Buried charges detection
From Proteopedia
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<span class="text-red">This page is under development. [[User:Eric Martz|Eric Martz]] 20:04, 8 February 2021 (UTC)</span> | <span class="text-red">This page is under development. [[User:Eric Martz|Eric Martz]] 20:04, 8 February 2021 (UTC)</span> | ||
| - | 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'''<ref name="pace">PMID: 19164280</ref>. Although the highly hydrophilic sidechains of these amino acids tend to be on the surfaces of soluble proteins, they are often found buried<ref name="pace" />. 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<ref name="pace" />. Buried ionizable | + | 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'''<ref name="pace">PMID: 19164280</ref>. Although the highly hydrophilic sidechains of these amino acids tend to be on the surfaces of soluble proteins, they are often found buried<ref name="pace" />. 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<ref name="pace" /><ref name="lesser">PMID: 2217164</ref>. Buried ionizable sidechain pKa's shift due to dehydration, net charge of the protein, hydrogen bonds, and other environmental influences<ref name="pace" /><ref name="thurlkill">PMID: 16934292</ref>. This may leave them uncharged, or charged over a wider range of pH's than would be expected from their intrinsic pKa's. |
==Protein Stability== | ==Protein Stability== | ||
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==Notes to myself== | ==Notes to myself== | ||
| - | Burial 1990, awaiting interlibrary | + | Burial 1990, awaiting interlibrary |
==References Cited== | ==References Cited== | ||
<references /> | <references /> | ||
Revision as of 19:31, 9 February 2021
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[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][2]. Buried ionizable sidechain pKa's shift due to dehydration, net charge of the protein, hydrogen bonds, and other environmental influences[1][3]. This may leave them uncharged, or charged over a wider range of pH's than would be expected from their intrinsic pKa's.
Protein Stability
Buried ionizable sidechains engaged in multiple hydrogen bonds contribute to protein stability, while those lacking such interactions contribute to instability[1][4]. Thermophilic proteins often have fewer buried ionizable sidechains[4]. 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
References Cited
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 4.0 4.1 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
