Protein allostery plays central roles in regulation of enzyme catalysis, signaling conduction and cellular metabolism. In this research, the interdomain allostery of postsynaptic density protein 95 (PSD-95), a key component of the postsynapse, was studied using NMR and other biophysical methods. Previous research has identified numerous PSD-95 interaction partners and revealed many PSD-95 mediated biological functions. Interestingly, interdomain allostery within PSD-95 has been found between PDZ3 and the following SH3/GK, and these allosteric events are regulated by phosphorylation. However, the structural mechanism of interdomain allostery and phosphorylation regulation is not addressed by in vivo studies on biological functions or in vitro studies on excised domains. In this dissertation, we studied the structural and dynamic effects of phosphorylation at the PDZ3/SH3 linker (Y397, S415 and S418). Upon phosphorylation, we found that the C-extension α-helix of PDZ3 is unfolded and undocked. We further examined the PDZ3-SH3 construct and showed that phosphorylation interrupts the domain interaction between PDZ3 and SH3. Using chemical shift perturbation and paramagnetic relaxation enhancement, we identified the PDZ3-SH3 interface. These experiments also suggested that CRIPT binding moves PDZ3 away from SH3. To understand interdomain allostery, we modeled the PDZ3-SH3-GK structure using SAXS. Consistent with PRE results, we found PDZ3 is mainly docked to the Hook domain region of the SH3 domain, and CRIPT binding reshuffles the domain packing between PDZ3 and SH3-GK. To obtain a high resolution structural model of PDZ3-SH3-GK, we carried out Rosetta simulations in the presence of PRE and chemical shift perturbation constraints. We found that the PDZ3 domain uses its peptide binding groove to interact with the PDZ3-SH3 linker. This interaction brings PDZ3 close to SH3, whereas it can be disrupted by CRIPT binding. This Rosetta model also reveals that the positively charged face of the Hook domain, which is the binding interface for calmodulin, is masked by the PDZ3 domain. Therefore the model provides a basis for understanding interdomain allostery between SH3 and PDZ3. In this research we also discussed the possible mechanism by which PDZ3 and GK allostery is transferred. Advisors/Committee Members: Zhang, Jun, Lee, Andrew, University of North Carolina at Chapel Hill.