ArticleProceedings of the National Academy of Sciences of the United States of America2005
A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 40 citations in OpenAlex.
- Article
- Graphene Nanopores for Protein Sequencing.Advanced functional materials · 2016Article
- A thorough anion-π interaction study in biomolecules: on the importance of cooperativity effects.Chemical science · 2016Article
- The role of the C-terminal helix of U1A protein in the interaction with U1hpII RNA.Nucleic acids research · 2013Article
- Article
- Putative molecular mechanisms underlying tandem CCCH zinc finger protein mediated plant growth, stress, and gene expression responses.Plant signaling & behavior · 2011Review
- Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis: the role of G8 tryptophan.The Journal of biological chemistry · 2009Article
- Mechanism of thermal decomposition of carbamoyl phosphate and its stabilization by aspartate and ornithine transcarbamoylases.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Explaining an unusually fast parasitic enzyme: folate tail-binding residues dictate substrate positioning and catalysis in Cryptosporidium hominis thymidylate synthase.Biochemistry · 2008Article
- Sequence-specific binding of single-stranded RNA: is there a code for recognition?Nucleic acids research · 2006Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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