Antibody-based detection of lysine modification of hepatic protein in mice treated with retrorsine

2020 ◽  
Vol 38 (4) ◽  
pp. 315-328
Author(s):  
Ting Cheng ◽  
Weiwei Li ◽  
Xiaojing Yang ◽  
Huali Wang ◽  
Fan Zhang ◽  
...  
Keyword(s):  
Lysine Modification

scholarly journals Small Mass but Strong Information: Diagnostic Ions Provide Crucial Clues to Correctly Identify Histone Lysine Modifications

Proteomes ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 18
Author(s):  
Alaa Hseiky ◽  
Marion Crespo ◽  
Sylvie Kieffer-Jaquinod ◽  
François Fenaille ◽  
Delphine Pflieger
Keyword(s):  
Amino Acid ◽  
Small Mass ◽  
Mass Region ◽  
Amino Acid Sequences ◽  
Lysine Modification ◽  
Lysine Residues ◽  
Two Factors ◽  
Low Mass ◽  
Diagnostic Ions

(1) Background: The proteomic analysis of histones constitutes a delicate task due to the combination of two factors: slight variations in the amino acid sequences of variants and the multiplicity of post-translational modifications (PTMs), particularly those occurring on lysine residues. (2) Methods: To dissect the relationship between both aspects, we carefully evaluated PTM identification on lysine 27 from histone H3 (H3K27) and the artefactual chemical modifications that may lead to erroneous PTM determination. H3K27 is a particularly interesting example because it can bear a range of PTMs and it sits nearby residues 29 and 31 that vary between H3 sequence variants. We discuss how the retention times, neutral losses and immonium/diagnostic ions observed in the MS/MS spectra of peptides bearing modified lysines detectable in the low-mass region might help validate the identification of modified sequences. (3) Results: Diagnostic ions carry key information, thereby avoiding potential mis-identifications due to either isobaric PTM combinations or isobaric amino acid-PTM combinations. This also includes cases where chemical formylation or acetylation of peptide N-termini artefactually occurs during sample processing or simply in the timeframe of LC-MS/MS analysis. Finally, in the very subtle case of positional isomers possibly corresponding to a given mass of lysine modification, the immonium and diagnostic ions may allow the identification of the in vivo structure.

Site-Specific Systematic Analysis of Lysine Modification Crosstalk

PROTEOMICS ◽  
2018 ◽  
Vol 18 (9) ◽  
pp. 1700292 ◽  
Author(s):  
Hao-Dong Xu ◽  
Li-Na Wang ◽  
Ping-Ping Wen ◽  
Shao-Ping Shi ◽  
Jian-Ding Qiu
Keyword(s):  
Systematic Analysis ◽  
Site Specific ◽  
Lysine Modification

scholarly journals Altered specificity of Hint-W123Q supports a role for Hint inhibition by ASW in avian sex determination

2004 ◽  
Vol 20 (1) ◽  
pp. 12-14 ◽  
Author(s):  
Kristen P. Parks ◽  
Heather Seidle ◽  
Nathan Wright ◽  
Jeffrey B. Sperry ◽  
Pawel Bieganowski ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Sex Determination ◽  
Dominant Negative ◽  
Z Chromosome ◽  
Enzyme Specificity ◽  
W Chromosome ◽  
Dominant Component ◽  
Lysine Modification ◽  
Female Specific

Hint is a universally conserved, dimeric AMP-lysine hydrolase encoded on the avian Z chromosome. Tandemly repeated on the female-specific W chromosome, Asw encodes a potentially sex-determining, dominant-negative Hint dimerization partner whose substrate-interacting residues were specifically altered in evolution. To test the hypothesis that Gln127 of Asw is responsible for depression and/or alteration of Hint enzyme activity, a corresponding mutant was created in the chicken Hint homodimer, and a novel substrate was developed that links reversal of AMP-lysine modification to aminomethylcoumarin release. Strikingly, the Hint-W123Q substitution reduced kcat/ Km for AMP-lysine hydrolysis 17-fold, while it increased specificity for AMP- para-nitroaniline hydrolysis by 160-fold. The resulting 2,700-fold switch in enzyme specificity suggests that Gln127 could be the dominant component of Asw dominant negativity in avian feminization.

scholarly journals Active-site characterization of S1 nuclease I. Affinity purification and influence of amino-group modification

1992 ◽  
Vol 285 (2) ◽  
pp. 489-494 ◽  
Author(s):  
S Gite ◽  
G Reddy ◽  
V Shankar
Keyword(s):  
Active Site ◽  
Affinity Purification ◽  
Simple Procedure ◽  
Binding Studies ◽  
S1 Nuclease ◽  
Lysine Modification ◽  
Group Modification ◽  
Substrate Protection ◽  
Kinetics Of

A simple procedure, involving heat-treatment, DEAE-Sephadex, AMP-Sepharose and Bio-Gel P-60 chromatography, was developed for the purification of S1 nuclease to homogeneity from commercially available Takadiastase powder. Chemical modification of the amino groups of purified S1 nuclease revealed that lysine is essential for single-stranded DNAase, RNAase and phosphomonoesterase activities associated with the enzyme. The kinetics of inactivation suggested the involvement of a single lysine residue in the active site of the enzyme. Additionally, lysine modification was accompanied by a concomitant loss of all the activities of the enzyme, indicating the presence of a common catalytic site responsible for the hydrolysis of single-stranded DNA, RNA and 3′-AMP. Substrate-protection and inhibitor-binding studies on enzyme modified with 2,4,6-trinitrobenzenesulphonic acid showed that lysine may be involved in the substrate binding.

