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Non-covalent interactions across subunit interfaces in Sm proteins

Authorized Users Only
2011
Authors
Zarić, Božidarka
Jovanović, Vesna B.
Stojanović, Srđan
Article (Published version)
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Abstract
The distinguishing property of Sm protein associations is their high stability. In order to understand this property, we analyzed the interface non-covalent interactions and compared the properties of the Sm protein interfaces with those of a test set, Binding Interface Database (BID). The comparison revealed that the main differences between interfaces of Sm proteins and those of the BID set are the content of charged residues, hydrogen bonds, salt bridges, and conservation scores of interface residues. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surface, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Both interfaces of Sm proteins and of test set have a similar number of hydrophobic interactions per 100 angstrom(2). The interfaces of Sm proteins have substantially more hydrogen bonds than... the interfaces in test set. The results show clearly that the interfaces of Sm proteins form more salt bridges compared with test set. On average, there are about 16 salt bridges per interface. The high conservation score of amino acids that are involved in non-covalent interactions in protein interfaces is an additional strong argument for their importance. The overriding conclusion from this study is that the non-covalent interactions in Sm protein interfaces considerably contribute to stability of higher order structures.

Keywords:
Interface / Sm proteins / Hydrogen bonds / Hydrophobic interactions / Salt bridges
Source:
Journal of Theoretical Biology, 2011, 271, 1, 18-26
Publisher:
  • Academic Press Ltd- Elsevier Science Ltd, London
Funding / projects:
  • Proučavanje odnosa reaktivnosti, nekovalentnih interakcija i strukture molekula i modelovanje hemijskih sistema (RS-142037)
  • Ispitivanje strukture i funkcije biološki važnih makromolekula u fiziološkim i patološkim stanjima (RS-142020)

DOI: 10.1016/j.jtbi.2010.11.025

ISSN: 0022-5193

PubMed: 21095194

WoS: 000286492100003

Scopus: 2-s2.0-78649761217
[ Google Scholar ]
5
4
URI
https://cer.ihtm.bg.ac.rs/handle/123456789/924
Collections
  • Radovi istraživača / Researchers' publications
Institution/Community
IHTM
TY  - JOUR
AU  - Zarić, Božidarka
AU  - Jovanović, Vesna B.
AU  - Stojanović, Srđan
PY  - 2011
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/924
AB  - The distinguishing property of Sm protein associations is their high stability. In order to understand this property, we analyzed the interface non-covalent interactions and compared the properties of the Sm protein interfaces with those of a test set, Binding Interface Database (BID). The comparison revealed that the main differences between interfaces of Sm proteins and those of the BID set are the content of charged residues, hydrogen bonds, salt bridges, and conservation scores of interface residues. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surface, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Both interfaces of Sm proteins and of test set have a similar number of hydrophobic interactions per 100 angstrom(2). The interfaces of Sm proteins have substantially more hydrogen bonds than the interfaces in test set. The results show clearly that the interfaces of Sm proteins form more salt bridges compared with test set. On average, there are about 16 salt bridges per interface. The high conservation score of amino acids that are involved in non-covalent interactions in protein interfaces is an additional strong argument for their importance. The overriding conclusion from this study is that the non-covalent interactions in Sm protein interfaces considerably contribute to stability of higher order structures.
PB  - Academic Press Ltd- Elsevier Science Ltd, London
T2  - Journal of Theoretical Biology
T1  - Non-covalent interactions across subunit interfaces in Sm proteins
VL  - 271
IS  - 1
SP  - 18
EP  - 26
DO  - 10.1016/j.jtbi.2010.11.025
ER  - 
@article{
author = "Zarić, Božidarka and Jovanović, Vesna B. and Stojanović, Srđan",
year = "2011",
abstract = "The distinguishing property of Sm protein associations is their high stability. In order to understand this property, we analyzed the interface non-covalent interactions and compared the properties of the Sm protein interfaces with those of a test set, Binding Interface Database (BID). The comparison revealed that the main differences between interfaces of Sm proteins and those of the BID set are the content of charged residues, hydrogen bonds, salt bridges, and conservation scores of interface residues. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surface, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Both interfaces of Sm proteins and of test set have a similar number of hydrophobic interactions per 100 angstrom(2). The interfaces of Sm proteins have substantially more hydrogen bonds than the interfaces in test set. The results show clearly that the interfaces of Sm proteins form more salt bridges compared with test set. On average, there are about 16 salt bridges per interface. The high conservation score of amino acids that are involved in non-covalent interactions in protein interfaces is an additional strong argument for their importance. The overriding conclusion from this study is that the non-covalent interactions in Sm protein interfaces considerably contribute to stability of higher order structures.",
publisher = "Academic Press Ltd- Elsevier Science Ltd, London",
journal = "Journal of Theoretical Biology",
title = "Non-covalent interactions across subunit interfaces in Sm proteins",
volume = "271",
number = "1",
pages = "18-26",
doi = "10.1016/j.jtbi.2010.11.025"
}
Zarić, B., Jovanović, V. B.,& Stojanović, S.. (2011). Non-covalent interactions across subunit interfaces in Sm proteins. in Journal of Theoretical Biology
Academic Press Ltd- Elsevier Science Ltd, London., 271(1), 18-26.
https://doi.org/10.1016/j.jtbi.2010.11.025
Zarić B, Jovanović VB, Stojanović S. Non-covalent interactions across subunit interfaces in Sm proteins. in Journal of Theoretical Biology. 2011;271(1):18-26.
doi:10.1016/j.jtbi.2010.11.025 .
Zarić, Božidarka, Jovanović, Vesna B., Stojanović, Srđan, "Non-covalent interactions across subunit interfaces in Sm proteins" in Journal of Theoretical Biology, 271, no. 1 (2011):18-26,
https://doi.org/10.1016/j.jtbi.2010.11.025 . .

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