Aromatic π-networks in Sm/LSm protein interfaces
Aromatična π-mreža u interfejsima Sm/LSm proteina
Abstract
In this work, we have analyzed the influence of π-π interactions on stability and properties of Sm/LSm assemblies. The residues were found to be involved in π-π interactions much more frequently than Tyr or His. Similarly, the Phe-Phe π-π interacting pair had the highest frequency of occurrence. Furthermore, a significant number of π-networks were observed at the interface of Sm/LSm proteins. Generally speaking, the distance between the interacting pairs was in the range of 5-6 Å. 3π and 7π-networks were found to frequently have plane-plane angles less than 60º. Solvent accessibility pattern of Sm/LSm proteins revealed that all of the interacting residues were from buried areas. Moreover, most of the π-π interacting residues of Sm/LSm proteins were evolutionary conserved and were in the strand regions. A high percentage of these residues could be considered as stabilization centers that (significantly) contribute to the net stability of Sm/LSm proteins.
U ovom radu smo analizirali uticaj π-π interakcija na stabilnost i osobine Sm/LSm proteinskih agregata. Ostatak fenilalanina znatno češće uzima učešće u π-π interakcijama u odnosu na His i Tyr. Slično, Phe-Phe π-π interagujući parovi su najučestaliji. Prepoznat je značajan broj π-mreža u interfejsima Sm/LSm proteinima. U većini slučajeva, rastojanje između interagujućih parova aminokiselina bilo je u opsegu 5-6 Å. Za 3π i 7π-mreže, prsten-prsten uglovi manji od 60º su bili učestaliji. Razmatrajući delove Sm/LSm proteina dostupne rastvaraču, može se zaključiti da se svi interagujući parovi nalaze u unutrašnjim regionima. Pored toga, većina π-π interagujućih aminokiselinskih ostataka je evoluciono konzervativan i nalazi se u regionima sa nabranom strukturom. Veliki broj ovih ostataka se može smatrati stabilizacionim centrima, koji (značajno) doprinose ukupnoj stabilnost Sm/LSm proteina.
Keywords:
aromatic π-networks / Sm/LSm proteins / interfaces / stabilization centers / conservation score / aromatična π-mreža / Sm/LSm proteini / interfejs / stabilizacioni centri / skor konzervativnostiSource:
Facta universitatis - series: Physics, Chemistry and Technology, 2014, 12, 1, 27-39Publisher:
- Univerzitet u Nišu
Funding / projects:
- The study of physicochemical and biochemical processes in living environment that have impacts on pollution and the investigation of possibilities for minimizing the consequences (RS-172001)
- Rational design and synthesis of biologically active and coordination compounds and functional materials, relevant for (bio)nanotechnology (RS-172035)
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Institution/Community
IHTMTY - JOUR AU - Breberina, Luka M. AU - Nikolić, Milan AU - Stojanović, Srđan PY - 2014 UR - https://cer.ihtm.bg.ac.rs/handle/123456789/1468 AB - In this work, we have analyzed the influence of π-π interactions on stability and properties of Sm/LSm assemblies. The residues were found to be involved in π-π interactions much more frequently than Tyr or His. Similarly, the Phe-Phe π-π interacting pair had the highest frequency of occurrence. Furthermore, a significant number of π-networks were observed at the interface of Sm/LSm proteins. Generally speaking, the distance between the interacting pairs was in the range of 5-6 Å. 3π and 7π-networks were found to frequently have plane-plane angles less than 60º. Solvent accessibility pattern of Sm/LSm proteins revealed that all of the interacting residues were from buried areas. Moreover, most of the π-π interacting residues of Sm/LSm proteins were evolutionary conserved and were in the strand regions. A high percentage of these residues could be considered as stabilization centers that (significantly) contribute to the net stability of Sm/LSm proteins. AB - U ovom radu smo analizirali uticaj π-π interakcija na stabilnost i osobine Sm/LSm proteinskih agregata. Ostatak fenilalanina znatno