Ubiquitin (Ub) is a protein that serves several important functions in all eukaryotes. Its role involves post-translational modification of target proteins which results in signaling for cellular activities of various kinds. Given several malignancies and neurodegenerative diseases caused by defects that arise in ubiquitin mediated pathways, understanding all the variations in ubiquitin based signaling and the selectivity and specificity involved in the pathways is imperative in potentially targeting and treating various ailments that are caused by the disruption within said pathways. For this purpose, this study examined possible therapeutic methods that could target the ubiquitin-proteasome system at the ubiquitin chain level. Binding studies utilizing NMR in addition to various SDS PAGE gel assays and crystallography were important in understanding how select therapeutic molecules interacted with ubiquitin chains. A secondary study involved Rub1, a protein that is very similar to ubiquitin in terms of sequence and structure. Comparative mutation-based gel assays, NMR analysis and mass spectrometry methods were explored with the goal of incorporating Rub1 within ubiquitin conjugation pathways and making polyRub1 chains. In addition, NMR, DSC, and CD based temperature studies were performed to further understand the structural differences between these closely related proteins and hopefully gain more insight into the seemingly special functional nature of ubiquitin.