Availability of NHS-biotin labeling to identify free protein lysine revealed by experiment and MD simulation

Muraoka, Aiichiro; Matsuura, Yoshinori; Naitow, Hisashi; Ihara, Makoto; Kunishima, N.

doi:10.1016/j.ab.2018.07.009

Cited by 6 publications

(4 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This was highlighted through the use of labeling reagents such as Nhydroxysuccinimide-biotin (NHS-biotin), which also involves a nucleophilic attack by primary amines on the NHS group. Here, biotinylation was significantly correlated with four factors relevant to the local environment of lysine residues; the solvent accessibility, the electrostatic energy, the number of hydrogen bonds, and the estimated pKa value of the sidechain (158). In agreement with this, nucleophilic attack by primary amines on biotinyl-5'-AMP is dependent on the side chain pKa, which can vary based on the pH of the local environment as well as the biochemical properties of amino acids in the vicinity of the amine group (159,160).…”

Section: Other Experimental Considerationsmentioning

confidence: 99%

Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches

Samavarchi-Tehrani

Samson

Gingras

2020

Molecular & Cellular Proteomics

163

150

View full text Add to dashboard Cite

The study of protein subcellular distribution, their assembly into complexes and the set of proteins with which they interact with is essential to our understanding of fundamental biological processes. Complementary to traditional assays, proximity-dependent biotinylation (PDB) approaches coupled with mass spectrometry (such as BioID or APEX) have emerged as powerful techniques to study proximal protein interactions and the subcellular proteome in the context of living cells and organisms. Since their introduction in 2012, PDB approaches have been used in an increasing number of studies and the enzymes themselves have been subjected to intensive optimization. How these enzymes have been optimized and considerations for their use in proteomics experiments are important questions. Here, we review the structural diversity and mechanisms of the two main classes of PDB enzymes: the biotin protein ligases (BioID) and the peroxidases (APEX). We describe the engineering of these enzymes for PDB and review emerging applications, including the development of PDB for coincidence detection (split-PDB). Lastly, we briefly review enzyme selection and experimental design guidelines and reflect on the labeling chemistries and their implication for data interpretation.

show abstract

Section: Other Experimental Considerationsmentioning

confidence: 99%

Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches

Samavarchi-Tehrani

Samson

Gingras

2020

Molecular & Cellular Proteomics

163

150

View full text Add to dashboard Cite

show abstract

“…Biotinylation remains an instrumental approach to confer multifunctional properties to proteins via the exploitation of the extremely strong biotin-streptavidin interaction. 1 For this purpose, researchers have employed mostly chemical [2][3][4] and enzymatic [5][6][7][8] approaches to append biotin molecules to proteins of interest for subsequent docking onto streptavidin-associated technologies. Unfortunately, many available chemical conjugation approaches are stochastic and non-orthogonal and oen yield heterogeneous products with compromised functionality.…”

Section: Introductionmentioning

confidence: 99%

Sortase A transpeptidation produces seamless, unbranched biotinylated nanobodies for multivalent and multifunctional applications

et al. 2023

View full text Add to dashboard Cite

show abstract

“…At least 20 post-translational modifications (PTMs) of ε-amino groups of lysine residues have been reported under physiological conditions. These include mono-, di-, and trimethylation, − ADP-ribosylation, , formylation, ,, hydroxylation, lipoylation, biotinylation, ubiquitination, ,, neddylation, and sumoylation. , Several acyl-CoA-dependent lysine modifications have been reported, including acetylation, butyrylation, propionylation, glutarylation, crotonylation, malonylation, and succinylation . Carbamylation is another common PTM of lysine residues that results from the reaction with reactive cyanatefrom dietary sources of thiocyanates, degradation of urea, or cigarette smokingto form ε-carbamyl-lysine (homocitrulline). , …”

Section: Introductionmentioning

confidence: 99%

“…22 At least 20 posttranslational modifications (PTMs) of ε-amino groups of lysine residues have been reported under physiological conditions. These include mono-, di-, and trimethylation, 23−26 ADP-ribosylation, 27,28 formylation, 26,29,30 hydroxylation, 31 lipoylation, 32 biotinylation, 33 ubiquitination, 26,34,35 neddylation, 36 and sumoylation. 26,36 Several acyl-CoA-dependent lysine modifications have been reported, including acetylation, butyrylation, 37 propionylation, 37 glutarylation, 38 crotonylation, 39 malonylation, 40 and succinylation.…”

Section: ■ Introductionmentioning

confidence: 99%

Extending the HSA-Cys34-Adductomics Pipeline to Modifications at Lys525

Grigoryan

Imani

Dudoit

et al. 2021

Chem. Res. Toxicol.

View full text Add to dashboard Cite

We previously developed an adductomics pipeline that employed nanoflow liquid chromatography and highresolution tandem mass spectrometry (nLC−HR-MS/MS) plus informatics to perform an untargeted detection of modifications to Cys34 in the tryptic T3 peptide of human serum albumin (HSA) ( 21 ALVLIAFAQYLQQC 34 PFEDHVK 41 ). In order to detect these peptide modifications without targeting specific masses, the pipeline interrogates MS2 ions that are signatures of the T3 peptide. The pipeline had been pilot-tested with archived plasma from healthy human subjects, and several of the 43 Cys34 adducts were highly associated with the smoking status. In the current investigation, we adapted the pipeline to include modifications to the ε-amino group of Lys525a major glycation site in HSA and thereby extend the coverage to products of Schiff bases that cannot be produced at Cys34. Because trypsin is generally unable to digest proteins at modified lysines, our pipeline detects miscleaved tryptic peptides with the sequence 525 KQTALVELVK 534 . Adducts of both Lys525 and Cys34 are measured in a single nLC−HR-MS/MS run by increasing the mass range of precursor ions in MS1 scans and including both triply and doubly charged precursor ions for collision-induced dissociation fragmentation. For proof of principle, we applied the Cys34/Lys525 pipeline to archived plasma specimens from a subset of the same volunteer subjects used in the original investigation. Twelve modified Lys525 peptides were detected, including products of glycation (fructosyl-lysine plus advanced-glycated-end products), acetylation, and elimination of ammonia and water. Surprisingly, the carbamylated and glycated adducts were present at significantly lower levels in smoking subjects. By including a larger class of in vivo nucleophilic substitution reactions, the Cys34/Lys525 adductomics pipeline expands exposomic investigations of unknown human exposure to reactive electrophiles derived from both exogenous and endogenous sources.

show abstract

Availability of NHS-biotin labeling to identify free protein lysine revealed by experiment and MD simulation

Cited by 6 publications

References 34 publications

Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches

Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches

Sortase A transpeptidation produces seamless, unbranched biotinylated nanobodies for multivalent and multifunctional applications

Extending the HSA-Cys34-Adductomics Pipeline to Modifications at Lys525

Contact Info

Product

Resources

About