Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa

Research output: Contribution to journalJournal articlepeer-review

Standard

Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa. / Liu, Chao; Wu, Ting; Shu, Xin; Li, Shang-Tong; Wang, Daniel R.; Wang, Nanxi; Zhou, Rong; Yang, Hao; Jiang, Hong; Hendriks, Ivo A.; Gong, Pengyun; Zhang, Long; Nielsen, Michael L.; Li, Kui; Wang, Lei; Yang, Bing.

In: Advanced Biology, Vol. 5, No. 3, 2000308, 2021.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Liu, C, Wu, T, Shu, X, Li, S-T, Wang, DR, Wang, N, Zhou, R, Yang, H, Jiang, H, Hendriks, IA, Gong, P, Zhang, L, Nielsen, ML, Li, K, Wang, L & Yang, B 2021, 'Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa', Advanced Biology, vol. 5, no. 3, 2000308. https://doi.org/10.1002/adbi.202000308

APA

Liu, C., Wu, T., Shu, X., Li, S-T., Wang, D. R., Wang, N., Zhou, R., Yang, H., Jiang, H., Hendriks, I. A., Gong, P., Zhang, L., Nielsen, M. L., Li, K., Wang, L., & Yang, B. (2021). Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa. Advanced Biology, 5(3), [2000308]. https://doi.org/10.1002/adbi.202000308

Vancouver

Liu C, Wu T, Shu X, Li S-T, Wang DR, Wang N et al. Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa. Advanced Biology. 2021;5(3). 2000308. https://doi.org/10.1002/adbi.202000308

Author

Liu, Chao ; Wu, Ting ; Shu, Xin ; Li, Shang-Tong ; Wang, Daniel R. ; Wang, Nanxi ; Zhou, Rong ; Yang, Hao ; Jiang, Hong ; Hendriks, Ivo A. ; Gong, Pengyun ; Zhang, Long ; Nielsen, Michael L. ; Li, Kui ; Wang, Lei ; Yang, Bing. / Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa. In: Advanced Biology. 2021 ; Vol. 5, No. 3.

Bibtex

@article{7c6166bf57a443578d1f1b6b36c79252,
title = "Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa",
abstract = "Protein crosslinks occur endogenously such as modifications by ubiquitin-like proteins for signaling, or exogenously through genetically encoded chemical crosslinkers (GECX) for studying elusive protein-protein interactions. However, it remains challenging to identify these protein crosslinks efficiently at the proteomic scale. Herein, software OpenUaa is developed for identifying protein crosslinks generated by genetically encoded unnatural amino acids and endogenous protein conjugation. OpenUaa features inclusive and open search capability, dramatically improving identification sensitivity and coverage. Integrating GECX with OpenUaa, the direct interactome of thioredoxin is identified in Escherichia coli cells, yielding 289 crosslinked peptides and corresponding to 205 direct binding protein of thioredoxin. These identified direct binders provide evidence for thioredoxin's regulation of redox state and mitochondria energy metabolism. When identifying endogenous conjugation of small ubiquitin-like modifier (SUMO), OpenUaa also markedly improves coverage of SUMOylated peptides by ≈92%, revealing new SUMO targets. GECX-OpenUaa will enable efficient identification of direct interactomes of various proteins in live cells.",
author = "Chao Liu and Ting Wu and Xin Shu and Shang-Tong Li and Wang, {Daniel R.} and Nanxi Wang and Rong Zhou and Hao Yang and Hong Jiang and Hendriks, {Ivo A.} and Pengyun Gong and Long Zhang and Nielsen, {Michael L.} and Kui Li and Lei Wang and Bing Yang",
year = "2021",
doi = "10.1002/adbi.202000308",
language = "English",
volume = "5",
journal = "Advanced Biology",
issn = "2701-0198",
publisher = "Wiley",
number = "3",

}

RIS

TY - JOUR

T1 - Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa

AU - Liu, Chao

AU - Wu, Ting

AU - Shu, Xin

AU - Li, Shang-Tong

AU - Wang, Daniel R.

AU - Wang, Nanxi

AU - Zhou, Rong

AU - Yang, Hao

AU - Jiang, Hong

AU - Hendriks, Ivo A.

AU - Gong, Pengyun

AU - Zhang, Long

AU - Nielsen, Michael L.

AU - Li, Kui

AU - Wang, Lei

AU - Yang, Bing

PY - 2021

Y1 - 2021

N2 - Protein crosslinks occur endogenously such as modifications by ubiquitin-like proteins for signaling, or exogenously through genetically encoded chemical crosslinkers (GECX) for studying elusive protein-protein interactions. However, it remains challenging to identify these protein crosslinks efficiently at the proteomic scale. Herein, software OpenUaa is developed for identifying protein crosslinks generated by genetically encoded unnatural amino acids and endogenous protein conjugation. OpenUaa features inclusive and open search capability, dramatically improving identification sensitivity and coverage. Integrating GECX with OpenUaa, the direct interactome of thioredoxin is identified in Escherichia coli cells, yielding 289 crosslinked peptides and corresponding to 205 direct binding protein of thioredoxin. These identified direct binders provide evidence for thioredoxin's regulation of redox state and mitochondria energy metabolism. When identifying endogenous conjugation of small ubiquitin-like modifier (SUMO), OpenUaa also markedly improves coverage of SUMOylated peptides by ≈92%, revealing new SUMO targets. GECX-OpenUaa will enable efficient identification of direct interactomes of various proteins in live cells.

AB - Protein crosslinks occur endogenously such as modifications by ubiquitin-like proteins for signaling, or exogenously through genetically encoded chemical crosslinkers (GECX) for studying elusive protein-protein interactions. However, it remains challenging to identify these protein crosslinks efficiently at the proteomic scale. Herein, software OpenUaa is developed for identifying protein crosslinks generated by genetically encoded unnatural amino acids and endogenous protein conjugation. OpenUaa features inclusive and open search capability, dramatically improving identification sensitivity and coverage. Integrating GECX with OpenUaa, the direct interactome of thioredoxin is identified in Escherichia coli cells, yielding 289 crosslinked peptides and corresponding to 205 direct binding protein of thioredoxin. These identified direct binders provide evidence for thioredoxin's regulation of redox state and mitochondria energy metabolism. When identifying endogenous conjugation of small ubiquitin-like modifier (SUMO), OpenUaa also markedly improves coverage of SUMOylated peptides by ≈92%, revealing new SUMO targets. GECX-OpenUaa will enable efficient identification of direct interactomes of various proteins in live cells.

U2 - 10.1002/adbi.202000308

DO - 10.1002/adbi.202000308

M3 - Journal article

C2 - 33729691

VL - 5

JO - Advanced Biology

JF - Advanced Biology

SN - 2701-0198

IS - 3

M1 - 2000308

ER -

ID: 259630879