Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces
Само за регистроване кориснике
2019
Чланак у часопису (Објављена верзија)
,
Wiley
Метаподаци
Приказ свих података о документуАпстракт
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.
Кључне речи:
Phycocyanins / Interface / Hydrogen bonds / Hydrophobic interactions / Salt bridgesИзвор:
Molecular Informatics, 2019, 38, 11-12, 1800145-Издавач:
- Wiley
Финансирање / пројекти:
- Проучавање физичкохемијских и биохемијских процеса у животној средини који утичу на загађење и истраживање могућности за минимизирање последица (RS-172001)
- Рационални дизајн и синтеза биолошки активних и координационих једињења и функционалних материјала, релевантних у (био)нанотехнологији (RS-172035)
DOI: 10.1002/minf.201800145
ISSN: 1868-1743; 1868-1751
WoS: 000620702900001
Scopus: 2-s2.0-85073932130
Институција/група
IHTMTY - JOUR AU - Breberina, Luka AU - Zlatović, Mario AU - Nikolić, Milan AU - Stojanović, Srđan PY - 2019 UR - https://cer.ihtm.bg.ac.rs/handle/123456789/3233 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 - Wiley 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 and Zlatović, Mario and Nikolić, Milan and Stojanović, Srđan", 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 = "Wiley", 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., Zlatović, M., Nikolić, M.,& Stojanović, S.. (2019). Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces. in Molecular Informatics Wiley., 38(11-12), 1800145. https://doi.org/10.1002/minf.201800145
Breberina L, Zlatović M, Nikolić M, Stojanović S. 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, Zlatović, Mario, Nikolić, Milan, Stojanović, Srđan, "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 . .