Warning: Constant ABSPATH already defined in D:\www\www164\blog\wp-config.php on line 31 {"id":403,"date":"2020-06-20T16:26:50","date_gmt":"2020-06-20T14:26:50","guid":{"rendered":"https:\/\/www.protpi.ch\/blog\/?p=403"},"modified":"2020-12-03T18:02:27","modified_gmt":"2020-12-03T16:02:27","slug":"amidation","status":"publish","type":"post","link":"https:\/\/www.protpi.ch\/blog\/bioinformatics\/2020\/06\/amidation\/","title":{"rendered":"Amidation"},"content":{"rendered":"\n

Amidation is one of the most common post-translational modification in which the C-terminal carboxyl group is replaced by an amide group\u200b1\u20135\u200b<\/sup><\/span>. Amidation plays an important role in peptidesand peptide hormones. More than half of all mammalian peptide hormones and more than 80 % of all insect hormones have amidated C-termini\u200b1\u200b<\/sup><\/span>. The mechanism of amidation is different depending on whether the modification takes place in vivo<\/em> or in vitro<\/em>. Amidation makes a peptide less susceptible to proteolytic degradation, which increases its half-life in the bloodstream\u200b2\u200b<\/sup><\/span>. By replacing the ionizable carboxyl group at the C-terminus with a nonionizable amide group,the physicochemical properties of the peptide can be altered. One example would be increased hydrophobicity under physiological conditions, which is essential for bioactive peptides involved in receptor recognition and signal transduction\u200b2\u20134\u200b<\/sup><\/span>. In addition, amidation influences the binding affinity of the peptides to their G-protein coupled receptors\u200b2,4\u200b<\/sup><\/span>.<\/p>\n\n\n\n

Amidation (in vivo<\/em>)<\/h2>\n\n\n\n

Overview<\/h3>\n\n\n\n

Amidation in vivo<\/em> is a common post-translational modification in peptides and peptide hormonesin which the N-C\u03b1 bond of a C-terminal glycine is cleaved in two steps by the bifunctional enzyme peptidylglycine-\u03b1-amidating monooxygenase (PAM), resulting in an amidated C-terminus.<\/p>\n\n\n\n

pKa<\/td>NC<\/td>Loss<\/td>Gain<\/td>Deltamass<\/td>H<\/td>AA<\/td>UV-Spec<\/td>Pattern<\/td><\/tr>
–<\/td>No<\/td>C2<\/sub>H3<\/sub>O2<\/sub><\/td>H<\/td>Av: -58.0362
M: -58.0055<\/td>		– 3<\/td>$<\/td>–<\/td>(?<=G)$<\/td><\/tr><\/tbody><\/table>
Physicochemical properties of amidation (in vivo<\/em>) that are stored in the modification database of Prot pi (NC: Native charge; H: Relative hydrophobicity; AA: Modified amino acid; Pattern: Regex for sequence-motif  recognition).<\/figcaption><\/figure>\n\n\n\n

In-depth mechanism<\/h3>\n\n\n\n

Amidation in vivo<\/em> is one of the last modifications in peptide maturation and occurs in the trans-Golgi network or in secretory vesicles\u200b2\u200b<\/sup><\/span>. It is not simply the result of a transamination reaction, but is performed by the bifunctional enzyme peptidylglycine-\u03b1-amidating monooxygenase (PAM), which catalyses the reaction in two steps\u200b1\u20133,5\u200b<\/sup><\/span>. PAM is an integral membrane proteine that specifically recognizes C-terminal glycines and amidates them. PAM has two enzymatic domains inside the secretory pathway lumen and a small C-terminal domain in the cytosol. The catalytic domain involved in the first step is called peptidylglycine \u03b1-hydroxylating monooxygenase (PHM). PHM uses peptidylglycine as substrate and converts it into an \u03b1-hydroxyglycine intermediate. The presence of copper, ascorbate as well as molecular oxygen is required for this reaction to occur. The second catalytic domain is called peptidyl-\u03b1-hydroxyglycine \u03b1-amidating lyase (PAL). PAL is a zinc dependent enzyme which converts the \u03b1-hydroxyglycine intermediate into an amidated peptide by cleaving the N-C\u03b1 bond and simultaneously releases glyoxylate\u200b1,2\u200b<\/sup><\/span>. The amidated peptide shows a mass loss of 58 Da compared to its precursor\u200b5\u200b<\/sup><\/span>. Additionally, in RPLC since the carboxyl group is protonated and thus more hydrophobic than the amide group, the hydrophobicity of the protein is lowered by 3 (+ 1 glycine clipping \/ – 4 amidation). The mechanism of amidation in vivo<\/em> is shown in figure 1.<\/p>\n\n\n\n

\"\"
Figure 1: Mechanism of amidation in vivo<\/em>. The reaction is catalysed by the bifunctional enzyme PAM. First, PHM, which requires copper, ascorbate and molecular oxygen, converts a peptylglycine into an \u03b1-hydroxyglycine intermediate. The intermediate is then converted into an amidated peptide by PAL, which is a zinc dependent enzyme. Glyoxylate is released in the process.<\/figcaption><\/figure>\n\n\n\n

