Protein domains are the basic functional modules that maintain cell functions at a molecule level. Previous studies have mainly focused on the functions of isolated protein domains. The general objective of this thesis is to understand functions and regulations of multi-domain containing proteins. The study is based on two protein classes: naturally occurred BAR domain-containing proteins and artificially engineered calcium indicators. BAR domain super-family proteins BAR (Bin/Amphiphysin/Rvs) domain super-family proteins are peripheral membrane proteins that regulate membrane curvatures during the membrane remodeling events such as endocytosis, vesicular trafficking and cell growth. Via multiple biophysical approaches, I systematically studied BAR domain functions in Sorting Nexin 9, Endophilin and Pacsins at the presence of other protein domains. Two major findings are presented in this thesis. First I show that the diverse membrane sculpture activity of BAR domains is encoded in their unique molecular structures, and is influenced by membrane properties. Second, I show that this function diversity is highly regulated by other protein domains. Some protein domains have synergetic effects and play important roles in regulating cellular membrane remodeling. This work is significant in that it provides the molecular basis for the functional diversity of BAR domains and established the regulatory mechanism of BAR domain mediated-membrane deformation process. Genetically Encoded Calcium Indicators Genetically encoded calcium indicator GCAMP is an artificially designed multi-domain containing protein that can be endogenously expressed in cells to monitor calcium signals. The molecular mechanisms of its signal response and fast kinetics are poorly understood. Using fluorescent spectrometry and site-directed mutagenesis, I show that the calcium-dependent brightness of GCAMP is due to the different protonation states of the chromophore. Structural characterization of GCAMP reveals that the calmodulin domain regulates chromophore protonation states via a sophisticated water-mediated hydrogen bond network. This finding provided a general scheme for designing GCAMP-like sensors. Furthermore, I show that distinct electron properties of the protonated and deprotonated chromophore can be applied to design color switchable fluorescent proteins. This finding provides a novel approach to design the ratio metric pH sensors with an improved sensitivity.