Salt bridges
From Proteopedia
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A salt bridge is generally considered to exist when the centers of charge are 4 Å or less apart<ref>Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997. Page 192.</ref>. The center of charge of the arginine sidechain is the zeta carbon<ref name='GD'>PMID: 10449714</ref>. The energetic significance of such complementary charge pairs is a complex function of the local environment. | A salt bridge is generally considered to exist when the centers of charge are 4 Å or less apart<ref>Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997. Page 192.</ref>. The center of charge of the arginine sidechain is the zeta carbon<ref name='GD'>PMID: 10449714</ref>. The energetic significance of such complementary charge pairs is a complex function of the local environment. | ||
| - | Proteins from [[extremophiles|thermophiles]] have more salt bridges than do proteins from mesophiles<ref>PMID: 11793224</ref><ref>PMID: 11577980</ref>. These additional salt bridges contribute to stability, resisting denaturation by high temperature<ref>PMID: 21720566</ref><ref>PMID: 31360001</ref>. | + | Proteins from [[extremophiles|thermophiles]] have more salt bridges than do proteins from mesophiles<ref>PMID: 11793224</ref><ref name="kumar">PMID: 11577980</ref>. These additional salt bridges contribute to stability, resisting denaturation by high temperature<ref>PMID: 21720566</ref><ref>PMID: 31360001</ref>. |
==Examples== | ==Examples== | ||
===Thermophile vs. mesophile=== | ===Thermophile vs. mesophile=== | ||
| - | Glutamate dehydrogenase structures have been determined at about 2 Å resolution for both a thermophile, ''Pyrococcus furiosus'' ([[1gtm]]), and a mesophile, ''Clostridium symbiosum'' ([[1hrd]]). The thermophile's protein has 1.7 fold more N and O atoms engaged in salt bridges than does the protein from the mesophile (301 vs. 175 respectively, as counted by [[FirstGlance]]. | + | Glutamate dehydrogenase structures have been determined at about 2 Å resolution for both a thermophile, ''Pyrococcus furiosus'' ([[1gtm]]), and a mesophile, ''Clostridium symbiosum'' ([[1hrd]])<ref name="kumar" />. The thermophile's protein has 1.7 fold more N and O atoms engaged in salt bridges than does the protein from the mesophile (301 vs. 175 respectively, as counted by [[FirstGlance]]. |
===Ultraviolet-B receptor=== | ===Ultraviolet-B receptor=== | ||
Revision as of 01:24, 10 November 2019
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Visualization
Putative salt bridges can be displayed by FirstGlance in Jmol.
References
- ↑ Donald JE, Kulp DW, DeGrado WF. Salt bridges: geometrically specific, designable interactions. Proteins. 2011 Mar;79(3):898-915. doi: 10.1002/prot.22927. Epub 2011 Jan 5. PMID:21287621 doi:http://dx.doi.org/10.1002/prot.22927
- ↑ Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997. Page 192.
- ↑ Gallivan JP, Dougherty DA. Cation-pi interactions in structural biology. Proc Natl Acad Sci U S A. 1999 Aug 17;96(17):9459-64. PMID:10449714
- ↑ Das R, Gerstein M. The stability of thermophilic proteins: a study based on comprehensive genome comparison. Funct Integr Genomics. 2000 May;1(1):76-88. PMID:11793224 doi:10.1007/s101420000003
- ↑ 5.0 5.1 Kumar S, Nussinov R. How do thermophilic proteins deal with heat? Cell Mol Life Sci. 2001 Aug;58(9):1216-33. PMID:11577980
- ↑ Chan CH, Yu TH, Wong KB. Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding. PLoS One. 2011;6(6):e21624. Epub 2011 Jun 24. PMID:21720566 doi:10.1371/journal.pone.0021624
- ↑ Bandyopadhyay AK, Islam RNU, Mitra D, Banerjee S, Goswami A. Stability of buried and networked salt-bridges (BNSB)in thermophilic proteins. Bioinformation. 2019 Feb 3;15(1):61-67. doi: 10.6026/97320630015061. eCollection , 2019. PMID:31360001 doi:http://dx.doi.org/10.6026/97320630015061
- ↑ Wu D, Hu Q, Yan Z, Chen W, Yan C, Huang X, Zhang J, Yang P, Deng H, Wang J, Deng X, Shi Y. Structural basis of ultraviolet-B perception by UVR8. Nature. 2012 Feb 29;484(7393):214-9. doi: 10.1038/nature10931. PMID:22388820 doi:10.1038/nature10931
