Buried charges detection - Revision history

Eric Martz: /* Definitions of "Buried" */

Eric Martz — Tue, 09 Feb 2021 21:57:46 GMT

Definitions of "Buried"

←Older revision		Revision as of 21:57, 9 February 2021
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	==Definitions of "Buried"==		==Definitions of "Buried"==
	The most common definition of ''buried'' is based on the loss of solvent-accessible surface area (SAS) of an amino acid in the folded protein, compared to its surface area in an unfolded state, such as when it is the middle residue of a tripeptide<ref name="kajander" />. Kajander ''et al.''<ref name="kajander" /> defined charged groups with <5% SAS as ''fully buried'', and those with 5-25% SAS as ''partially buried''.		The most common definition of ''buried'' is based on the loss of solvent-accessible surface area (SAS) of an amino acid in the folded protein, compared to its surface area in an unfolded state, such as when it is the middle residue of a tripeptide<ref name="kajander" />. Kajander ''et al.''<ref name="kajander" /> defined charged groups with <5% SAS as ''fully buried'', and those with 5-25% SAS as ''partially buried''.
		+
		+	Many buried ionizable sidechains form salt bridges with nearby opposite charges, and others form usually multiple hydrogen bonds. Few have neither<ref name="kajander" />. Some, of course, may be involved in a functional site.

	By the SAS definition, charged groups may be buried, yet likely exposed to solvent some of the time due to thermal motion and their proximity to the molecular surface. An example is Lys191 in hemocyanin [[1lla\|1LLA]]. Its sidechain amino is buried, but some of the methylene (-CH<sub>2</sub>) sidechain groups are partly exposed on the surface<ref name="kajander" />.		By the SAS definition, charged groups may be buried, yet likely exposed to solvent some of the time due to thermal motion and their proximity to the molecular surface. An example is Lys191 in hemocyanin [[1lla\|1LLA]]. Its sidechain amino is buried, but some of the methylene (-CH<sub>2</sub>) sidechain groups are partly exposed on the surface<ref name="kajander" />.

Eric Martz: /* Definitions of "Buried" */

Eric Martz — Tue, 09 Feb 2021 20:40:15 GMT

Definitions of "Buried"

←Older revision		Revision as of 20:40, 9 February 2021
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	==Definitions of "Buried"==		==Definitions of "Buried"==
	The most common definition of ''buried'' is based on the loss of solvent-accessible surface area (SAS) of an amino acid in the folded protein, compared to its surface area in an unfolded state, such as when it is the middle residue of a tripeptide<ref name="kajander" />. Kajander ''et al.''<ref name="kajander" /> defined charged groups with <5% SAS as ''fully buried'', and those with 5-25% SAS as ''partially buried''.		The most common definition of ''buried'' is based on the loss of solvent-accessible surface area (SAS) of an amino acid in the folded protein, compared to its surface area in an unfolded state, such as when it is the middle residue of a tripeptide<ref name="kajander" />. Kajander ''et al.''<ref name="kajander" /> defined charged groups with <5% SAS as ''fully buried'', and those with 5-25% SAS as ''partially buried''.
		+
		+	By the SAS definition, charged groups may be buried, yet likely exposed to solvent some of the time due to thermal motion and their proximity to the molecular surface. An example is Lys191 in hemocyanin [[1lla\|1LLA]]. Its sidechain amino is buried, but some of the methylene (-CH<sub>2</sub>) sidechain groups are partly exposed on the surface<ref name="kajander" />.

	==References Cited==		==References Cited==
	<references />		<references />

Eric Martz: /* Definitions of "Buried" */

Eric Martz — Tue, 09 Feb 2021 20:04:31 GMT

Definitions of "Buried"

←Older revision		Revision as of 20:04, 9 February 2021
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	==Definitions of "Buried"==		==Definitions of "Buried"==
-	The most common definition of ''buried'' is based on the loss of solvent-accessible surface area of an amino acid in the folded protein, compared to its surface area in an unfolded state, such as when it is the middle residue of a tripeptide<ref name="kajander" />.	+	The most common definition of ''buried'' is based on the loss of solvent-accessible surface area (SAS) of an amino acid in the folded protein, compared to its surface area in an unfolded state, such as when it is the middle residue of a tripeptide<ref name="kajander" />. Kajander ''et al.''<ref name="kajander" /> defined charged groups with <5% SAS as ''fully buried'', and those with 5-25% SAS as ''partially buried''.

