Unknown

Dataset Information

0

A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding.


ABSTRACT: We present a close electronic view of the protein-base interface for the N-terminal domain of the human protein U1A. Combining accurate mixed quantum mechanics/molecular mechanics techniques and protein structure prediction methods, we provide a detailed electronic structure description of the protein-RNA stacking interactions. Our analysis indicates the evolution of the protein structure optimizing the interaction between Asp-92 and the RNA bases. The results show a direct coupling of the C-terminal tail and Asp-92, providing a direct rationalization of the experimentally determined role of the C-terminal domain in RNA binding. Here, we propose a mechanism where a protein side chain, with a delocalized electronic pi system, assists in the nucleotide binding. The binding mechanism involves a short-range interaction of the side chain with the nucleotide base and an electronic long-range interaction through a sandwich-stacking motif. The structural motif of the binding mechanism is observed in similar protein-RNA interactions and in various protein-ATP-binding sites.

SUBMITTER: Guallar V 

PROVIDER: S-EPMC554833 | biostudies-literature | 2005 Mar

REPOSITORIES: biostudies-literature

altmetric image

Publications

A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding.

Guallar Victor V   Borrelli Kenneth W KW  

Proceedings of the National Academy of Sciences of the United States of America 20050307 11


We present a close electronic view of the protein-base interface for the N-terminal domain of the human protein U1A. Combining accurate mixed quantum mechanics/molecular mechanics techniques and protein structure prediction methods, we provide a detailed electronic structure description of the protein-RNA stacking interactions. Our analysis indicates the evolution of the protein structure optimizing the interaction between Asp-92 and the RNA bases. The results show a direct coupling of the C-ter  ...[more]

Similar Datasets

| S-EPMC3835729 | biostudies-literature
| S-EPMC3732173 | biostudies-literature
| S-EPMC6506629 | biostudies-literature
| S-EPMC1326249 | biostudies-literature
| S-EPMC8695263 | biostudies-literature
| S-EPMC1484440 | biostudies-literature
| S-EPMC3375920 | biostudies-literature
| S-EPMC5775260 | biostudies-literature
| S-EPMC3661757 | biostudies-literature
| S-EPMC5374631 | biostudies-literature