Calmodulin (CaM) is a ubiquitous intracellular protein that regulates biological activities of numerous enzymes and ion channels. Upon responding Ca2+ concentration change, Ca2+- dependent CaM activates the hydrolyzation of cGMP by PDE and Ca2+ releasing channel activity of ryanodine receptor. In this dissertation, a series of CaM variants were engineered to enhance Ca2+ binding affinities by increasing the number of negative charged residues in individual EF-hand. The capability of shifting the biphasic Ca2+-activation profile of RyR1 is significantly altered by changing Ca2+ binding affinity of CaM at the C-terminal. This indicates that examining Ca2+-CaM affinity is a valid strategy to tune the activation profile of CaM-regulated ion channels. To further understand interactions between CaM and RyR1, NMR was used to determine their binding mode. To dissect roles of structural components of CaM in metal binding and regulation of biological functions of target proteins, we created half-CaMs and Del-CaM. Binding affinities of these variants to Ca2+, Tb3+ and Gd3+ were determined by fluorescence spectroscopy; functional studies were conducted using single channel analysis and PDE function assay. Another objective of my dissertation is to design a protein based contrast agent for molecular imaging. CaM was selected as the scaffold protein for designing Gd3+ based MRI contrast agent by modifying metal binding sites as well as grafting a biomarker peptide into the linker region to specifically target cancers with efficient and optimized modifications. The physical kinetic properties and animal imaging effects of these designed contrast agents were investigated by various methods.