. Furthermore a complete and near error-free assignment of chemical shifts obtained by the NMR experiments is needed, due to the static, or deterministic, assignment. In this thesis I present Chemshift, a module for handling chemical shift assignments, implemented in the protein structure determination program Phaistos. This module treats both the assignment of experimental data, as well as the weighing compared to physical terms, in a probabilistic framework where no data is discarded. Provided a partial assignment of NMR peaks, the module is able to improve the assignment with the intension to utilise this in the protein folding with little bias.