Molecular Dynamics and Thermodynamics of Protein-RNA Interactions: Mutation of a Conserved Aromatic Residue Modifies Stacking Interactions and Structural Adaptation in the U1A-Stem Loop 2 RNA Complex
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- 作者：Dukagjin M. Blakaj ; Kevin J. McConnell ; David L. Beveridge ; and Anne M. Baranger
- 刊名：Journal of the American Chemical Society
- 出版年：2001
- 出版时间：March 21, 2001
- 年：2001
- 卷：123
- 期：11
- 页码：2548 - 2551
- 全文大小：236K
- 年卷期：v.123,no.11(March 21, 2001)
- ISSN：1520-5126
文摘
Molecular dynamics (MD) simulations and free energy component analysis have been performedto evaluate the molecular origins of the 5.5 kcal/mol destabilization of the complex formed between theN-terminal RNP domain of U1A and stem loop 2 of U1 snRNA upon mutation of a conserved aromaticresidue, Phe56, to Ala. MD simulations, including counterions and water, have been carried out on the wildtype and Phe56Ala peptide-stem loop 2 RNA complexes, the free wild type and Phe56Ala peptides, and thefree stem loop 2 RNA. The MD structure of the Phe56Ala-stem loop 2 complex is similar to that of the wildtype complex except the stacking interaction between Phe56 and A6 of stem loop 2 is absent and loop 3 of thepeptide is more dynamic. However, the MD simulations predict large changes in the structure and dynamicsof helix C and increased dynamic range of loop 3 for the free Phe56Ala peptide compared to the wild typepeptide. Since helix C and loop 3 are highly variable regions of RNP domains, this indicates that a significantcontribution to the reduced affinity of the Phe56Ala peptide for RNA results from cooperation between highlyconserved and highly variable regions of the RNP domain of U1A. Surprisingly, these structural effects, whichare manifested as cooperative free energy changes, occur in the free peptide, rather than in the complex, andare revealed only by study of both the initial and final states of the complexation process. Free energy componentanalysis correctly accounts for the destabilization of the Phe56Ala-stem loop 2 complex, and indicates that~80% of the destabilization is due to the loss of the stacking interaction and ~20% is due to differences inU1A adaptation.