کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
2829395 1162806 2007 14 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
A study of collective atomic fluctuations and cooperativity in the U1A–RNA complex based on molecular dynamics simulations
موضوعات مرتبط
علوم زیستی و بیوفناوری بیوشیمی، ژنتیک و زیست شناسی مولکولی زیست شناسی مولکولی
پیش نمایش صفحه اول مقاله
A study of collective atomic fluctuations and cooperativity in the U1A–RNA complex based on molecular dynamics simulations
چکیده انگلیسی

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.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Structural Biology - Volume 157, Issue 3, March 2007, Pages 500–513
نویسندگان
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