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Mapping Free Energy Landscapes of Proteins with Application to Kinase Catalytic Domains
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Date
2021
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Chemistry
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http://dx.doi.org/10.34944/dspace/6863
Abstract
One of the most attractive systems in drug design is protein kinases that can be inhibited by small molecules blocking the kinase activity when binding into the kinase catalytic active site. However, it is not always trivial how to design potent drug inhibitors that target a protein kinase family specifically and in fact, the design of protein kinase inhibitors has occupied a great amount of time and cost. Learning about the conformational landscape of the protein kinase families and extracting conformational states as potent drug targets can indeed be of great benefit to ligand optimization and addressing many questions in drug design. This dissertation provides insights into exploring the conformational landscape of protein kinase domains from two perspectives: I) Structural analysis of protein kinases available from public databases II) Free energy calculations to obtain the free energy cost associated with conformational transitions in protein kinases. In the first part of this dissertation, we cover the historical background of various structural studies and conformational classifications that have been carried out on protein kinases. We go over the most frequently observed inactive conformational states of protein kinases and analyze their statistics according to the families and discuss the structural features distinguishing two particular states: 1) The closest inactive state to the active state that could be a potential target of type-I inhibitors 2) The inactive state that is mostly targeted by Type-II inhibitors. We explain the challenges encountered in the classification of the Gly-Rich loop which is directly involved in ligand binding into the binding pocket. We also discuss the lessons on the conformational landscape of protein kinase domains taken from the residue-residue contact frequency map and the structural observations. The second part of this dissertation deals with the development and application of an alchemical free energy method called R-FEP-R. We pay close attention to the fundamental statistical mechanics of the R-FEP-R 1.0 method developed in the Levy lab and discuss how it is applicable to estimate the free energy cost between two stable conformational states including a side chain or N/C terminal conformational changes. We then extend the method to an adapted version R-FEP-R 2.0 that can be applied to loop conformational changes as well as side-chain conformational changes. Extending our studies, we show that our method does not encounter some challenges, such as the determination of collective variables or a physical pathway, that is usually dealt with in other methods (such as Umbrella Sampling), and in fact, it is more efficient. We apply our method to determine the free energy difference between two stable conformations of protein Ubiquitin, a regulatory protein that has been found in the bound state with USP (Ubiquitin-Specific Protease) in a less frequent conformational state than its ground state.
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