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Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces

Samo za registrovane korisnike
2019
Autori
Breberina, Luka M.
Zlatović, Mario
Nikolić, Milan
Stojanović, Srđan Đ.
Članak u časopisu (Objavljena verzija)
Metapodaci
Prikaz svih podataka o dokumentu
Apstrakt
Protein-protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non-redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call “standard-size” interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water-bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein-protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contr...ibutes to 9.3 %±1.7 % on average in these complexes. Moreover, there is about 1.9 %±1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than −16 kJ mol−1, while most of them have energy in the range from −6 to −14 kJ mol−1. The non-covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein-bioactive compound interactions.

Ključne reči:
Hydrogen bonds / Hydrophobic interactions / Interface / Phycocyanins / Salt bridges
Izvor:
Molecular Informatics, 2019, 38, 11-12, 1800145-
Izdavač:
  • Willey
Finansiranje / projekti:
  • Proučavanje fizičkohemijskih i biohemijskih procesa u životnoj sredini koji utiču na zagađenje i istraživanje mogućnosti za minimiziranje posledica (RS-172001)
  • Racionalni dizajn i sinteza biološki aktivnih i koordinacionih jedinjenja i funkcionalnih materijala, relevantnih u (bio)nanotehnologiji (RS-172035)

DOI: 10.1002/minf.201800145

ISSN: 1868-1743

WoS: 000620702900001

Scopus: 2-s2.0-85073932130
[ Google Scholar ]
2
2
URI
https://cherry.chem.bg.ac.rs/handle/123456789/3790
Kolekcije
  • Publikacije
Institucija/grupa
Hemijski fakultet
TY  - JOUR
AU  - Breberina, Luka M.
AU  - Zlatović, Mario
AU  - Nikolić, Milan
AU  - Stojanović, Srđan Đ.
PY  - 2019
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3790
AB  - Protein-protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non-redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call “standard-size” interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water-bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein-protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contributes to 9.3 %±1.7 % on average in these complexes. Moreover, there is about 1.9 %±1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than −16 kJ mol−1, while most of them have energy in the range from −6 to −14 kJ mol−1. The non-covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein-bioactive compound interactions.
PB  - Willey
T2  - Molecular Informatics
T1  - Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces
VL  - 38
IS  - 11-12
SP  - 1800145
DO  - 10.1002/minf.201800145
ER  - 
@article{
author = "Breberina, Luka M. and Zlatović, Mario and Nikolić, Milan and Stojanović, Srđan Đ.",
year = "2019",
abstract = "Protein-protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non-redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call “standard-size” interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water-bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein-protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contributes to 9.3 %±1.7 % on average in these complexes. Moreover, there is about 1.9 %±1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than −16 kJ mol−1, while most of them have energy in the range from −6 to −14 kJ mol−1. The non-covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein-bioactive compound interactions.",
publisher = "Willey",
journal = "Molecular Informatics",
title = "Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces",
volume = "38",
number = "11-12",
pages = "1800145",
doi = "10.1002/minf.201800145"
}
Breberina, L. M., Zlatović, M., Nikolić, M.,& Stojanović, S. Đ.. (2019). Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces. in Molecular Informatics
Willey., 38(11-12), 1800145.
https://doi.org/10.1002/minf.201800145
Breberina LM, Zlatović M, Nikolić M, Stojanović SĐ. Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces. in Molecular Informatics. 2019;38(11-12):1800145.
doi:10.1002/minf.201800145 .
Breberina, Luka M., Zlatović, Mario, Nikolić, Milan, Stojanović, Srđan Đ., "Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces" in Molecular Informatics, 38, no. 11-12 (2019):1800145,
https://doi.org/10.1002/minf.201800145 . .

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