Amino acid composition - Revision history

Eric Martz: /* Example */

Eric Martz — Fri, 24 Apr 2020 21:57:30 GMT

Example

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-	\|[[Image:Composition-by-pir-for-2ace.png]]	+	\|[[Image:Composition-by-pir-for-2ace.png\|center]]
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	\|This composition bar graph was created by the Protein Information Resource's (PIR's) [https://proteininformationresource.org/pirwww/search/comp_mw.shtml Composition/Molecular Weight Calculator]. Protein sequences are easily obtained from [http://UniProt.Org UniProt.Org] or by viewing a PDB entry in [http://firstglance.jmol.org FirstGlance in Jmol] and clicking on Sequences. You may wish to align the genomic full-length sequence from UniProt with the experimentally crystallized sequence. Here are [http://firstglance.jmol.org/seqalign.htm instructions].		\|This composition bar graph was created by the Protein Information Resource's (PIR's) [https://proteininformationresource.org/pirwww/search/comp_mw.shtml Composition/Molecular Weight Calculator]. Protein sequences are easily obtained from [http://UniProt.Org UniProt.Org] or by viewing a PDB entry in [http://firstglance.jmol.org FirstGlance in Jmol] and clicking on Sequences. You may wish to align the genomic full-length sequence from UniProt with the experimentally crystallized sequence. Here are [http://firstglance.jmol.org/seqalign.htm instructions].

Eric Martz: /* Average Compositions */

Eric Martz — Fri, 24 Apr 2020 21:56:55 GMT

Average Compositions

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	[[Image:Composition-caruso-200.png\|770px\|center]]		[[Image:Composition-caruso-200.png\|770px\|center]]

-	~~Above~~ percentages were determined for several thousand sequences of diverse proteins of length 200 residues, with sequence identities below 50%<ref name="length" />. These data are included in the above-linked spreadsheet.	+	The above percentages were determined for several thousand sequences of diverse proteins of length 200 residues, with sequence identities below 50%<ref name="length" />. These data are included in the above-linked spreadsheet.

	==Determinants of Amino Acid Composition==		==Determinants of Amino Acid Composition==

Eric Martz: /* Example */

Eric Martz — Fri, 24 Apr 2020 17:25:44 GMT

Example

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	\|[[Image:Composition-by-pir-for-2ace.png]]		\|[[Image:Composition-by-pir-for-2ace.png]]
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-	\|This composition bar graph was created by the Protein Information Resource's (PIR's) [https://proteininformationresource.org/pirwww/search/comp_mw.shtml Composition/Molecular Weight Calculator]. Protein sequences are easily obtained from [http://UniProt.Org UniProt.Org] or by viewing a PDB entry in [http://firstglance.jmol.org FirstGlance in Jmol] and clicking on Sequences.	+	\|This composition bar graph was created by the Protein Information Resource's (PIR's) [https://proteininformationresource.org/pirwww/search/comp_mw.shtml Composition/Molecular Weight Calculator]. Protein sequences are easily obtained from [http://UniProt.Org UniProt.Org] or by viewing a PDB entry in [http://firstglance.jmol.org FirstGlance in Jmol] and clicking on Sequences. You may wish to align the genomic full-length sequence from UniProt with the experimentally crystallized sequence. Here are [http://firstglance.jmol.org/seqalign.htm instructions].
	\|}		\|}

Eric Martz at 01:29, 24 April 2020

Eric Martz — Fri, 24 Apr 2020 01:29:35 GMT

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-	The ''amino acid composition'' of a protein refers to the percentages of each amino acid in the sequence of that protein. The percentage, sometimes called the Mole percentage, is calculated for each of the [[amino acids\|22 standard amino acids]] as the ~~number~~ of a that amino acid divided by the total number of amino acids in the protein chain or molecule.	+	The ''amino acid composition'' of a protein refers to the percentages of each amino acid in the sequence of that protein. The percentage, sometimes called the Mole percentage, is calculated for each of the [[amino acids\|22 standard amino acids]] as the count of that amino acid divided by the total number of amino acids in the protein chain or molecule.

	==Example==		==Example==

Eric Martz at 01:21, 24 April 2020

Eric Martz — Fri, 24 Apr 2020 01:21:19 GMT

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	[[Image:Composition-caruso-200.png\|770px\|center]]		[[Image:Composition-caruso-200.png\|770px\|center]]

-	Above percentages were determined for several thousand sequences of diverse proteins of length 200 residues, with sequence identities below 50%.	+	Above percentages were determined for several thousand sequences of diverse proteins of length 200 residues, with sequence identities below 50%<ref name="length" />. These data are included in the above-linked spreadsheet.

