<p> To quote famous physicist and Nobel laureate, Dr. Richard Feynman, &ldquo;&hellip;everything that living things do can be understood in terms of the jigglings and wigglings of atoms.&rdquo; It is these jigglings and wigglings of atoms that form the focus of my dissertation, which studies the structural dynamics of two different allosteric proteins through computational simulations. Protein allostery is a field that has been investigated widely. But the structural details of how signals initiating at one site transmit through the network of residues in different proteins and result in the alteration of their functional states, still remains largely unresolved. Here, we independently study the kinesin motor protein and the neuromuscular acetylcholine receptor (nAChR) &ndash; both of which play crucial roles in cellular signaling. Kinesins are intracellular porters, carrying organelles, molecules and other cargo within the cell, while nAChRs are transmembrane receptors that aid in intercellular communication at nerve-to-muscle synapses. These two protein families are structurally and functionally very different, but both are allosteric in nature, with interesting protein dynamics that efficiently convert chemical energy to mechanical motions in order to perform their cellular functions.</p><p> The total timescale of an entire allosteric transition is currently too long for complete all-atom molecular dynamics simulations. Thus, in this dissertation, for both the projects, we begin at different equilibrium states of the proteins and carry out comparative analyses of conformation and dynamics at those states, which aids in elucidating the structural and functional correlates for these systems.</p><p> For the kinesin-microtubule (KIN-MT) system, we have built atomistic structure models for the key nucleotide-binding states of the kinesin-MT complex from lower resolution cryo-EM maps, by suitably modifying the MD potential with the EM map force. We have also studied ligand-protein (ADP/ATP-kinesin) interactions and predicted the sequence of structural changes in kinesin-MT complex during its conformational transitions between important biochemical states and pinpointed key contributing residues.</p><p> Simultaneously, we have also characterized the transmitter binding sites of neuromuscular acetylcholine receptors and analyzed the energy asymmetries between the fetal and adult endplate receptors. Through large-scale simulations of the fetal and adult binding sites, we have come across compelling evidence of the structural causes that explain these asymmetries and were successful in identifying the minimum construct that is both necessary and sufficient to exchange the function between adult and fetal binding sites in AChRs. Our <i> in silico</i> models and predictions act as important tools to further guide mutational and functional experiments.</p>