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Anatomy of noncovalent interactions between the nucleobases or ribose and ?-containing amino acids in RNA-protein complexes.

ABSTRACT: A set of >300 nonredundant high-resolution RNA-protein complexes were rigorously searched for ?-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an RNA nucleobase (denoted ?-? interaction) or ribose moiety (denoted sugar-?). The resulting dataset of >1500 RNA-protein ?-contacts were visually inspected and classified based on the interaction type, and amino acids and RNA components involved. More than 80% of structures searched contained at least one RNA-protein ?-interaction, with ?-? contacts making up 59% of the identified interactions. RNA-protein ?-? and sugar-? contacts exhibit a range in the RNA and protein components involved, relative monomer orientations and quantum mechanically predicted binding energies. Interestingly, ?-? and sugar-? interactions occur more frequently with RNA (4.8 contacts/structure) than DNA (2.6). Moreover, the maximum stability is greater for RNA-protein contacts than DNA-protein interactions. In addition to highlighting distinct differences between RNA and DNA-protein binding, this work has generated the largest dataset of RNA-protein ?-interactions to date, thereby underscoring that RNA-protein ?-contacts are ubiquitous in nature, and key to the stability and function of RNA-protein complexes.

SUBMITTER: Wilson KA

PROVIDER: S-EPMC7913691 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA-protein complexes.

Wilson Katie A KA Kung Ryan W RW D'souza Simmone S Wetmore Stacey D SD

Nucleic acids research 20210201 4

A set of >300 nonredundant high-resolution RNA-protein complexes were rigorously searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an RNA nucleobase (denoted π-π interaction) or ribose moiety (denoted sugar-π). The resulting dataset of >1500 RNA-protein π-contacts were visually inspected and classified based on the interaction type, and amino acids and RNA components involved. More than 80% of structures searched contained at least one RNA-protein π-interactio ...[more]

PMID: 33544852

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Project description:Geometric (HOMA) and magnetic (NICS) indices of aromaticity were estimated for aromatic rings of amino acids and nucleobases. Cartesian coordinates were taken directly either from PDB files deposited in public databases at the finest resolution available (? 1.5 Å), or from structures resulting from full gradient geometry optimization in a hybrid QM/MM approach. Significant environmental effects imposing alterations of HOMA values were noted for all aromatic rings analysed. Furthermore, even extra fine resolution (? 1.0 Å) is not sufficient for direct estimation of HOMA values based on Cartesian coordinates provided by PDB files. The values of mean bond errors seem to be much higher than the 0.05 Å often reported for PDB files. The use of quantum chemistry geometry optimization is strongly advised; even a simple QM/MM model comprising only the aromatic substructure within the QM region and the rest of biomolecule treated classically within the MM framework proved to be a promising means of describing aromaticity inside native environments. According to the results presented, three consequences of the interaction with the environment can be observed that induce changes in structural and magnetic indices of aromaticity. First, broad ranges of HOMA or NICS values are usually obtained for different conformations of nearest neighborhood. Next, these values and their means can differ significantly from those characterising isolated monomers. The most significant increase in aromaticities is expected for the six-membered rings of guanine, thymine and cytosine. The same trend was also noticed for all amino acids inside proteins but this effect was much smaller, reaching the highest value for the five-membered ring of tryptophan. Explicit water solutions impose similar changes on HOMA and NICS distributions. Thus, environment effects of protein, DNA and even explicit water molecules are non-negligible sources of aromaticity changes appearing in the rings of nucleobases and aromatic amino acids residues.

Dataset Information

Anatomy of noncovalent interactions between the nucleobases or ribose and ?-containing amino acids in RNA-protein complexes.

Publications

Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA-protein complexes.

Similar Datasets

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