Cation-pi interactions in high resolution protein-RNA complex crystal structures
Само за регистроване кориснике
2013
Чланак у часопису (Објављена верзија)

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In this work, we have analyzed the influence of cation-pi interactions to the stability of 59 high resolution protein-RNA complex crystal structures. The total number of Lys and Arg are similar in the dataset as well as the number of their interactions. On the other hand, the aromatic chains of purines are exhibiting more cation-pi interactions than pyrimidines. 35% of the total interactions in the dataset are involved in the formation of multiple cation-pi interactions. The multiple cation-pi interactions have been conserved more than the single interactions. The analysis of the geometry of the cation-pi interactions has revealed that the average distance (d) value falls into distinct ranges corresponding to the multiple (4.28 angstrom) and single (5.50 angstrom) cation-pi interactions. The G-Arg pair has the strongest interaction energy of -3.68 kcal mol(-1) among all the possible pairs of amino acids and bases. Further, we found that the cation-pi interactions due to five-membered r...ings of A and G are stronger than that with the atoms in six-membered rings. 8.7% stabilizing residues are involved in building cation-pi interactions with the nucleic bases. There are three types of structural motifs significantly over-represented in protein-RNA interfaces: beta-turn-ir, niche-4r and st-staple. Tetraloops and kink-turns are the most abundant RNA motifs in protein-RNA interfaces. Amino acids deployed in the protein-RNA interfaces are deposited in helices, sheets and coils. Arg and Lys, involved in cation-pi interactions, prefer to be in the solvent exposed surface. The results from this study might be used for structure-based prediction and as scaffolds for future protein-RNA complex design.
Кључне речи:
Cation-pi interactions / Proteins / RNA / Interfaces / Stabilization centersИзвор:
Computational Biology and Chemistry, 2013, 47, 105-112Издавач:
- Elsevier Sci Ltd, Oxford
Финансирање / пројекти:
- Организовање одрживе производње органског узгоја јагњади као подршка руралног развоја (RS-31085)
- Проучавање физичкохемијских и биохемијских процеса у животној средини који утичу на загађење и истраживање могућности за минимизирање последица (RS-172001)
- Аберације ћелијског циклуса и утицај оксидативног стреса на неуродегенеративне процесе и малигну трансформацију ћелије (RS-173034)
DOI: 10.1016/j.compbiolchem.2013.08.005
ISSN: 1476-9271
PubMed: 24055762
WoS: 000329270700015
Scopus: 2-s2.0-84884578304
Институција/група
IHTMTY - JOUR AU - Borozan, Sunčica AU - Dimitrijević, Blagoje P. AU - Stojanović, Srđan PY - 2013 UR - https://cer.ihtm.bg.ac.rs/handle/123456789/1247 AB - In this work, we have analyzed the influence of cation-pi interactions to the stability of 59 high resolution protein-RNA complex crystal structures. The total number of Lys and Arg are similar in the dataset as well as the number of their interactions. On the other hand, the aromatic chains of purines are exhibiting more cation-pi interactions than pyrimidines. 35% of the total interactions in the dataset are involved in the formation of multiple cation-pi interactions. The multiple cation-pi interactions have been conserved more than the single interactions. The analysis of the geometry of the cation-pi interactions has revealed that the average distance (d) value falls into distinct ranges corresponding to the multiple (4.28 angstrom) and single (5.50 angstrom) cation-pi interactions. The G-Arg pair has the strongest interaction energy of -3.68 kcal mol(-1) among all the possible pairs of amino acids and bases. Further, we found that the cation-pi interactions due to five-membered rings of A and G are stronger than that with the atoms in six-membered rings. 8.7% stabilizing residues are involved in building cation-pi interactions with the nucleic bases. There are three types of structural motifs significantly over-represented in protein-RNA interfaces: beta-turn-ir, niche-4r and st-staple. Tetraloops and kink-turns are the most abundant RNA motifs in protein-RNA interfaces. Amino acids deployed in the protein-RNA interfaces are deposited in helices, sheets and coils. Arg and Lys, involved in cation-pi interactions, prefer to be in the solvent exposed surface. The results from this study might be used for structure-based prediction and as scaffolds for future protein-RNA complex design. PB - Elsevier Sci Ltd, Oxford T2 - Computational Biology and Chemistry T1 - Cation-pi interactions in high resolution protein-RNA complex crystal structures VL - 47 SP - 105 EP - 112 DO - 10.1016/j.compbiolchem.2013.08.005 ER -
@article{ author = "Borozan, Sunčica and Dimitrijević, Blagoje P. and Stojanović, Srđan", year = "2013", abstract = "In this work, we have analyzed the influence of cation-pi interactions to the stability of 59 high resolution protein-RNA complex crystal structures. The total number of Lys and Arg are similar in the dataset as well as the number of their interactions. On the other hand, the aromatic chains of purines are exhibiting more cation-pi interactions than pyrimidines. 35% of the total interactions in the dataset are involved in the formation of multiple cation-pi interactions. The multiple cation-pi interactions have been conserved more than the single interactions. The analysis of the geometry of the cation-pi interactions has revealed that the average distance (d) value falls into distinct ranges corresponding to the multiple (4.28 angstrom) and single (5.50 angstrom) cation-pi interactions. The G-Arg pair has the strongest interaction energy of -3.68 kcal mol(-1) among all the possible pairs of amino acids and bases. Further, we found that the cation-pi interactions due to five-membered rings of A and G are stronger than that with the atoms in six-membered rings. 8.7% stabilizing residues are involved in building cation-pi interactions with the nucleic bases. There are three types of structural motifs significantly over-represented in protein-RNA interfaces: beta-turn-ir, niche-4r and st-staple. Tetraloops and kink-turns are the most abundant RNA motifs in protein-RNA interfaces. Amino acids deployed in the protein-RNA interfaces are deposited in helices, sheets and coils. Arg and Lys, involved in cation-pi interactions, prefer to be in the solvent exposed surface. The results from this study might be used for structure-based prediction and as scaffolds for future protein-RNA complex design.", publisher = "Elsevier Sci Ltd, Oxford", journal = "Computational Biology and Chemistry", title = "Cation-pi interactions in high resolution protein-RNA complex crystal structures", volume = "47", pages = "105-112", doi = "10.1016/j.compbiolchem.2013.08.005" }
Borozan, S., Dimitrijević, B. P.,& Stojanović, S.. (2013). Cation-pi interactions in high resolution protein-RNA complex crystal structures. in Computational Biology and Chemistry Elsevier Sci Ltd, Oxford., 47, 105-112. https://doi.org/10.1016/j.compbiolchem.2013.08.005
Borozan S, Dimitrijević BP, Stojanović S. Cation-pi interactions in high resolution protein-RNA complex crystal structures. in Computational Biology and Chemistry. 2013;47:105-112. doi:10.1016/j.compbiolchem.2013.08.005 .
Borozan, Sunčica, Dimitrijević, Blagoje P., Stojanović, Srđan, "Cation-pi interactions in high resolution protein-RNA complex crystal structures" in Computational Biology and Chemistry, 47 (2013):105-112, https://doi.org/10.1016/j.compbiolchem.2013.08.005 . .