	==References Cited==		==References Cited==
	<references />		<references />

Eric Martz: /* Protein Stability */

Eric Martz — Tue, 09 Feb 2021 20:00:37 GMT

Protein Stability

←Older revision		Revision as of 20:00, 9 February 2021
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	Buried ionizable sidechains engaged in multiple hydrogen bonds, or in [[salt bridges]], contribute to protein stability, while those lacking such interactions contribute to instability<ref name="pace" /><ref name="kajander">PMID: 11080642</ref>. Thermophilic proteins often have fewer buried ionizable sidechains<ref name="kajander" />. Stability does not increase with protein size<ref name="pace" />. 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<ref name="pace" />.		Buried ionizable sidechains engaged in multiple hydrogen bonds, or in [[salt bridges]], contribute to protein stability, while those lacking such interactions contribute to instability<ref name="pace" /><ref name="kajander">PMID: 11080642</ref>. Thermophilic proteins often have fewer buried ionizable sidechains<ref name="kajander" />. Stability does not increase with protein size<ref name="pace" />. 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<ref name="pace" />.
		+
		+	==Definitions of "Buried"==
		+	The most common definition of ''buried'' is based on the loss of solvent-accessible surface area of an amino acid in the folded protein, compared to its surface area in an unfolded state, such as when it is the middle residue of a tripeptide<ref name="kajander" />.

	==References Cited==		==References Cited==
	<references />		<references />

Eric Martz: /* Protein Stability */

Eric Martz — Tue, 09 Feb 2021 19:35:56 GMT

Protein Stability

←Older revision		Revision as of 19:35, 9 February 2021
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	==Protein Stability==		==Protein Stability==

-	Buried ionizable sidechains engaged in multiple hydrogen bonds contribute to protein stability, while those lacking such interactions contribute to instability<ref name="pace" /><ref name="kajander">PMID: 11080642</ref>. Thermophilic proteins often have fewer buried ionizable sidechains<ref name="kajander" />. Stability does not increase with protein size<ref name="pace" />. 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<ref name="pace" />.	+	Buried ionizable sidechains engaged in multiple hydrogen bonds, or in [[salt bridges]], contribute to protein stability, while those lacking such interactions contribute to instability<ref name="pace" /><ref name="kajander">PMID: 11080642</ref>. Thermophilic proteins often have fewer buried ionizable sidechains<ref name="kajander" />. Stability does not increase with protein size<ref name="pace" />. 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<ref name="pace" />.
-		+
-		+

	==References Cited==		==References Cited==
	<references />		<references />

Eric Martz: /* Notes to myself */

Eric Martz — Tue, 09 Feb 2021 19:32:07 GMT

Notes to myself

←Older revision		Revision as of 19:32, 9 February 2021
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	Buried ionizable sidechains engaged in multiple hydrogen bonds contribute to protein stability, while those lacking such interactions contribute to instability<ref name="pace" /><ref name="kajander">PMID: 11080642</ref>. Thermophilic proteins often have fewer buried ionizable sidechains<ref name="kajander" />. Stability does not increase with protein size<ref name="pace" />. 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<ref name="pace" />.		Buried ionizable sidechains engaged in multiple hydrogen bonds contribute to protein stability, while those lacking such interactions contribute to instability<ref name="pace" /><ref name="kajander">PMID: 11080642</ref>. Thermophilic proteins often have fewer buried ionizable sidechains<ref name="kajander" />. Stability does not increase with protein size<ref name="pace" />. 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<ref name="pace" />.

-	==Notes to myself==

-	Burial 1990, awaiting interlibrary

	==References Cited==		==References Cited==
	<references />		<references />

Eric Martz at 19:31, 9 February 2021

Eric Martz — Tue, 09 Feb 2021 19:31:14 GMT

←Older revision		Revision as of 19:31, 9 February 2021
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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 ~~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>.	+	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~~<ref name="lesser">PMID: 2217164</ref>~~	+	Burial 1990, awaiting interlibrary

	==References Cited==		==References Cited==
	<references />		<references />

Eric Martz at 19:28, 9 February 2021

Eric Martz — Tue, 09 Feb 2021 19:28:17 GMT

←Older revision		Revision as of 19:28, 9 February 2021
Line 1:		Line 1:
	<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 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>.	+	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 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==

Eric Martz at 19:26, 9 February 2021

Eric Martz — Tue, 09 Feb 2021 19:26:43 GMT

←Older revision		Revision as of 19:26, 9 February 2021
Line 1:		Line 1:
	<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" /><ref name="thurlkill">PMID: 16934292</ref>.	+	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 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==

Eric Martz at 00:51, 9 February 2021

Eric Martz — Tue, 09 Feb 2021 00:51:41 GMT

←Older revision		Revision as of 00:51, 9 February 2021
Line 5:		Line 5:
	==Protein Stability==		==Protein Stability==

-	Buried ionizable sidechains engaged in multiple hydrogen bonds contribute to protein stability, while those lacking such interactions contribute to instability<ref name="pace" />. Stability does not increase with protein size<ref name="pace" />. 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<ref name="pace" />.	+	Buried ionizable sidechains engaged in multiple hydrogen bonds contribute to protein stability, while those lacking such interactions contribute to instability<ref name="pace" /><ref name="kajander">PMID: 11080642</ref>. Thermophilic proteins often have fewer buried ionizable sidechains<ref name="kajander" />. Stability does not increase with protein size<ref name="pace" />. 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<ref name="pace" />.

	==Notes to myself==		==Notes to myself==