Protein Interactions and Fluctuations in a Proteomic Network using an Elastic Network Model |
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| Authors: | Melik C Demirel Ozlem Keskin |
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| Institution: | 1. College of Engineering Pennsylvania State University , University Park , PA , 16802 , USA;2. Center of Computational Biology and Bioinformatics , College of Engineering Koc University , 34450 , Istanbul , Turkey;3. Laboratory of Experimental , Computational Biology , NCI-Frederick, NIH, Frederick , MD , 21702 , USA |
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| Abstract: | Abstract A set of protein conformations are analyzed by normal mode analysis. An elastic network model is used to obtain fluctuation and cooperativity of residues with low amplitude fluctuations across different species. Slow modes that are associated with the function of proteins have common features among different protein structures. We show that the degree of flexibility of the protein is important for proteins to interact with other proteins and as the species gets more complex its proteins become more flexible. In the complex organism, higher cooperativity arises due to protein structure and connectivity. |
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