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 a nitrogen-oxygen atom pair in sidechains of (Arg,Lys)-(Asp,Glu) are ≤ 4.0 Å apart[2]. The charged atoms could also be the amino-termini or carboxy-termini of protein chains or within non-protein ligands. The energetic significance of such complementary charge pairs is a complex function of the local environment[2]. Proteins from thermophiles have more salt bridges than do proteins from mesophiles[3][4][5]. These additional salt bridges contribute to stability, resisting denaturation by high temperature[6][7]. ContentsExamplesThermophile 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). Many of the extra salt bridges in the thermophilic enzyme cluster around the active site[8]. 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[9]. 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.)
| ||||||||||||
Visualization
Putative protein-protein salt bridges involving charged amino acid sidechains and/or charged chain termini can be displayed by 1cbr. 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.
