Salt bridges

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In proteins, salt bridges<ref>PMID: 21287621</ref> 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<sup>+</sup> or SO<sub>4</sub><sup>=</sup>, and amino acid side-chains.
In proteins, salt bridges<ref>PMID: 21287621</ref> 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<sup>+</sup> or SO<sub>4</sub><sup>=</sup>, and amino acid side-chains.
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A salt bridge is generally considered to exist when the centers of charge are 4 &Aring; 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.
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A salt bridge is generally considered to exist when the centers of charge are 4 &Aring; or less apart (<ref>Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997. Page 192.</ref> and see legend to Table 6 in ref. <ref>PMID:11080642</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:19164280</ref><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>.
Proteins from [[extremophiles|thermophiles]] have more salt bridges than do proteins from mesophiles<ref>PMID:19164280</ref><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>.

Current revision

Salt bridge between retinoic acid(-) and arg131(+) in 1cbr.

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Visualization

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.

References

  1. ↑ 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
  2. ↑ Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997. Page 192.
  3. ↑ Kajander T, Kahn PC, Passila SH, Cohen DC, Lehtio L, Adolfsen W, Warwicker J, Schell U, Goldman A. Buried charged surface in proteins. Structure. 2000 Nov 15;8(11):1203-14. PMID:11080642
  4. ↑ 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
  5. ↑ Pace CN, Grimsley GR, Scholtz JM. Protein ionizable groups: pK values and their contribution to protein stability and solubility. J Biol Chem. 2009 May 15;284(20):13285-9. doi: 10.1074/jbc.R800080200. Epub 2009 , Jan 21. PMID:19164280 doi:http://dx.doi.org/10.1074/jbc.R800080200
  6. ↑ 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
  7. ↑ 7.0 7.1 Kumar S, Nussinov R. How do thermophilic proteins deal with heat? Cell Mol Life Sci. 2001 Aug;58(9):1216-33. PMID:11577980
  8. ↑ 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
  9. ↑ 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
  10. ↑ Kumar S, Ma B, Tsai CJ, Nussinov R. Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers. Proteins. 2000 Mar 1;38(4):368-83. doi:, 10.1002/(sici)1097-0134(20000301)38:4<368::aid-prot3>3.0.co;2-r. PMID:10707024 doi:<368::aid-prot3>3.0.co;2-r http://dx.doi.org/10.1002/(sici)1097-0134(20000301)38:4<368::aid-prot3>3.0.co;2-r
  11. ↑ 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

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