Buried charges detection

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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[1]. In fact, on average, about half of the charged sidechain oxygens or nitrogens of Arg, Asp, and Glu are buried, while about one third of Lys sidechain nitrogens 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][2].

Protein Stability

Buried ionizable sidechains engaged in multiple hydrogen bonds contribute to protein stability, while those lacking such interactions contribute to instability[1][3]. Thermophilic proteins often have fewer buried ionizable sidechains[3]. 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[4]

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. ↑ Thurlkill RL, Grimsley GR, Scholtz JM, Pace CN. Hydrogen bonding markedly reduces the pK of buried carboxyl groups in proteins. J Mol Biol. 2006 Sep 22;362(3):594-604. doi: 10.1016/j.jmb.2006.07.056. Epub 2006, Jul 29. PMID:16934292 doi:http://dx.doi.org/10.1016/j.jmb.2006.07.056
  3. ↑ 3.0 3.1 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. ↑ 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

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