The award, funded by the Systems and Synthetic Biology Program in MCB, the Biotechnology, Biochemical and Biomass Engineering Program in CBET, and EPSCoR, is aimed at understanding the fundamental process of macromolecular assembly within cells. Many cellular functions are carried out by large protein complexes known as "molecular machines". The cell does not synthesize these machines as single, active units, but rather as a set of protein parts that must be assembled into a particular structure in order for the machine to function. Despite decades of research, it is still unclear exactly how assembly processes ensure the efficient and reliable production of these machines within cells. A major barrier to understanding assembly has been a comparative lack of theoretical investigation into the assembly process. This grant focuses on overcoming this problem by combining novel computational simulation techniques with experimental tests to study the assembly of the proteasome. This massive molecular machine is primarily responsible for disposing of damaged or unwanted proteins by cutting them into smaller pieces that can be eventually reused by the cell, and accurate assembly is crucial for its function. Findings from this research will not only provide insight into the assembly of the proteasome itself, but also shed light on the general principles of efficient macromolecular assembly. These general principles will likely be applicable to a wide array of cellular machines, and could eventually be applied to the design of synthetic materials that can self-assemble reliably in a wide range of environments.
This grant will also support ongoing outreach activities at the University of Kansas. In particular, the proposed research will be integrated into a recently-developed program in which high school students are exposed to the importance of modeling and quantitative biology. This work will also be used as a platform to recruit undergraduate and graduate students from underrepresented backgrounds both to KU and the labs in which this research will be performed. These efforts will focus on leveraging existing undergraduate research programs at KU aimed at minority students and will strengthen recruiting efforts at national conferences such as ABRCMS and SACNAS.
proteasome consists of a proteolytically active Core Particle (CP), containing 14 alpha and 14 beta proteins arranged in an alpha7beta7beta7alpha7 pattern, and a Regulatory Particle (RP) that binds the alpha rings and controls which substrates are degraded. The enzyme is only active if the subunits adopt this specific three-dimensional structure, making efficient assembly crucial for proteasome function. Extensive experimental study has led to the proposal of a number of hypothetical proteasome assembly mechanisms, governing everything from the self-assembly of prokaryotic CPs in vitro to the chaperone-assisted assembly of eukaryotic RPs in vivo. To date, however, there has been no attempt to make a formal or mathematical model of this process. It is thus difficult to fully evaluate current assembly mechanisms, since their predictions have never been formally established or quantitatively tested.
A major focus of research in the Deeds lab involves using a combination of computational models and experimental tests to overcome this problem. The proposed research will leverage novel simulation tools that allow for efficient simulation of proteasome assembly. Predictions from these simulations will be tested and validated against in vitro and in vivo experimental data obtained by collaborators. The unprecedented combination of modeling and experiment has the potential to fundamentally transform our understanding of how certain mechanisms, such as assembly chaperones, act to increase the reliability and efficiency of assembly. While this proposal is focused on a particular model system, our work will begin to elucidate a set of general principles of macromolecular assembly, principles that could be applied to our understanding of other large machines or to the design of novel nanomaterials that self-assemble with high yields in vitro or in vivo.
