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Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions.
J Biomol Struct Dyn. 2014; 32(10):1686-704.JB

Abstract

The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, and uracil, are structurally similar, but the proteins that bind to them are able to discriminate them and form interactions. Since nonbonded interactions are responsible for molecular recognition processes in biological systems, our work attempts to understand some of the underlying principles of such recognition of pyrimidine molecular structures by proteins. The preferences of the amino acid residues to contact the pyrimidine bases in terms of nonbonded interactions; amino acid residue-ligand atom preferences; main chain and side chain atom contributions of amino acid residues; and solvent-accessible surface area of ligand atoms when forming complexes are analyzed. Our analysis shows that the amino acid residues, tyrosine and phenyl alanine, are highly involved in the pyrimidine interactions. Arginine prefers contacts with the cytosine base. The similarities and differences that exist between the interactions of the amino acid residues with each of the three pyrimidine base atoms in our analysis provide insights that can be exploited in designing specific inhibitors competitive to the ligands.

Authors+Show Affiliations

a Department of Bioinformatics, School of Life Sciences , Bharathidasan University , Tiruchirappalli 620 024 , Tamilnadu , India .No affiliation info available

Pub Type(s)

Journal Article

Language

eng

PubMed ID

24028440

Citation

Usha, S, and S Selvaraj. "Structure-wise Discrimination of Cytosine, Thymine, and Uracil By Proteins in Terms of Their Nonbonded Interactions." Journal of Biomolecular Structure & Dynamics, vol. 32, no. 10, 2014, pp. 1686-704.
Usha S, Selvaraj S. Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions. J Biomol Struct Dyn. 2014;32(10):1686-704.
Usha, S., & Selvaraj, S. (2014). Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions. Journal of Biomolecular Structure & Dynamics, 32(10), 1686-704. https://doi.org/10.1080/07391102.2013.832384
Usha S, Selvaraj S. Structure-wise Discrimination of Cytosine, Thymine, and Uracil By Proteins in Terms of Their Nonbonded Interactions. J Biomol Struct Dyn. 2014;32(10):1686-704. PubMed PMID: 24028440.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions. AU - Usha,S, AU - Selvaraj,S, Y1 - 2013/09/13/ PY - 2013/9/14/entrez PY - 2013/9/14/pubmed PY - 2015/2/28/medline KW - atom–atom contacts KW - computation KW - nonbonded interactions KW - protein–pyrimidine KW - pyrimidines KW - residue preferences SP - 1686 EP - 704 JF - Journal of biomolecular structure & dynamics JO - J Biomol Struct Dyn VL - 32 IS - 10 N2 - The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, and uracil, are structurally similar, but the proteins that bind to them are able to discriminate them and form interactions. Since nonbonded interactions are responsible for molecular recognition processes in biological systems, our work attempts to understand some of the underlying principles of such recognition of pyrimidine molecular structures by proteins. The preferences of the amino acid residues to contact the pyrimidine bases in terms of nonbonded interactions; amino acid residue-ligand atom preferences; main chain and side chain atom contributions of amino acid residues; and solvent-accessible surface area of ligand atoms when forming complexes are analyzed. Our analysis shows that the amino acid residues, tyrosine and phenyl alanine, are highly involved in the pyrimidine interactions. Arginine prefers contacts with the cytosine base. The similarities and differences that exist between the interactions of the amino acid residues with each of the three pyrimidine base atoms in our analysis provide insights that can be exploited in designing specific inhibitors competitive to the ligands. SN - 1538-0254 UR - https://www.unboundmedicine.com/medline/citation/24028440/Structure_wise_discrimination_of_cytosine_thymine_and_uracil_by_proteins_in_terms_of_their_nonbonded_interactions_ L2 - https://www.tandfonline.com/doi/full/10.1080/07391102.2013.832384 DB - PRIME DP - Unbound Medicine ER -