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posted 02. March 2006 19:01
Dependency Map of Proteins in the Small Ribosomal Subunit
Kay Hamacher, Joanna Trylska, J. Andrew McCammon
The ribosome acts as the protein–production facility of the cell. Interfering with its assembly will shut down the function of the cell. The bacterial ribosome^ differs from the eukaryotic^ one. Both properties together prompt for the development of antibiotics targeting the bacterial ribosome. To target this macromolecular complex most efficiently, one needs to understand the assembly process. The smaller subunit consists of 21 proteins and a 1500 nucleotide long RNA^ chain. This size makes it unfeasible to treat the assembly process with conventional computational techniques^. To overcome this size limit, this paper introduces a new approach which computes energetic and entropic^ contributions to the binding energy of individual proteins. By systematic Gedanken experiments and an accompanying analysis procedure we were able to deduce the binding dependencies of the proteins and the influences of their respective absence or presence onto other proteins. From the obtained influence map we can deduce potential target proteins for drug development or other binding hindering experiments.
Received: July 11, 2005; Accepted: December 30, 2005; Published: February 17, 2006
Copyright: © 2006 Hamacher et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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[Link-underlined terms with ^ indicate linked entry in ISCID Encyclopedia of Science and Philosophy as added by ISCID News Editor]
To read the full research article, visit PLoS Computational Biology
[ 02. March 2006, 19:06: Message edited by: ISCID News Editor ]