Browsing by Subject "UBD"
Now showing 1 - 2 of 2
Results Per Page
Sort Options
Item The determinants of chain type specificity and the mechanism of polyubiquitination by HECT E3s(2010-12) Kim, Hyung Cheol; Huibregtse, Jon M.; Appling, Dean; Johnson, Arlen; Paull, Tanya; Stevens, ScottUbiquitination is a post-translational modification that can take several forms. Some proteins are modified with a single ubiquitin molecule, while others are modified with polyubiquitin chains. Each type of ubiquitination is thought to have distinct biological functions. The best-characterized types of ubiquitin modification are K48-linked polyubiquitination, which serves as a signal for proteasomal degradation and K63-linked polyubiquitination, which has non-proteolytic functions such in DNA repair, signaling, and endocytosis. HECT ubiquitin ligases (HECT E3s) form a class of E3s, defined by a C terminal catalytic domain. Several lines of evidence suggested that the HECT E3s assemble a polyubiquitin chain in a sequential manner with one molecule of ubiquitin at a time being conjugated to the distal ubiquitin of the chain. In the process of chain elongation, not all HECT E3s target a common internal lysine of ubiquitin, leading to diversification of chain type specificity in HECT E3s. For example, yeast Rsp5 forms K63 chains, while human E6AP forms K48 chains. Two important mechanistic questions were addressed in my work: 1) what are the determinants of chain type specificity of HECT E3s, and 2) what allows the distal ubiquitin of a chain to be continuously oriented near the active site of the HECT domain in the course of a sequential polyubiquitination reaction? I have determined that the chain type specificity of Rsp5 is a function solely of the HECT domain. Further, through the generation of chimeric HECT E3s, I demonstrated that chain type specificity determinants are located within the last 60 amino acids of the C lobe of the HECT domain. To address the second question, we solved the structure of Rsp5 HECT domain in complex with non-covalently bound ubiquitin in collaboration with Jue Chen’s laboratory (Purdue University). From the structure, we found that the N lobe of the HECT domain binds ubiquitin in a manner distinct from other known ubiquitin binding domains, and I have shown that Rsp5 proteins defective for ubiquitin binding are defective for chain elongation. We hypothesize that the ubiquitin binding site functions in the recruitment of the distal ubiquitin of polyubiquitin chain for efficient polyubiquitination.Item Managed Pressure Drilling Candidate Selection(2010-07-14) Nauduri, Anantha S.Managed Pressure Drilling now at the pinnacle of the 'Oil Well Drilling' evolution tree, has itself been coined in 2003. It is an umbrella term for a few new drilling techniques and some preexisting drilling techniques, all of them aiming to solve several drilling problems, including non-productive time and/or drilling flat time issues. These techniques, now sub-classifications of Managed Pressure Drilling, are referred to as 'Variations' and 'Methods' of Managed Pressure Drilling. Although using Managed Pressure Drilling for drilling wells has several benefits, not all wells that seem a potential candidate for Managed Pressure Drilling, need Managed Pressure Drilling. The drilling industry has numerous simulators and software models to perform drilling hydraulics calculations and simulations. Most of them are designed for conventional well hydraulics, while some can perform Underbalanced Drilling calculations, and a select few can perform Managed Pressure Drilling calculations. Most of the few available Managed Pressure Drilling models are modified Underbalanced Drilling versions that fit Managed Pressure Drilling needs. However, none of them focus on Managed Pressure Drilling and its candidate selection alone. An 'Managed Pressure Drilling Candidate Selection Model and software' that can act as a preliminary screen to determine the utility of Managed Pressure Drilling for potential candidate wells are developed as a part of this research dissertation. The model and a flow diagram identify the key steps in candidate selection. The software performs the basic hydraulic calculations and provides useful results in the form of tables, plots and graphs that would help in making better engineering decisions. An additional Managed Pressure Drilling worldwide wells database with basic information on a few Managed Pressure Drilling projects has also been compiled that can act as a basic guide on the Managed Pressure Drilling variation and project frequencies and aid in Managed Pressure Drilling candidate selection.