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Aromatic π-networks in Sm/LSm protein interfaces

Aromatična π-mreža u interfejsima Sm/LSm proteina

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2014
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Authors
Breberina, Luka M.
Nikolić, Milan
Stojanović, Srđan
Article (Published version)
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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 konzervativnosti
Source:
Facta universitatis - series: Physics, Chemistry and Technology, 2014, 12, 1, 27-39
Publisher:
  • 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)

DOI: 10.2298/FUPCT1401027B

ISSN: 0354-4656

[ Google Scholar ]
URI
https://cer.ihtm.bg.ac.rs/handle/123456789/1468
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  • Radovi istraživača / Researchers' publications
Institution/Community
IHTM
TY  - 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 . .

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