Protein molecules can undergo a wide variety of conformational transitions occurring over a series of time and distance scales, ranging from large-scale structural reorganizations required for folding to more localized and subtle motions required for function. Furthermore, the dynamics and mechanisms of such motions and transitions delicately depend on many factors and, as a result, it is not always easy, or even possible, to use existing experimental techniques to arrive at a molecular level understanding of the conformational event of interest. Therefore, this thesis aims to develop and utilize non-natural chemical modification strategies, namely molecular cross-linkers and unnatural amino acids as site-specific spectroscopic probes, in combination with various spectroscopic methods to examine, in great detail, certain aspects of protein folding and functional dynamics, and to manipulate protein self-assemblies. Specifically, we first demonstrate how strategically placed molecular constraints can be used to manipulate features of the protein folding free energy landscape, thus, allowing direct measurement of key components via temperature-jump kinetic studies, such as folding from a transition-state structure or the effect of internal friction on the folding mechanism. Secondly, we utilize a photolabile non-natural amino acid, Lys(nvoc), to probe the mechanism of protein misfolding in a β-hairpin model and identify an aggregation gatekeeper that tunes the aggregation propensity. We further develop a method where the induced-charge produced by photocleavage of Lys(nvoc) can be used to target and destabilize hydrophobic regions of amyloid fibril assemblies, resulting in complete disassembly, Finally, we highlight new useful properties of a site-specific spectroscopic probe, 5-cyanotryptophan (TrpCN), by demonstrating (1) how the frequency and linewidth of the infrared nitrile stretching vibration is sensitive to multiple hydrogen bonding interactions and solvent polarity, (2) that the fluorescence emission, quantum yield, and lifetime is extremely sensitive to hydration, and serves as a convenient fluorescence probe of protein solvation status, and (3) that the unique characteristics of TrpCN can be used to target the structure, local environment, and mechanism of the tryptophan gate in the M2 membrane proton channel of the influenza A virus.