Amino Acids: Difference between revisions
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==22 Standard Amino Acids and Mnemonics== | ==22 Standard Amino Acids and Mnemonics== | ||
Here are the names of the twenty-two standard amino acids, with their three and one-letter<ref>A one-letter notation for amino acid sequences (definitive rules). IUPAC—IUB Commission on Biochemical Nomenclature, pages 639-645, International Union of Pure and Applied Chemistry and International Union of Biochemistry, Butterworths, London, 1971. [ | Here are the names of the twenty-two standard amino acids, with their three and one-letter<ref>A one-letter notation for amino acid sequences (definitive rules). IUPAC—IUB Commission on Biochemical Nomenclature, pages 639-645, International Union of Pure and Applied Chemistry and International Union of Biochemistry, Butterworths, London, 1971. [https://old.iupac.org/publications/pac/1972/pdf/3104x0639.pdf Full Text].</ref> abbreviations. Mnemonic names are intended to help you to remember the one-letter codes, but are not the correct names. | ||
<center> | <center> | ||
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</tr> | </tr> | ||
<tr><td colspan="4"><center> | <tr><td colspan="4"><center> | ||
<nowiki>*</nowiki>Since the mid-20th century, there were 20 standard amino acids. | <nowiki>*</nowiki>Since the mid-20th century, there were 20 standard amino acids. Early in the 21st Century, | ||
genetically encoded | genetically encoded | ||
[[#Unusual_Amino_Acids|Selenocysteine and Pyrrolysine]] have been included as standard. | [[#Unusual_Amino_Acids|Selenocysteine and Pyrrolysine]] have been included as standard by the World Wide Protein Data Bank<ref name="pdb22" />. | ||
<br> | <br> | ||
† Asx: Asn or Asp; Glx: Gln or Glu; Unk: unknown. | † Asx: Asn or Asp; Glx: Gln or Glu; Unk: unknown. | ||
<br> | <br> | ||
[http:// | [http://old.iupac.org/publications/pac/1972/pdf/3104x0639.pdf IUPAC/IUB 1971 publication] defining one-letter codes. | ||
</center></td></tr> | </center></td></tr> | ||
</table> | </table> | ||
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==L- and D-Amino Acids== | ==L- and D-Amino Acids== | ||
<table border='1' cellpadding='3' align='right' hspace="8"><tr><td colspan='2'> | <table border='1' cellpadding='3' align='right' hspace="8" class="wikitable" style="margin:0px 0px 0px 8px;"><tr><td colspan='2'> | ||
PDB Nomenclature | PDB Nomenclature | ||
</td></tr><tr><td> | </td></tr><tr><td> | ||
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</td></tr><tr><td> | </td></tr><tr><td> | ||
ALA<br>ARG<br>ASN<br>ASP<br>CYS<br>GLN<br>GLU<br>HIS<br>ILE<br>LEU<br>LYS<br>MET<br> | ALA<br>ARG<br>ASN<br>ASP<br>CYS<br>GLN<br>GLU<br>HIS<br>ILE<br>LEU<br>LYS<br>MET<br> | ||
PHE<br>PRO<br>SER<br>THR<br>TRP<br>TYR<br>VAL | PHE<br>PRO<br>PYL<br>SEC<br>SER<br>THR<br>TRP<br>TYR<br>VAL | ||
</td><td> | </td><td> | ||
DAL<br>DAR<br>DSG<br>DAS<br>DCY<br>DGN<br>DGL<br>DHI<br>DIL<br>DLE<br>DLY<br>MED<br> | DAL<br>DAR<br>DSG<br>DAS<br>DCY<br>DGN<br>DGL<br>DHI<br>DIL<br>DLE<br>DLY<br>MED<br> | ||
DPN<br>DPR<br>DSN<br>DTH<br>DTR<br>DTY<br>DVA | DPN<br>DPR<br>?<ref name="ddd">In January, 2022, no D-selenocysteine nor D-pyrrolysine were present in the [[wwPDB]], according to David Armstrong of PDBe.</ref><br>?<ref name="ddd" /><br>DSN<br>DTH<br>DTR<br>DTY<br>DVA | ||
</td></tr></table> | </td></tr></table> | ||
The asymmetric α-carbon in | The asymmetric α-carbon in 21 of the standard amino acids (all except glycine) is a chiral (stereogenic) center<ref name='chirality' />. Thus, each amino acid can exist in either of two optical isomers or enantiomers (mirror images), designated the L-form and D-form. Nearly all naturally-occuring amino acids are L-amino acids, so named because they are analogous to the L-form of glyceraldehyde<ref name='chirality'>See [http://en.wikipedia.org/wiki/Chirality_(chemistry) Chirality in Wikipedia]].</ref>. (Not all L-amino acids are levorotatory; some rotate polarized light clockwise<ref name='chirality' />). | ||