češće uzima učešće u π-π interakcijama u odnosu na His i Tyr. Slično, Phe-Phe π-π interagujući parovi su najučestaliji. Prepoznat je značajan broj π-mreža u interfejsima Sm/LSm proteinima. U većini slučajeva, rastojanje između interagujućih parova aminokiselina bilo je u opsegu 5-6 Å. Za 3π i 7π-mreže, prsten-prsten uglovi manji od 60º su bili učestaliji. Razmatrajući delove Sm/LSm proteina dostupne rastvaraču, može se zaključiti da se svi interagujući parovi nalaze u unutrašnjim regionima. Pored toga, većina π-π interagujućih aminokiselinskih ostataka je evoluciono konzervativan i nalazi se u regionima sa nabranom strukturom. Veliki broj ovih ostataka se može smatrati stabilizacionim centrima, koji (značajno) doprinose ukupnoj stabilnost Sm/LSm proteina. PB - Univerzitet u Nišu T2 - Facta universitatis - series: Physics, Chemistry and Technology T1 - Aromatic π-networks in Sm/LSm protein interfaces T1 - Aromatična π-mreža u interfejsima Sm/LSm proteina VL - 12 IS - 1 SP - 27 EP - 39 DO - 10.2298/FUPCT1401027B ER -
@article{ author = "Breberina, Luka M. and Nikolić, Milan and Stojanović, Srđan", year = "2014", abstract = "In this work, we have analyzed the influence of π-π interactions on stability and properties of Sm/LSm assemblies. The residues were found to be involved in π-π interactions much more frequently than Tyr or His. Similarly, the Phe-Phe π-π interacting pair had the highest frequency of occurrence. Furthermore, a significant number of π-networks were observed at the interface of Sm/LSm proteins. Generally speaking, the distance between the interacting pairs was in the range of 5-6 Å. 3π and 7π-networks were found to frequently have plane-plane angles less than 60º. Solvent accessibility pattern of Sm/LSm proteins revealed that all of the interacting residues were from buried areas. Moreover, most of the π-π interacting residues of Sm/LSm proteins were evolutionary conserved and were in the strand regions. A high percentage of these residues could be considered as stabilization centers that (significantly) contribute to the net stability of Sm/LSm proteins., U ovom radu smo analizirali uticaj π-π interakcija na stabilnost i osobine Sm/LSm proteinskih agregata. Ostatak fenilalanina znatno češće uzima učešće u π-π interakcijama u odnosu na His i Tyr. Slično, Phe-Phe π-π interagujući parovi su najučestaliji. Prepoznat je značajan broj π-mreža u interfejsima Sm/LSm proteinima. U većini slučajeva, rastojanje između interagujućih parova aminokiselina bilo je u opsegu 5-6 Å. Za 3π i 7π-mreže, prsten-prsten uglovi manji od 60º su bili učestaliji. Razmatrajući delove Sm/LSm proteina dostupne rastvaraču, može se zaključiti da se svi interagujući parovi nalaze u unutrašnjim regionima. Pored toga, većina π-π interagujućih aminokiselinskih ostataka je evoluciono konzervativan i nalazi se u regionima sa nabranom strukturom. Veliki broj ovih ostataka se može smatrati stabilizacionim centrima, koji (značajno) doprinose ukupnoj stabilnost Sm/LSm proteina.", publisher = "Univerzitet u Nišu", journal = "Facta universitatis - series: Physics, Chemistry and Technology", title = "Aromatic π-networks in Sm/LSm protein interfaces, Aromatična π-mreža u interfejsima Sm/LSm proteina", volume = "12", number = "1", pages = "27-39", doi = "10.2298/FUPCT1401027B" }
Breberina, L. M., Nikolić, M.,& Stojanović, S.. (2014). Aromatic π-networks in Sm/LSm protein interfaces. in Facta universitatis - series: Physics, Chemistry and Technology Univerzitet u Nišu., 12(1), 27-39. https://doi.org/10.2298/FUPCT1401027B
Breberina LM, Nikolić M, Stojanović S. Aromatic π-networks in Sm/LSm protein interfaces. in Facta universitatis - series: Physics, Chemistry and Technology. 2014;12(1):27-39. doi:10.2298/FUPCT1401027B .
Breberina, Luka M., Nikolić, Milan, Stojanović, Srđan, "Aromatic π-networks in Sm/LSm protein interfaces" in Facta universitatis - series: Physics, Chemistry and Technology, 12, no. 1 (2014):27-39, https://doi.org/10.2298/FUPCT1401027B . .