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Bioinformatics and Computational Biology Summer Institute |
Research Projects for Fellows, June 20 - August 6, 2005
P6: Analyzing Domain-Swapping Mechanism of Ribonuclease A Dimers and Trimers
| Title: | Analyzing Domain-Swapping Mechanism of Ribonuclease A Dimers and Trimers |
| Mentors: | Dr. Robert Jernigan |
| Description: | Domain-swapping is an evolutionary mechanism that creates oligomers by juxtaposition of similar monomers.
Although the advantages of oligomers over monomers are unclear, a recently proposed mechanism for amyloid fiber formation
(responsible for Alzheimer's disease, mad cow disease and others) involving domain swapping has increased the importance of
understanding domain-swapped proteins. In this project, the intern will look at domain-swapped protein dynamics of monomers, dimers,
and trimers to analyze possible mechanism(s) of this structural change. RNase A is a particularly interesting protein since
(1) it has two distinct different domain-swapped dimers, and (2) has mobile “hinge” regions. In this project,
the intern will develop a sense of biologically important issues by reading the literature, learn to use/develop computer code,
and relate protein dynamics predictions to experimental results.
The intern is expected to be familiar with computational languages (FORTRAN is preferable). When there is a lack of knowledge, motivation and interest can substitute. |
| Web Resources: | |
| References: | Kundu S, Jernigan RL., Molecular mechanism of domain swapping in proteins: an analysis of slower motions., Biophysical Journal, 86(6):3846-54, 2004 |