Amidation (in vitro<\/em>)<\/h2>\n\n\n\n

Overview<\/h3>\n\n\n\n

Amidation in vitro<\/em> is an artificial modification that can be introduced at the C-terminus of a protein whereby the carboxyl group is replaced by an amide group. The C-terminal amide can be formed by chemical synthesis or by catalysation of carboxypeptidase-Y.<\/p>\n\n\n\n

pKa<\/td>NC<\/td>Loss<\/td>Gain<\/td>Deltamass<\/td>H<\/td>AA<\/td>UV-Spec<\/td>Pattern<\/td><\/tr>
–<\/td>No<\/td>OH<\/td>NH2<\/td>Av: -0.9848
M: -0.9840<\/td>		– 4<\/td>$<\/td>–<\/td>–<\/td><\/tr><\/tbody><\/table>
Physicochemical properties of amidation (in vitro<\/em>) that are stored in the modification database of Prot pi (NC: Native charge; H: Relative hydrophobicity; AA: Modified amino acid; Pattern: Regex for sequence-motif  recognition).<\/figcaption><\/figure>\n\n\n\n

In-depth mechanism<\/h3>\n\n\n\n

Much research has been carried out to develop a more efficient amidation reaction, in particular due to its industrial application in the production of peptid amides for therapeutic purposes. Therefore, several methods have been developed. Four methods in particular have proved successful. These four methods include amidation by an \u03b1-amidating enzyme from a natural source, amidation by a recombinant \u03b1-amidating enzyme, enzymatic transacylation by carboxypeptidase-Y and chemical synthesis\u200b1\u200b<\/sup><\/span>. For the latter two methods, it is not necessary that a glycine is present at the C-terminus. The carboxyl group is directly exchanged for an amide group without partially cleaving off the C-terminal glycine. Therefore, with these two methods only a mass loss of 1 Da occurs compared to its precursor\u200b3,4\u200b<\/sup><\/span>. Also, the hydrophobicity in RPLC is reduced by 4 because the partial clipping of the C-terminal glycine is no longer carried out. The mechanism for amidation of the C-terminus by carboxypeptidase-Y and chemical synthesis is shown in figure 2.<\/p>\n\n\n\n

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Figure 2: Abbreviated mechanism of amidationin vitro. The C-terminal carboxyl group canreplaced by an amide group by chemical synthesis or carboxypeptidase-Y.<\/figcaption><\/figure>\n\n\n\n

References<\/p>\n\n\n\n

  1. \n
    1. <\/div>
    Kim K-H, Seong BL. Peptide amidation: Production of peptide hormonesin vivo andin vitro. Biotechnology and Bioprocess Engineering<\/i>. 2001;6:244\u2013251. doi:10.1007\/BF02931985<\/a><\/div>\n <\/div>\n<\/li>
  2. \n
    2. <\/div>
    Kumar D, Eipper BA, Mains REBT-RM in BS. Amidation\u2606. In: Reference Module in Biomedical Sciences<\/i>. Elsevier; 2014:1\u20135. doi:https:\/\/doi.org\/10.1016\/B978-0-12-801238-3.04040-X<\/a><\/div>\n <\/div>\n<\/li>
  3. \n
    3. <\/div>
    Cui W, Niu S, Zheng L, et al. Prediction of protein amidation sites by feature selection and analysis. Molecular Genetics and Genomics<\/i>. 2013;288:391\u2013400. doi:10.1007\/s00438-013-0760-x<\/a><\/div>\n <\/div>\n<\/li>
  4. \n
    4. <\/div>
    Marino G, Eckhard U, Overall CM. Protein Termini and Their Modifications Revealed by Positional Proteomics. ACS Chemical Biology<\/i>. 2015;10:1754\u20131764. doi:10.1021\/acschembio.5b00189<\/a><\/div>\n <\/div>\n<\/li>
  5. \n
    5. <\/div>
    An Z, Chen Y, Koomen JM, Merkler DJ. A mass spectrometry-based method to screen for \u0251-amidated peptides. Proteomics<\/i>. 2012;12:173\u2013182. doi:10.1002\/pmic.201100327<\/a><\/div>\n <\/div>\n<\/li><\/ol><\/section>\n","protected":false},"excerpt":{"rendered":"

    Amidation is one of the most common post-translational modification in which the C-terminal carboxyl group is replaced by an amide group\u200b1\u20135\u200b. Amidation plays an important role in peptidesand peptide hormones. More than half of all mammalian peptide hormones and more than 80 % of all insect hormones have amidated C-termini\u200b1\u200b. The mechanism of amidation is […]<\/p>\n","protected":false},"author":11,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[26],"tags":[41,43,42,40,57],"class_list":["post-403","post","type-post","status-publish","format-standard","hentry","category-bioinformatics","tag-hormones","tag-in-vitro","tag-in-vivo","tag-peptide","tag-post-translational-modification"],"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/www.protpi.ch\/blog\/wp-json\/wp\/v2\/posts\/403","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.protpi.ch\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.protpi.ch\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.protpi.ch\/blog\/wp-json\/wp\/v2\/users\/11"}],"replies":[{"embeddable":true,"href":"https:\/\/www.protpi.ch\/blog\/wp-json\/wp\/v2\/comments?post=403"}],"version-history":[{"count":14,"href":"https:\/\/www.protpi.ch\/blog\/wp-json\/wp\/v2\/posts\/403\/revisions"}],"predecessor-version":[{"id":542,"href":"https:\/\/www.protpi.ch\/blog\/wp-json\/wp\/v2\/posts\/403\/revisions\/542"}],"wp:attachment":[{"href":"https:\/\/www.protpi.ch\/blog\/wp-json\/wp\/v2\/media?parent=403"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.protpi.ch\/blog\/wp-json\/wp\/v2\/categories?post=403"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.protpi.ch\/blog\/wp-json\/wp\/v2\/tags?post=403"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}