Salt bridges
In proteins, salt bridges[1] occur between amino acid side-chains with opposite positive or negative full-electron charges, namely, (at neutral pH) Glu- or Asp- vs. Arg+ or Lys+. They may also occur between ionized organic ligands, such as acetylcholine+ (or example at right: 1cbr), or inorganic ions, such as K+ or SO4=, and amino acid side-chains. A salt bridge is generally considered to exist when the centers of charge are 4 Å or less apart[2]. The center of charge of the arginine sidechain is the zeta carbon[3]. The energetic significance of such complementary charge pairs is a complex function of the local environment. Proteins from thermophiles have more salt bridges than do proteins from mesophiles[4][5]. These additional salt bridges contribute to stability, resisting denaturation by high temperature[6][7]. ExamplesThermophile vs. mesophileGlutamate dehydrogenase structures have been determined at about 2 Å resolution for both a thermophile, Pyrococcus furiosus (1gtm), and a mesophile, Clostridium symbiosum (1hrd)[5]. 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 receptorUVR8 is an ultraviolet-B receptor in plants such as Arabidopsis. It is a homodimer that, upon irradiation, dissociates into a monomer involved in transcriptional activation of UV protective proteins[8]. Unexpectedly, high ionic strength was found to dissociate the dimer. The homodimer 4dnw contains many salt bridges and cation-pi interactions at the interface. More. Chains and clumps of salt bridges6nie contains a chain of salt bridges: D236-K170-D140-R237-E120-K301. The chain branches at R237 which is salt bridged to D119. A branched chain could be described as a "clump". (K301 is an unusual monomeric amino acid ligand.)
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VisualizationVisualization
Putative protein-protein salt bridges involving charged amino acid sidechains and/or charged chain termini can be displayed by FirstGlance in Jmol. Salt bridges to ligands can be visualized using the Contacts & Non-covalent interactions tool, after selecting the ligand as the target for the display. Such a case is illustrated above in JSmol.
ReferencesReferences
- ↑ 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