A maximum entropy-based approach for the description of the conformational ensemble of calmodulin from paramagnetic NMR
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Characterizing protein dynamics is an essential step towards a better understanding of protein function. Experimentally, we can access information about protein dynamics from paramagnetic NMR data such as pseudocontact shifts, which integrate ensemble-averaged information about the motion of proteins. In this report, we recognize that the relative position of the two domains of calmodulin can be represented as the evolution of one of the domains in the space of Euclidean motions. From this perspective, we suggest a maximum entropy-based approach for finding a probability distribution on SE(3) satisfying experimental NMR measurements. While sampling of SE(3) is performed with the ensemble generator EOM, the proposed framework can be extended to uniform sampling of the space of Euclidean motions. At the end of this study, we find that the most represented protein conformations for calmodulin corresponds to conformations in which both protein domains are in close contact, despite being largely different from each other. Such a representation agrees with the random coil linker model, and sharply differs with the extended crystal structure of calmodulin.
CitationThelot, Francois (2016). A maximum entropy-based approach for the description of the conformational ensemble of calmodulin from paramagnetic NMR. Honors thesis, Duke University. Retrieved from https://hdl.handle.net/10161/11973.
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Rights for Collection: Undergraduate Honors Theses and Student papers