Salt bridges: Difference between revisions
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) No edit summary |
||
| (17 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
<StructureSection load='' size='300' side='right' caption='Salt bridge between retinoic acid(-) and arg131(+) in [[1cbr]].' scene='Salt_bridges/Salt_bridge/2'> | |||
<!-- | |||
<applet load='1cbr' size='300' frame='true' align='right' caption='Salt bridge between retinoic acid(-) and arg131(+) in [[1cbr]].' | <applet load='1cbr' size='300' frame='true' align='right' caption='Salt bridge between retinoic acid(-) and arg131(+) in [[1cbr]].' | ||
scene='Salt_bridges/Salt_bridge/ | scene='Salt_bridges/Salt_bridge/2' /> | ||
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<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. | |||
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. [[Suggestions_for_new_articles#April:_Ultraviolet-B_Photoreceptor_Dimer_to_Monomer|More]]. | 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 /> | ||