More than 700 entries in the [[PDB]] contain one or more D amino acids. Although D-amino acids are rare in nature, they do occur (see [http://en.wikipedia.org/wiki/Chirality_(chemistry)#D-Amino_Acid_Natural_Abundance natural abundance in Wikipedia]). D-alanine (DAL) occurs in over 100 entries in the [[PDB]], D-leucine (DLE), D-phenylalanine (DPN), D-serine (DSN), and D-valine (DVA) each occur in over 50. Some of these entries are chemically synthesized, not naturally occuring. Gramicidin is a naturally occuring antibiotic containing several D-amino acids, e.g. [[1nrm]]. [[4glu]] is the 102 amino acid chain of VEGF-A synthesized entirely from D-amino acids. | More than 700 entries in the [[PDB]] contain one or more D amino acids. Although D-amino acids are rare in nature, they do occur (see [http://en.wikipedia.org/wiki/Chirality_(chemistry)#D-Amino_Acid_Natural_Abundance natural abundance in Wikipedia]). D-alanine (DAL) occurs in over 100 entries in the [[PDB]], D-leucine (DLE), D-phenylalanine (DPN), D-serine (DSN), and D-valine (DVA) each occur in over 50. Some of these entries are chemically synthesized, not naturally occuring. Gramicidin is a naturally occuring antibiotic containing several D-amino acids, e.g. [[1nrm]]. [[4glu]] is the 102 amino acid chain of VEGF-A synthesized entirely from D-amino acids. | ||
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===Selenocysteine: the 21st amino acid=== | ===Selenocysteine: the 21st amino acid=== | ||
Rare proteins in all domains of life include '''[[Selenocysteine|selenocysteine (Sec, U)]]''', designated the 21st amino acid<ref name='21st'>PMID: 11028985</ref>. | Rare proteins in all domains of life include '''[[Selenocysteine|selenocysteine (Sec, U)]]''', designated the 21st amino acid<ref name='21st'>PMID: 11028985</ref>. In 2024, over 90 entries in the [[PDB]] include selenocysteine, identified as SEC. | ||
===Pyrrolysine: the 22nd amino acid=== | ===Pyrrolysine: the 22nd amino acid=== | ||
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===Postranslational modifications=== | ===Postranslational modifications=== | ||
Many unusual amino acids are formed by enzyme-catalyzed reactions that modify a standard amino acid after it has been included in a polypeptide; these are called post-translational modifications. Among them: | Many unusual amino acids are formed by enzyme-catalyzed reactions that modify a genetically encoded standard amino acid after it has been included in a polypeptide; these are called post-translational modifications. Among them: | ||
* phosphorylation of serine, threonine, or tyrosine | * phosphorylation of serine, threonine, or tyrosine | ||
** Example: C kinase [[1bkx]] | ** Example: C kinase [[1bkx]] | ||
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==Structure, Properties, Behaviors in Proteins== | ==Structure, Properties, Behaviors in Proteins== | ||
Angel Herráez has provided a [http://biomodel.uah.es/en/model1/prot/aa-intro.htm tutorial introduction to amino acid structure] in which | Angel Herráez has provided a [http://biomodel.uah.es/en/model1/prot/aa-intro.htm tutorial introduction to amino acid structure] in which 20 amino acids may be visualized in 3D using JSmol. | ||
Please help to expand the list below to include all | Please help to expand the list below to include all 22 amino acids. | ||
===Glycine=== | ===Glycine=== | ||
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*[[Standard Residues]] | *[[Standard Residues]] | ||
*[http://en.wikipedia.org/wiki/Amino_acids Amino Acids in Wikipedia] | *[http://en.wikipedia.org/wiki/Amino_acids Amino Acids in Wikipedia] | ||
*[ | *[[Basics of Protein Structure]] | ||
==References== | ==References== | ||
<references /> | <references /> | ||