Salt bridges: Difference between revisions
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<applet load='1cbr' size='300' frame='true' align='right' caption='Salt bridge between retinoic acid(-) and arg131(+) in 1cbr.' | <StructureSection load='' size='300' side='right' caption='Salt bridge between retinoic acid(-) and arg131(+) in [[1cbr]].' scene='Salt_bridges/Salt_bridge/2'> | ||
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In proteins, salt bridges 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 | <applet load='1cbr' size='300' frame='true' align='right' caption='Salt bridge between retinoic acid(-) and arg131(+) in [[1cbr]].' | ||
scene='Salt_bridges/Salt_bridge/2' /> | |||
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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. | |||
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> 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>. | |||
==Examples== | ==Examples== | ||
===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]])<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]]). Many of the extra salt bridges in the thermophilic enzyme cluster around the active site<ref name="kumar2000">PMID:10707024</ref>. | |||
===Ultraviolet-B receptor=== | ===Ultraviolet-B receptor=== | ||
UVR8 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<ref>PMID:22388820</ref>. Unexpectedly, high ionic strength was found to dissociate the dimer. The homodimer [[4dnw]] contains many [[salt bridges]] and [[cation-pi interactions]] at the interface. | UVR8 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<ref>PMID:22388820</ref>. Unexpectedly, high ionic strength was found to dissociate the dimer. The homodimer [[4dnw]] contains many [[salt bridges]] and [[cation-pi interactions]] at the interface. [[Suggestions_for_new_articles#April:_Ultraviolet-B_Photoreceptor_Dimer_to_Monomer|More]]. | ||
===Chains and clumps of salt bridges=== | |||
[[6nie]] 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.) | |||
</StructureSection> | |||
==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 <i>Contacts & Non-covalent interactions</i> tool, after selecting the ligand as the target for the display. Such a case is illustrated above in JSmol. | |||
==References== | ==References== | ||
<references /> | <references /> | ||
Latest revision as of 00:01, 10 February 2021
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] and see legend to Table 6 in ref. [3]). The center of charge of the arginine sidechain is the zeta carbon[4]. 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[5][6][7]. These additional salt bridges contribute to stability, resisting denaturation by high temperature[8][9]. 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)[7]. 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). Many of the extra salt bridges in the thermophilic enzyme cluster around the active site[10]. 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[11]. 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.
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 7.0 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
- ↑ 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
- ↑ 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
- ↑ 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