Deamidation of human proteins

Robinson, Noah E.; Robinson, Arthur L.

doi:10.1073/pnas.221463198

Cited by 256 publications

(264 citation statements)

References 34 publications

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“…It was noticed that the neighboring residues next to the deamidated asparagines (N 85 and N 87 ) were glycines. The observed pattern of deamidation was consistent with the findings that glycine was observed as the most common (N ϩ 1) neighboring residue in proteins in which deamidation was established and characterized [24,25]. Accordingly, theoretical values of the deamidated peptide FVQNALNGNGDPNNMDR are m/z 631.93 and 947.41 for triply charged and doubly charged species, respectively, considering that the methionine is oxidized.…”

Section: Identification Of R95k Substitutionsupporting

confidence: 87%

Identification of amino acid substitutions in avian influenza virus (H5N1) matrix protein 1 by using nanoelectrospray MS and MS/MS

Liu

Song

Lee

et al. 2009

J. Am. Soc. Mass Spectrom.

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Matrix protein 1 (M1), the major structural protein of the avian influenza virus, plays a critical role in regulation of viral RNA transcription via interaction with RNA and transportation of RNP cores. Mutations in M1 have been frequently observed in the highly virulent avian influenza H5N1 virus, which might be crucial to the pathogenic function. Here we report the characterization of mutated peptides in M1 purified from highly pathogenic avian influenza virus H5N1 by nanoelectrospray MS and MS/MS analyses on a quadrupole-time-of-flight mass spectrometer (Q-TOFMS). The specificity of tandem mass spectrometry allowed the identification of six amino acid (AA) substitutions in M1, including R95K, A166V, I168T, N207S, N224S, and R230K. Two commonly observed modifications such as oxidation and deamidation were accurately assigned in the protein. Bioinformatics analysis suggested some relationship between the amino acid substitution and structural property of M1 protein.Discussions on de novo sequencing of MS/MS spectra, especially in dealing with the AA substitutions, were provided. (J Am Soc Mass Spectrom 2009, 20, 312-320)

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Section: Identification Of R95k Substitutionsupporting

confidence: 87%

Identification of amino acid substitutions in avian influenza virus (H5N1) matrix protein 1 by using nanoelectrospray MS and MS/MS

Liu

Song

Lee

et al. 2009

J. Am. Soc. Mass Spectrom.

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“…It is now clear that in addition to the primary structure, the rate of asparagine deamidation is controlled by the secondary and tertiary structure of the protein (10). A corollary to this is that the rate of deamidation of an asparagine can be altered by a change in secondary or tertiary structure such as might occur if the protein is subject to a posttranslational modification or a change in the interaction with a binding partner (10).…”

Section: The Molecular Clock Hypothesis Of Deamidationmentioning

confidence: 99%

“…A corollary to this is that the rate of deamidation of an asparagine can be altered by a change in secondary or tertiary structure such as might occur if the protein is subject to a posttranslational modification or a change in the interaction with a binding partner (10). Therefore, even though the underlying deamidation rate is set by the protein sequence surrounding the asparagine that undergoes deamidation, the process is subject to multiple levels of control within the protein.…”

Section: The Molecular Clock Hypothesis Of Deamidationmentioning

confidence: 99%

“…Using this formula, which has proven to be extraordinarily accurate, they demonstrated that deamidation must be widespread. They first computed the predicted deamidation half-life of 126 human proteins included in the Brookhaven Protein Data Bank and found that 4% of these proteins would be predicted to have a single-site deamidation half-life of less than 1 day, and 13% would be predicted to have a single-site deamidation half-life of less than 5 days when incubated in a physiologic phosphate buffer (10). They then computed the predicted deamidation half-lives for all of the asparagines in the 49 Drosophila proteins for which 3D structures were registered in the Protein Data Bank.…”

Section: The Molecular Clock Hypothesis Of Deamidationmentioning

confidence: 99%

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Chronoregulation by Asparagine Deamidation

