Buried charges detection: Difference between revisions
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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 in the hydrophobic cores<ref name="pace" />. In fact, on average, about '''half of Arg, Asp, and Glu sidechains are buried''', while about '''one third of Lys''' sidechains are buried<ref name="pace" />. 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<ref name="pace" />. | 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 in the hydrophobic cores<ref name="pace" />. In fact, on average, about '''half of Arg, Asp, and Glu sidechains are buried''', while about '''one third of Lys''' sidechains are buried<ref name="pace" />. 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<ref name="pace" /><ref name="thurlkill">PMID: 16934292</ref>. | ||
==Protein Stability== | ==Protein Stability== | ||
Revision as of 03:45, 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 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][2].
Protein StabilityProtein 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 myselfNotes to myself
Burial 1990, awaiting interlibrary[3]
References CitedReferences 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
- ↑ 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
- ↑ 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