Deamidation of Glutaminyl and Asparaginyl Residues in Peptides and Proteins

Robinson, Arthur L.; Rudd, Colette J.

doi:10.1016/b978-0-12-152808-9.50013-4

Cited by 421 publications

(539 citation statements)

References 182 publications

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“…S7). As in other palaeoproteomes, the presence of such semitryptic peptides is not uncommon and is likely the result of protein diagenesis (23,25,(35)(36)(37). In addition, all three spectra contain a hydroxylated proline on the same position (COL10α1 position 135), further demonstrating consistency among our peptide-spectrum matches.…”

Section: Resultssupporting

confidence: 53%

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

Welker

Hajdinjak

Talamo

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

290

260

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In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this "transitional" assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation. Here we provide further evidence for a Neandertal-Châtelperronian association at the Grotte du Renne through biomolecular and chronological analysis. We identified 28 additional hominin specimens through zooarchaeology by mass spectrometry (ZooMS) screening of morphologically uninformative bone specimens from Châtelperronian layers at the Grotte du Renne. Next, we obtain an ancient hominin bone proteome through liquid chromatography-MS/MS analysis and error-tolerant amino acid sequence analysis. Analysis of this palaeoproteome allows us to provide phylogenetic and physiological information on these ancient hominin specimens. We distinguish Late Pleistocene clades within the genus Homo based on ancient protein evidence through the identification of an archaic-derived amino acid sequence for the collagen type X, alpha-1 (COL10α1) protein. We support this by obtaining ancient mtDNA sequences, which indicate a Neandertal ancestry for these specimens. Direct accelerator mass spectometry radiocarbon dating and Bayesian modeling confirm that the hominin specimens date to the Châtelperronian at the Grotte du Renne.

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Section: Resultssupporting

confidence: 53%

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

Welker

Hajdinjak

Talamo

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

290

260

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“…Early work established that deamidation occurs in vitro and in vivo, and that the rates of deamidation depend on primary sequence, three-dimensional (3D) structure, pH, temperature, ionic strength, buffer ions, and other solution properties (1-11). It has been hypothesized (3,5,7,12,13) that Asn and Gln may serve, through deamidation, as molecular clocks which time biological processes such as protein turnover, homeostatic control, and organismic development and aging, as well as mediators of postsynthetic production of new proteins of unique biological value.Deamidation has been observed and characterized in a wide variety of proteins. It has been shown to regulate some timedependent biological processes (8, 9) and to correlate with others, such as development and aging.…”

mentioning

confidence: 99%

“…At neutral pH, deamidation introduces a negative charge at the reaction site and can also lead to structural isomerization. Early work established that deamidation occurs in vitro and in vivo, and that the rates of deamidation depend on primary sequence, three-dimensional (3D) structure, pH, temperature, ionic strength, buffer ions, and other solution properties (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11). It has been hypothesized (3,5,7,12,13) that Asn and Gln may serve, through deamidation, as molecular clocks which time biological processes such as protein turnover, homeostatic control, and organismic development and aging, as well as mediators of postsynthetic production of new proteins of unique biological value.…”

mentioning

confidence: 99%

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Deamidation of human proteins

Robinson

Robinson²

2001

Proc. Natl. Acad. Sci. U.S.A.

258

250

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Deamidation of asparaginyl and glutaminyl residues causes timedependent changes in charge and conformation of peptides and proteins. Quantitative and experimentally verified predictive calculations of the deamidation rates of 1,371 asparaginyl residues in a representative collection of 126 human proteins have been performed. These rates suggest that deamidation is a biologically relevant phenomenon in a remarkably large percentage of human proteins.in vivo deamidation ͉ asparaginyl residues D eamidation of asparaginyl (Asn) and glutaminyl (Gln) residues to produce aspartyl (Asp) and glutamyl (Glu) residues causes structurally and biologically important alterations in peptide and protein structures. At neutral pH, deamidation introduces a negative charge at the reaction site and can also lead to structural isomerization. Early work established that deamidation occurs in vitro and in vivo, and that the rates of deamidation depend on primary sequence, three-dimensional (3D) structure, pH, temperature, ionic strength, buffer ions, and other solution properties (1-11). It has been hypothesized (3,5,7,12,13) that Asn and Gln may serve, through deamidation, as molecular clocks which time biological processes such as protein turnover, homeostatic control, and organismic development and aging, as well as mediators of postsynthetic production of new proteins of unique biological value.Deamidation has been observed and characterized in a wide variety of proteins. It has been shown to regulate some timedependent biological processes (8, 9) and to correlate with others, such as development and aging. There are many reports of deamidation under physiological conditions in proteins of biological significance. For examples, see refs. 14-18.Extensive evidence suggests that deamidation of Asn at neutral pH usually proceeds through a cyclic imide reaction mechanism (19)(20)(21). Sometimes the Asp produced by deamidation is isomerized to isoAsp. The in vivo reversal of this isomerization has been widely reported, but reversal of deamidation itself and of the introduced negative charge has not been observed.Deamidation rates depend on the amino acid residues near Asn and Gln in the peptide chain with sequence-determined deamidation half-times at neutral pHs and 37°C in the range of 1-500 days for Asn and 100-Ͼ5,000 days for Gln (7, 13).Sequence-determined Asn and Gln deamidation rates are modulated by peptide and protein 3D structures. Deamidation of peptides is observed at both Asn and Gln, largely in accordance with sequence-controlled rates. Deamidation of proteins, which is usually slowed by 3D structure, occurs primarily at Asn except in very long-lived proteins where Gln deamidation is also observed. In a few instances, 3D structure has been reported to increase deamidation rate.The deamidation rates of individual Asn residues in a protein can be reliably predicted as a result of two recent advances. First, the sequence-controlled Asn deamidation rates of most of the 400 possible near-neighbor combinations in pentapeptide m...

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“…Acetic acid induced deamidation of wheat gluten was further found to inhibit SDS-stable aggregate formation whilst largely retaining its ability to form disulfide bonds (Liao et al, 2010). The rate of the deamidation reaction has been found to depend on primary sequence and pH under which the reaction takes place, but was independent of ionic strength for model peptides (Patel & Borchardt, 1990a, 1990bRobinson & Rudd, 1974;Tyler-Cross & Schirch, 1991), soy protein and egg white lysozyme (Zhang et al, 1993).…”

Section: Deamidationmentioning

confidence: 99%