A maximum entropy-based approach for the description of the conformational ensemble of calmodulin from paramagnetic NMR

dc.contributor.advisor

Donald, Bruce Randall

dc.contributor.advisor

Maggioni, Mauro

dc.contributor.author

Thelot, Francois

dc.date.accessioned

2016-05-04T21:23:58Z

dc.date.available

2017-05-08T04:30:05Z

dc.date.issued

2016-05-04

dc.department

Mathematics

dc.description.abstract

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.

dc.identifier.uri

https://hdl.handle.net/10161/11973

dc.language.iso

en_US

dc.subject

protein conformational ensemble

dc.subject

maximum entropy

dc.subject

calmodulin

dc.title

A maximum entropy-based approach for the description of the conformational ensemble of calmodulin from paramagnetic NMR

dc.type

Honors thesis

duke.embargo.months

18

Files

Original bundle

Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
thelot_thesis_final.pdf
Size:
1.95 MB
Format:
Adobe Portable Document Format
Description:
main