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
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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DOI：
10.1021/ja005538j
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发表时间：
2001-03-21
影响因子：
15
通讯作者：
Baranger, AM
中科院分区：
文献类型：
--
作者：
Blakaj, DM;McConnell, KJ;Baranger, AM
分子动力学（MD）模拟和自由能分量分析已经进行了评估的分子起源的5.5千卡/摩尔之间形成的复合物的不稳定的N-末端RNP结构域的U1 A和茎环2的U1 snRNA突变后的保守的芳香族残基，苯丙氨酸56，丙氨酸。已经对野生型和Phe 56 Ala肽-茎环2 RNA复合物、游离野生型和Phe 56 Ala肽以及游离茎环2 RNA进行了包括抗衡离子和水的MD模拟。Phe 56 Ala-茎环2复合物的MD结构类似于野生型复合物的MD结构，除了Phe 56和茎环2的A6之间的堆叠相互作用不存在并且肽的环3更具动态性。然而，MD模拟预测的螺旋C的结构和动力学的大的变化和增加的动态范围的环3的游离Phe 56 Ala肽相比，野生型肽。由于螺旋C和环3是RNP结构域的高度可变区，这表明U1 A的RNP结构域的高度保守区和高度可变区之间的合作导致Phe 56 Ala肽对RNA的亲和力降低。令人惊讶的是，这些结构的影响，表现为合作的自由能变化，发生在游离肽，而不是在复杂的，只有通过研究的初始和最终状态的络合过程中揭示。自由能分量分析正确地解释了Phe 5 BAla-茎环2复合物的不稳定性，并表明类似于80%的不稳定性是由于堆叠相互作用的损失，而类似于20%是由于U1 A适应的差异。
Molecular dynamics (MD) simulations and free energy component analysis have been performed to evaluate the molecular origins of the 5.5 kcal/mol destabilization of the complex formed between the N-terminal RNP domain of U1A and stem loop 2 of U1 snRNA upon mutation of a conserved aromatic residue, Phe56, to Ala. MD simulations, including counterions and water, have been carried out on the wild type and Phe56Ala peptide-stem loop 2 RNA complexes, the free wild type and Phe56Ala peptides, and the free stem loop 2 RNA. The MD structure of the Phe56Ala-stem loop 2 complex is similar to that of the wild type complex except the stacking interaction between Phe56 and A6 of stem loop 2 is absent and loop 3 of the peptide is more dynamic. However, the MD simulations predict large changes in the structure and dynamics of helix C and increased dynamic range of loop 3 for the free Phe56Ala peptide compared to the wild type peptide. Since helix C and loop 3 are highly variable regions of RNP domains, this indicates that a significant contribution to the reduced affinity of the Phe56Ala peptide for RNA results from cooperation between highly conserved and highly variable regions of the RNP domain of U1A. Surprisingly, these structural effects, which are manifested as cooperative free energy changes, occur in the free peptide, rather than in the complex, and are revealed only by study of both the initial and final states of the complexation process. Free energy component analysis correctly accounts for the destabilization of the Phe5BAla-stem loop 2 complex, and indicates that similar to 80% of the destabilization is due to the loss of the stacking interaction and similar to 20% is due to differences in U1A adaptation.