Oxidative surface mapping and molecular dynamics simulations
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For certain classes of biomolecular complexes, particularly those involving glycans binding to proteins, it is rarely possible to employ traditional methods such as x-ray crystallography or nuclear magnetic resonance to determine their structural features. Therefore, a contact surface mapping (footprinting) method that would be applicable in these cases could provide information for characterizing the 3D structures in these interactions. The protein surface mapping method described here employs hydroxyl radicals, generated by pulsed-laser induced photodissociation of hydrogen peroxide, to modify the amino acid side chains. Analysis of the extent and location of oxidation is subsequently determined by mass spectrometry. This data can then be combined with the predictions of an average solvent accessible surface area for each residue employing molecular dynamics simulations and molecular modeling to validate predicted 3D structures. Development of such a combined method is a contribution to the field of 3D structure modeling as well as experimental footprinting.