Corrigendum: Reversible Lysine Modification on Proteins by Using Functionalized Boronic Acids

2015 ◽  
Vol 22 (47) ◽  
pp. 16711-16711
Author(s):  
Pedro M. S. D. Cal ◽  
Raquel F. M. Frade ◽  
Carlos Cordeiro ◽  
Pedro M. P. Gois
Keyword(s):  
Boronic Acids ◽  
Lysine Modification

scholarly journals Acetylation: A lysine modification with neuroprotective effects in ischemic retinal degeneration

2014 ◽  
Vol 127 ◽  
pp. 124-131 ◽  
Author(s):  
Oday Alsarraf ◽  
Jie Fan ◽  
Mohammad Dahrouj ◽  
C. James Chou ◽  
Donald R. Menick ◽  
...  
Keyword(s):  
Retinal Degeneration ◽  
Neuroprotective Effects ◽  
Lysine Modification

scholarly journals Modification of pig M4 lactate dehydrogenase by pyridoxal 5'-phosphate. Demonstration of an essential lysine residue

1975 ◽  
Vol 149 (1) ◽  
pp. 107-113 ◽  
Author(s):  
S S Chen ◽  
P C Engel
Keyword(s):  
Lactate Dehydrogenase ◽  
Equilibrium Mixture ◽  
Lysine Residue ◽  
Original Activity ◽  
Complete Inactivation ◽  
Lysine Modification ◽  
Covalently Bonded ◽  
Lysine Residues ◽  
Enzyme Protection ◽  
Schiff Base Formation

1. Pig M4 lactate dehydrogenase treated in the dark with pyridoxal 5'-phosphate at pH8.5 and 25 degrees C loses activity gradually. The maximum inactivation was 66%, and this did not increase with concentrations of pyridoxal 5'-phosphate above 1 mM. 2. Inactivation may be reversed by dialysis or made permanent by reducing the enzyme with NaBH4. 3. Spectral evidence indicates modification of lysine residues, and 6-N-pyridoxyl-lysine is present in the hydrolsate of inactivated, reduced enzyme. 4. A second cycle of treatment with pyridoxal 5'-phosphate and NaBH4 further decreases activity. After three cycles only 9% of the original activity remains. 5. Apparent Km values for lactate and NAD+ are unaltered in the partially inactivated enzyme. 6. These results suggest that the covalently modified enzyme is inactive; failure to achieve complete inactivation in a single treatment is due to the reversibility of Schiff-base formation and to the consequent presence of active non-covalently bonded enzyme-modifier complex in the equilibrium mixture. 7. Although several lysine residues per subunit are modified, only one appears to be essential for activity: pyruvate and NAD+ together (both 5mM) completely protect against inactivation, and there is a one-to-one relationship between enzyme protection and decreased lysine modification. 8. NAD+ or NADH alone gives only partial protection. Substrates give virtually none. 9. Pig H4 lactate dehydrogenase is also inactivated by pyridoxal 5'-phosphate. 10. The possible role of the essential lysine residue is discussed.

scholarly journals Hypermethylated in Cancer 1 (HIC1), a Tumor Suppressor Gene Epigenetically Deregulated in Hyperparathyroid Tumors by Histone H3 Lysine Modification

2012 ◽  
Vol 97 (7) ◽  
pp. E1307-E1315 ◽  
Author(s):  
Jessica Svedlund ◽  
Susanne Koskinen Edblom ◽  
Victor E. Marquez ◽  
Göran Åkerström ◽  
Peyman Björklund ◽  
...  
Keyword(s):  
Tumor Suppressor ◽  
Tumor Suppressor Gene ◽  
Histone H3 ◽  
Suppressor Gene ◽  
Lysine Modification

scholarly journals Conformational destabilization of Bacillus licheniformis α-amylase induced by lysine modification and calcium depletion.

2011 ◽  
Vol 58 (3) ◽  
Author(s):  
Cheau Yuaan Tan ◽  
Raja Noor Zaliha Binti Raja Abdul Rahman ◽  
Habsah Abdul Kadir ◽  
Saad Tayyab
Keyword(s):  
Bacillus Licheniformis ◽  
Polyacrylamide Gel Electrophoresis ◽  
Conformational Stability ◽  
Gel Chromatography ◽  
Salt Bridges ◽  
Amino Groups ◽  
Calcium Depletion ◽  
Chemically Modified ◽  
Lysine Modification ◽  
Conformational Alteration

Bacillus licheniformis α-amylase (BLA) was chemically modified using 100-fold molar excess of succinic anhydride over protein or 0.66 M potassium cyanate to obtain 42 % succinylated and 81 % carbamylated BLAs. Size and charge homogeneity of modified preparations was established by Sephacryl S-200 HR gel chromatography and polyacrylamide gel electrophoresis. Conformational alteration in these preparations was evident by the larger Stokes radii (3.40 nm for carbamylated and 3.34 nm for succinylated BLAs) compared to 2.43 nm obtained for native BLA. Urea denaturation results using mean residue ellipticity (MRE) as a probe also showed conformational destabilization based on the early start of transition as well as ΔG(D)(H(2)O) values obtained for both modified derivatives and Ca-depleted BLA. Decrease in ΔG(D)(H(2)O) value from 5,930 cal/mol (for native BLA) to 3,957 cal/mol (for succinylated BLA), 3,336 cal/mol (for carbamylated BLA) and 3,430 cal/mol for Ca-depleted BLA suggested reduced conformational stability upon modification of amino groups of BLA or depletion of calcium. Since both succinylation and carbamylation reactions abolish the positive charge on amino groups (both α- and ε- amino), the decrease in conformational stability can be ascribed to the disruption of salt bridges present in the protein which might have released the intrinsic calcium from its binding site.

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