Transient Pockets and Surface Hotspots Prediction.
Matteo De Chiara, Bottini Silvia, Morandi Edoardo, Cirri Simone, Andrea Bernini, Ottavia Spiga, Neri Niccolai · Use Siena air (University of Siena) · 2011
A new tool for identifying transient pockets on a protein surface, PSTP-finder, directly from trajectories of Molecular Dynamic simulations has been developed. An experimental procedure to validate the occurrence of transient pockets predicted by PSTP-finder, based on Nuclear Magnetic Resonance accessibility profiling of a paramagnetic probe on protein backbone amide hydrogens is also proposed. Sso7d, a chromatin protein of 62 residues from the hyperthermophilic archaeabacterium Sulfolobus solfataricus, has been used to test PSTP-finder and the NMR based validation procedure.