Abstract
Electron paramagnetic resonance studies on diamagnetic proteins are based on site-directed spin labelling and require relatively much effort for engineering cystein point mutations as well as expressing and labelling the protein. Therefore, it is advantageous to predict those sites and pairs of sites that can provide the most precise and most reliable information on accessibility and distances. Systematic site scans based on a rotamer library approach for spin label side groups allow for such predictions. Figures of merit are defined that can be used to rank sites according to their potential suitability in studies of structure and structural changes. Such site scans can still provide useful results if only a backbone model and the amino acid sequence of the protein are known.
Highlights
Site-directed spin labelling (SDSL) of proteins [12], has recently become a widespread technique, in particular, in combination with pulsed electron paramagnetic resonance (EPR) techniques for the measurement of distance distributions between two spin labels [13,17,20]
A more detailed study based on a molecular dynamics (MD) approach demonstrated that conformational distribution of the spin label can provide the major contribution to the width of the measured distance distributions [16]
To model this conformational distribution and to predict spin-to-spin distance distributions from a given model for the protein structure, we have developed a rotamer library approach [13] that is similar in spirit to an approach for understanding spin label dynamics [18,19]
Summary
Site-directed spin labelling (SDSL) of proteins [12], has recently become a widespread technique, in particular, in combination with pulsed electron paramagnetic resonance (EPR) techniques for the measurement of distance distributions between two spin labels [13,17,20]. A more detailed study based on a molecular dynamics (MD) approach demonstrated that conformational distribution of the spin label can provide the major contribution to the width of the measured distance distributions [16] To model this conformational distribution and to predict spin-to-spin distance distributions from a given model for the protein structure, we have developed a rotamer library approach [13] that is similar in spirit to an approach for understanding spin label dynamics [18,19]. The new rotamer library approach allows for prediction of the conformational distribution of a spin label with a common personal computer in a computation time between less than a minute and a few minutes This opens up the possibility to systematically scan a protein structure for favourable spin labelling sites and site pairs. We consider measurements of spin label accessibility [1] and distance measurements, as well as the study of structural changes
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