Ca2+ is a key second messenger governing many physiological functions. However, its concentration in the cytosol must be tightly regulated, as excessive Ca2+ can be toxic to cells. Voltage-Gated Calcium Channels (VGCCs) such as CaV1.2, an L-type Ca²⁺ channel abundantly expressed in the brain and heart, plays a key role in regulating the influx of Ca²⁺ which is critical for processes such as neuronal excitability, synaptic plasticity, learning, and memory, heart beats and vascular tone among others. Dysfunction of the CaV1.2 channel has also been implicated in the etiology of various disorders such as arrhythmias, autism, bipolar disorder, epilepsy, Timothy Syndrome, heart failure, and stroke. Thus, it is essential to understand how CaV1.2 activity is regulated, and how calcium homeostasis is maintained for proper physiological function. In this dissertation, I will first show how computational methods for protein structure prediction were used to build a complex model of CaV1.2 inactivation with available structural data. Initial electron density refinement and homology modeling for CaV1.2 was performed on the α11.2 pore forming subunit utilizing the cryogenic - electron microscopy (cryo-EM) structures of a homologous rabbit-derived isoform CaV1.1 (PDB ID: 6JP8). The published structures of ion channels are believed to represent the channel inactivated state, due to the conditions the proteins are subjected to during cryo-EM experiments. Also, the cryo-EM structures of CaV1.1 and CaV1.2 reveal a closed pore domain with each voltage-sensor domain pointing upward, which necessarily implies the channel must be in the inactivated state. Thus, my homology model of the α11.2 subunit was used as the basis for combining: (1) a de novo folding prediction of the proximal C-terminus (PCT) and (2) an NMR structure of the downstream IQ helix in complex with the calcium-binding protein calmodulin (CaM), creating a foundational model of the pore-forming α1 subunit of CaV1.2 in the inactivated state. Previous studies have shown that CaM binds to and modulates CaV1.2 activity. Further work has shown that under basal resting Ca²⁺ concentrations, CaM is pre-associated with the channel, and our model suggests that when the channel pore is opened, local Ca²⁺ influx drives a rapid inactivation of the channel, called Ca²⁺ dependent inactivation (CDI)—a negative feedback mechanism that prevents prolonged Ca²⁺ current into the cell. We propose that under resting conditions, half-calcified CaM binds to the IQ motif, which interacts with the EF-hands in the α11.2 c-terminus, preventing the formation of the α11.2 EF-hand/III-IV linker complex, which would otherwise block Ca²⁺ influx. Upon voltage stimulation, the channel activates and opens—leading to increased local Ca²⁺ concentrations. When Ca²⁺ binds to all four EF-hands of the CaM that is pre-associated with the α11.2 IQ motif, the fully-calcified CaM preferentially binds to the IQ helix and sequesters it from the pre-IQ EF-hands, allowing them to form a complex with the III-IV linker and thereby drive calcium-dependent inactivation. Using the results of my computational structure prediction of the proximal C-terminus and its associated III-IV linker to understand structural mechanisms of the CaV1.2 inactivation, I targeted several key interactions with site-directed mutagenesis to disrupt the PCT inactivation complex and utilizing electrophysiological testing and analyses—showed that this complex serves a key role in mediating not only CDI but also affects voltage-dependent inactivation (VDI). Altogether, this PhD thesis seeks to integrate computational methods for prediction of protein structure to better inform the traditional electrophysiological characterizations of ion channel activity states and ultimately dissect the biophysical mechanisms of ion channel function.