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Analys av korrelationen mellan NMR-kemiska skift och rotationsvinklar i proteiner
Analysis of the correlation of NMR chemical shifts to protein dihedral angles
It is well-known in the field of NMR (nuclear magnetic resonance), since quite some time ago, that chemical shift is related to the electromagnetic environment of the measured nucleus. For example is the chemical shift of a nucleus in a protein molecule affected by the relative positions of electronic orbitals of neighbouring atoms. This fact has been used to qualitatively determine the secondary structure type of small peptide chains in proteins with unknown molecular structure (see for example Wishart et al and Cornilescu et al). A more recent publication (Wang and Jardetsky) reports an extension of previous studies by presenting a quantification of the correlation using a statistical approach. Finding an accurate quantification of the correlation between the chemical shift and structure geometries have important implications for protein structure determination, and have a potential to extend current capabilities of NMR into analysis of protein folding and protein interactions.
Specific plan and suitable previous knowledge:
The student will analyze a database of chemical shifts and relate the chemical shifts to corresponding protein structures in other databases. The aim is to make a statistical quantification (analogously to Wang and Jardetsky) of the relationship between chemical shifts and associated peptide dihedral torsion angles. Using dihedral torsion angles rather than classifications of secondary structure elements is believed to improve the correlations (and thus structure predictions based on the chemical shift) significantly. Data may be collected from the databases by writing program scripts in for example Perl (or any other suitable programming language). Subsequent statistical analysis is probably best developed in C. Besides familiarity with these programming languages, experiences with any of the following may be advantageous: protein structures, NMR, database programming, and statistics.
Wishart, Sykes and Richards, Biochemistry 31, 1647-1651 (1992)
Cornilescu, Delaglio and Bax, J. Biomol. NMR 13, 289-302 (1999)
Wang and Jardetsky, Protein Science 11, 852-861 (2002)
NMR chemical shifts, Protein secondary structure, Dihedral torsion angles, Statistics, Database, Computer programming, C, Perl.
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