	==Determinants of Amino Acid Composition==		==Determinants of Amino Acid Composition==

Eric Martz at 01:19, 24 April 2020

Eric Martz — Fri, 24 Apr 2020 01:19:53 GMT

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	**Trp is constant at about 1.4% for lengths 75-200.		**Trp is constant at about 1.4% for lengths 75-200.
	*'''Linkers vs. domains''': Linkers between domains have more polar residues, while compact domains have more hydrophobic residues<ref name="linkers">PMID: 29426365</ref>.		*'''Linkers vs. domains''': Linkers between domains have more polar residues, while compact domains have more hydrophobic residues<ref name="linkers">PMID: 29426365</ref>.
-	*'''Habitat''': The environment in which an organism lives has a minor effect on the average composition of its proteins<ref name="~~habitat~~" />.	+	*'''Habitat''': The environment in which an organism lives has a minor effect on the average composition of its proteins<ref name="habitats" />.
	*Compositional variability ranks archaea > baceteria > eukaryotes<ref name="linkers" />.		*Compositional variability ranks archaea > baceteria > eukaryotes<ref name="linkers" />.

Eric Martz: /* Average Compositions */

Eric Martz — Fri, 24 Apr 2020 01:19:12 GMT

Average Compositions

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	==Average Compositions==		==Average Compositions==
	Average compositions have been calculated for large numbers of proteins from diverse taxa. These are tabulated in the downloadable spreadsheet [http://proteopedia.org/wiki/images/1/15/Amino-acid-composition.xlsx.zip amino-acid-composition.xlsx.zip]. It is reassuring to see the agreement between tabulations generated in 1993, 1998, and 2008 (citations are in the spreadsheet).		Average compositions have been calculated for large numbers of proteins from diverse taxa. These are tabulated in the downloadable spreadsheet [http://proteopedia.org/wiki/images/1/15/Amino-acid-composition.xlsx.zip amino-acid-composition.xlsx.zip]. It is reassuring to see the agreement between tabulations generated in 1993, 1998, and 2008 (citations are in the spreadsheet).
-	[[Image:~~Amino~~-~~acid~~-~~composition~~.~~xlsx.zip~~\|770px]]	+
		+	[[Image:Composition-caruso-200.png\|770px\|center]]
		+
		+	Above percentages were determined for several thousand sequences of diverse proteins of length 200 residues, with sequence identities below 50%.

	==Determinants of Amino Acid Composition==		==Determinants of Amino Acid Composition==

Eric Martz: /* Average Compositions */

Eric Martz — Fri, 24 Apr 2020 01:17:10 GMT

Average Compositions

←Older revision		Revision as of 01:17, 24 April 2020
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	==Average Compositions==		==Average Compositions==
	Average compositions have been calculated for large numbers of proteins from diverse taxa. These are tabulated in the downloadable spreadsheet [http://proteopedia.org/wiki/images/1/15/Amino-acid-composition.xlsx.zip amino-acid-composition.xlsx.zip]. It is reassuring to see the agreement between tabulations generated in 1993, 1998, and 2008 (citations are in the spreadsheet).		Average compositions have been calculated for large numbers of proteins from diverse taxa. These are tabulated in the downloadable spreadsheet [http://proteopedia.org/wiki/images/1/15/Amino-acid-composition.xlsx.zip amino-acid-composition.xlsx.zip]. It is reassuring to see the agreement between tabulations generated in 1993, 1998, and 2008 (citations are in the spreadsheet).
		+	[[Image:Amino-acid-composition.xlsx.zip\|770px]]

	==Determinants of Amino Acid Composition==		==Determinants of Amino Acid Composition==

Eric Martz: /* Example */

Eric Martz — Fri, 24 Apr 2020 00:58:21 GMT

Example

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	==Example==		==Example==
	As an example, here is the amino acid composition of acetylcholinesterase of ''Torpedo californica'' (the Pacific electric ray), whose structure is [[2ace]]. The [https://www.uniprot.org/uniprot/P04058#sequences canonical isoform sequence] has length 586. In its mature form, a signal peptide is removed from the amino-terminus, and a pro-peptide is removed from the carboxy-terminus, leaving a mature length of 537, with this composition:		As an example, here is the amino acid composition of acetylcholinesterase of ''Torpedo californica'' (the Pacific electric ray), whose structure is [[2ace]]. The [https://www.uniprot.org/uniprot/P04058#sequences canonical isoform sequence] has length 586. In its mature form, a signal peptide is removed from the amino-terminus, and a pro-peptide is removed from the carboxy-terminus, leaving a mature length of 537, with this composition:
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	\|[[Image:Composition-by-pir-for-2ace.png]]		\|[[Image:Composition-by-pir-for-2ace.png]]

Eric Martz: /* Example */

Eric Martz — Fri, 24 Apr 2020 00:57:25 GMT

Example

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	\|[[Image:Composition-by-pir-for-2ace.png]]		\|[[Image:Composition-by-pir-for-2ace.png]]
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-	\|This composition bar graph was created by the Protein Information Resource's (PIR's) [https://proteininformationresource.org/pirwww/search/comp_mw.shtml Composition/Molecular Weight Calculator].	+	\|This composition bar graph was created by the Protein Information Resource's (PIR's) [https://proteininformationresource.org/pirwww/search/comp_mw.shtml Composition/Molecular Weight Calculator]. Protein sequences are easily obtained from [http://UniProt.Org UniProt.Org] or by viewing a PDB entry in [http://firstglance.jmol.org FirstGlance in Jmol] and clicking on Sequences.
	\|}		\|}