期刊
STRUCTURE
卷 21, 期 7, 页码 1097-1106出版社
CELL PRESS
DOI: 10.1016/j.str.2013.05.014
关键词
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资金
- Swiss National Science Foundation (SNF) [200021_122120, 200020_138013]
- Swiss National Science Foundation (SNF) [200020_138013, 200021_122120] Funding Source: Swiss National Science Foundation (SNF)
Proteins often assemble in multimeric complexes to perform a specific biologic function. However, trapping these high-order conformations is difficult experimentally. Therefore, predicting how proteins assemble using in silico techniques can be of great help. The size of the associated conformational space and the fact that proteins are intrinsically flexible structures make this optimization problem extremely challenging. Nonetheless, known experimental spatial restraints can guide the search process, contributing to model biologically relevant states. We present here a swarm intelligence optimization protocol able to predict the arrangement of protein symmetric assemblies by exploiting a limited amount of experimental restraints and steric interactions. Importantly, within this scheme the native flexibility of each protein subunit is taken into account as extracted from molecular dynamics (MD) simulations. We show that this is a key ingredient for the prediction of biologically functional assemblies when, upon oligomerization, subunits explore activated states undergoing significant conformational changes.
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