Macroscopic characteristics of a peptide or protein are dependent on microscopic properties. One microscopic property that has an effect on the macroscopic characteristics is the oxidation of methionine. Here we show that oxidation strengthens the methionine-aromatic interaction by 0.5-1.4 kcal/mol and that oxidation plays a role in the structure and biological function of calmodulin and lymphotoxin-α/TNFR1 binding. Another microscopic property is the sequence of amino acids. We have also shown that the intrinsically disordered linker region of synaptotagmin I plays a role in modulating the binding of Ca2+ and the interaction with membrane. The final portion of this work determined the microscopic properties, in this case hydrophobic and electrostatic interactions within the dystrophin ABD1 to shed light on the underlying mechanism by which structural changes occur under physiological conditions. This work consisted of using thermodynamic and structural approaches and computational techniques, namely database searching and molecular dynamics simulations.