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- W2124383454 abstract "Cooperative interactions play an important role in recognition and binding in macromolecular systems. In this study, we find that cross-correlated atomic fluctuations can be used to identify cooperative networks in a protein–RNA system. The dynamics of the RRM-containing protein U1A–stem loop 2 RNA complex have been calculated theoretically from a 10 ns molecular dynamics (MD) simulation. The simulation was analyzed by calculating the covariance matrix of all atomic fluctuations. These matrix elements are then presented in the form of a two-dimensional grid, which displays fluctuations on a per residue basis. The results indicate the presence of strong, selective cross-correlated fluctuations throughout the RRM in U1A–RNA. The atomic fluctuations correspond well with previous biophysical studies in which a multiplicity of cooperative networks have been reported and indicate that the various networks identified in separate individual experiments are fluctuationally correlated into a hyper-network encompassing most of the RRM. The calculated results also correspond well with independent results from a statistical covariance analysis of 330 aligned RRM sequences. This method has significant implications as a predictive tool regarding cooperativity in the protein–nucleic acid recognition process." @default.
- W2124383454 created "2016-06-24" @default.
- W2124383454 creator A5031194172 @default.
- W2124383454 creator A5043639901 @default.
- W2124383454 creator A5062449462 @default.
- W2124383454 date "2007-03-01" @default.
- W2124383454 modified "2023-10-17" @default.
- W2124383454 title "A study of collective atomic fluctuations and cooperativity in the U1A–RNA complex based on molecular dynamics simulations" @default.
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