Abstract
Recent years have shown an increase in coarse-grained (CG) molecular dynamics simulations, providing structural and dynamic details of large proteins and enabling studies of self-assembly of biological materials. It is not easy to acquire such data experimentally, and access is also still limited in atomistic simulations.
During her PhD studies, Iwona Siuda used MARTINI CG models to study the dynamics of different globular and membrane proteins. In several cases, the MARTINI model was sufficient to study conformational changes of small, purely alpha-helical proteins. However, in studies of larger systems, the MARTINI model has to be combined with an elastic network extension called ELNEDIN to maintain the tertiary structure of the protein. For the purpose of studying conformational changes of proteins in an unbiased manner, the ELNEDIN model shows limitations, and a new model called domELNEDIN was therefore proposed as part of the work.
Iwona Siuda’s results from the CG simulations had biological implications that provide insights into possible mechanisms of the periplasmic leucine-binding protein, the sarco(endo)plasmic reticulum calcium pump, and several proteins from the saposin-like proteins family.
During her PhD studies, Iwona Siuda used MARTINI CG models to study the dynamics of different globular and membrane proteins. In several cases, the MARTINI model was sufficient to study conformational changes of small, purely alpha-helical proteins. However, in studies of larger systems, the MARTINI model has to be combined with an elastic network extension called ELNEDIN to maintain the tertiary structure of the protein. For the purpose of studying conformational changes of proteins in an unbiased manner, the ELNEDIN model shows limitations, and a new model called domELNEDIN was therefore proposed as part of the work.
Iwona Siuda’s results from the CG simulations had biological implications that provide insights into possible mechanisms of the periplasmic leucine-binding protein, the sarco(endo)plasmic reticulum calcium pump, and several proteins from the saposin-like proteins family.
| Original language | English |
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| Publisher | Aarhus University, Faculty of Science and Technology |
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| Number of pages | 164 |
| Commissioning body | Graduate School of Science and Technology |
| Publication status | Published - 5 Nov 2012 |