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.
Matteo De, C., Silvia, B., Edoardo, M., Simone, C., Bernini, A., Spiga, O., et al. (2011). Transient Pockets and Surface Hotspots Prediction.. In World Congress on Engineering and Technology.
Transient Pockets and Surface Hotspots Prediction.
BERNINI, ANDREA;SPIGA, OTTAVIA;NICCOLAI, NERI
2011-01-01
Abstract
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.
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https://hdl.handle.net/11365/33872
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