Weintraub

Deverman

2007

Sci. STKE

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Every asparagine in every protein undergoes nonenzymatic deamidation to aspartate or isoaspartate at a rate determined by the surrounding protein structure and cellular environment. Under physiologic conditions, the deamidation half-life of individual asparagines in proteins is proposed to range from less than a day to several centuries. More than 200 proteins have been shown to undergo deamidation to a meaningful degree, and modeling predicts that hundreds more undergo deamidation at rates that have the potential to be of biological consequence. Because deamidation converts an asparagine into an aspartate or isoaspartate, it introduces a negative charge into a protein and results in the isomerization of a residue. Therefore, deamidation has the potential to change protein function. Additionally, deamidation is thought to render some proteins more susceptible to degradation. In most instances in which asparagine deamidation has been identified in vivo, it is involved in pathology. Hence, deamidation has been viewed primarily as a form of protein damage. However, the pervasiveness and evolutionary persistence of these unstable asparagines suggest that they may have a beneficial role. Notably, the change of even a single neighboring amino acid can have a marked effect on the rate of deamidation of an asparagine. Therefore, the underlying rate of deamidation of any asparagine is genetically programmable. This characteristic, combined with the wide range of deamidation rates that can be programmed, imparts to asparagines the potential to serve as molecular timers that regulate protein function and stability.

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“…Although phosphorylation and acetylation have received the most attention, nonenzymatic deamidation of labile Asn residues is also a frequently occurring post-translational modification in proteins (42). The reaction mechanism of this hydrolytic reaction (6) and the main factors that determine the wide range of rate constants observed in individual proteins (and peptides) (42) are also well characterized.…”

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confidence: 99%

Deamidations in Recombinant Human Phenylalanine Hydroxylase

Carvalho

Solstad

Bjørgo

et al. 2003

Journal of Biological Chemistry

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Recombinant human phenylalanine hydroxylase (hPAH) expressed in Escherichia coli for 24 h at 28°C has been found by two-dimensional electrophoresis to exist as a mixture of four to five molecular forms as a result of nonenzymatic deamidation of labile Asn residues. The multiple deamidations alter the functional properties of the enzyme including its affinity for Lphenylalanine and tetrahydrobiopterin, catalytic efficiency, and substrate inhibition and also result in enzyme forms more susceptible to limited tryptic proteolysis. Phenylalanine hydroxylase (PAH, 1 phenylalanine 4-monooxygenase, EC 1.14.16.1) is a non-heme iron monooxygenase that catalyzes the hydroxylation of L-phenylalanine (L-Phe) to L-tyrosine (L-Tyr) in the presence of the natural cofactor (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (H 4 biopterin) and dioxygen. Mutations in the human enzyme (hPAH) leading to altered kinetic properties or reduced stability of the enzyme are associated with the autosomal recessive disorder phenylketonuria (PKU). hPAH isolated from liver (2) and as recombinant enzyme expressed in Escherichia coli (3, 4) has been found to exist as a mixture of 4 -5 molecular forms with the same apparent subunit molecular mass, but with different isoelectric points (pI). Isoelectric focusing and two-dimensional electrophoresis of recombinant hPAH expressed in E. coli for 24 h at 28°C revealed five components of decreasing staining intensity and decreasing pI (denoted hPAH I-V). This microheterogeneity was shown to be the result of nonenzymatic deamidations of Asn residues (1, 4). Mainly one band with the highest pI (hPAH I) was, however, detected after a short induction period of 2 h at 28°C, and this form was considered to represent the newly synthesized and most native, nondeamidated form of the enzyme. Thus, the microheterogeneity pattern is highly dependent on the induction time with IPTG in E. coli (4). Due to the relatively high rate of deamidation, the labile amide-containing residues have been considered to be Asn residues (4), and this conclusion has recently been confirmed by the demonstration of iso-Asp in several tryptic peptides of the highly deamidated full-length wt-hPAH (1). In the deamidation reaction Asn is converted to Asp and iso-Asp in a variable ratio, sometimes with iso-Asp as the main product (5, 6). The rate of Asn deamidation in proteins and peptides has been shown to be dependent on pH, temperature, and ionic strength (7) and on intrinsic factors like the nearest neighbor amino acids, particularly the residue in the (n ϩ 1) position (8 -10). The deamidation proceeds via a cyclic succinimide intermediate (6), and with glycine in the n ϩ 1 position the rate of deamidation is unusually rapid, whereas all the other 19 amino acid residues are more sterically hindered in the formation of the cyclic intermediate (11). Moreover, the rate of deamidation is also determined by the protein secondary and tertiary structure because the necessary flexibility for the formation of the cyclic intermediate may be limited in p...

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Deamidation of human proteins

Cited by 256 publications

References 34 publications

Identification of amino acid substitutions in avian influenza virus (H5N1) matrix protein 1 by using nanoelectrospray MS and MS/MS

Identification of amino acid substitutions in avian influenza virus (H5N1) matrix protein 1 by using nanoelectrospray MS and MS/MS

Chronoregulation by Asparagine Deamidation

Deamidations in Recombinant Human Phenylalanine Hydroxylase

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