Buried charges detection

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This page is under development. Eric Martz 20:04, 8 February 2021 (UTC)

The four common amino acids whose sidechains are fully charged from pH 5 to 9, in the absence of environmental effects, are Arg, Asp, Glu, & Lys^[1]. Although the highly hydrophilic sidechains of these amino acids tend to be on the surfaces of soluble proteins, they are often found buried in the hydrophobic cores^[1]. In fact, on average, about half of Arg, Asp, and Glu sidechains are buried, while about one third of Lys sidechains are buried^[1]. Buried ionizable sidechains may be uncharged because their pKa's shift due to dehydration, net charge of the protein, hydrogen bonds, and other environmental influences^[1].

Protein Stability

Buried ionizable sidechains engaged in multiple hydrogen bonds contribute to protein stability, while those lacking such interactions contribute to instability^[1]. Stability does not increase with protein size^[1]. The independence of protein stability vs. size appears related to burial of more ionizable sidechains that are not hydrogen bonded in large proteins. Proteins with <100 residues have on average 1.9 buried ionizable sidechains, while those with >300 residues average 4.9/100 residues^[1].

Notes to myself

Burial 1990, awaiting interlibrary^[2]

References Cited

1. ↑ ^{1.0 1.1 1.2 1.3 1.4 1.5 1.6} 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
2. ↑ Lesser GJ, Rose GD. Hydrophobicity of amino acid subgroups in proteins. Proteins. 1990;8(1):6-13. doi: 10.1002/prot.340080104. PMID:2217164 doi:http://dx.doi.org/10.1002/prot.340080104