Rotational and vibrational excitations may lead to changing proteins conformation. There are literature studies about the application of microwave radiation for this purpose.
As far as I know, in case of ionizing radiation, irradiation will produce many free radicals and ion pairs which will react with adjacent (within 2-3 nm proximity) molecule, in this case protein. While reacting with proteins, free radicals and ion pairs can modify amino acids and break peptide bonds; thus changes the conformation of protein. This is called indirect effect of ionizing radiation which is predominant in gamma radiation or X-ray which possess low Linear Energy Transfer (LET) property.
In the direct effect of ionizing radiation, predominant in case of alpha and beta radiation containing high Linear Energy Transfer (LET) property, protein denaturation/deformation will be caused directly by these particles through modification of amino acids and breakdown of peptide bonds.
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