Allosteric transition, the basis of signal transduction and central to the function of regulatory proteins (e.g., transcriptional factors), is widely involved in biological systems with conformational change as a key characteristic. Although end-state structures are known for many proteins, less is known about the underlying detailed mechanism of the allosteric transition. We have used LacI as a model system to investigate this process at the atomic level. The work in this thesis focuses on three regions of LacI: the core pivot region, the N-subdomain monomer-monomer interface, and the hinge region. Characterization of representative mutants (L148F, S151P, P320A, and Q60G/L148F) demonstrated that the core pivot region exerts long-range effects on LacI function. For L148F and S151P, operator and inducer binding are altered in an inverse fashion with binding for one ligand strengthened, and binding for the other ligand weakened. Further characterization of L148F and S 151P has indicated that the conformational equilibrium is shifted towards the induced state in L148F and towards the repressed end in S151P. This conclusion is supported by detailed thermodynamic ligand binding assays and UV difference spectra. Detailed unfolding/refolding studies further suggest that the intrinsic ligand-binding properties of L148F and S151P are altered. Global fitting of all ligand-binding data is underway to further characterize these shifts. Our data for K84 hydrophobic variants (K84A/L) disclose impeded allosteric response to inducer, a state that is supported by a unique pattern in UV difference spectra. Operator release kinetics for K84A/L in response to IPTG suggest that two inducer molecules are required to release operator DNA. Characterization of 13 substitutions at V52, including binding to operator sequence variants, indicates a dominant role of the protein-operator interaction in LacI allostery and high affinity operator binding. Moreover, subsets of mutants that decouple inducer binding and conformational change were identified. In summary, this thesis work emphasizes the key role of several regions in LacI allostery, identifies several LacI allosteric intermediates, and discloses intermediates trapped along the allosteric pathway by mutation that correlate with points along the TMD simulation.