Redox-active amino acids form catalytically active, one-electron oxidized radicals that occur as key intermediates in many biological electron transfer reactions. State-of-the-art quantum-mechanics/molecular-mechanics (QM/MM) and dynamical QM/MM (QM/MM MD) methods are used to characterize the electronic, vibrational, and magnetic properties of these radicals in proteins and enzymes. The proper modeling of the environmental effects, in combination with the available experimental data, makes possible the unambiguous assignment of the experimentally detected radical species to a specific site and the clarification of the nature (neutral or charged) of the intermediates. Furthermore, it allows to obtain a mechanistic description of the proton-coupled electron transfer process leading to the radical formation and to provide additional details on the role played by the nearby protein residues and solvent water molecules in affecting the spectral properties and the geometrical structure of the radical intermediates. The information obtained on these important reactive intermediates opens the way to a comprehensive understanding of amino acid radical-mediated electron transfer reactions.