Molecular dynamic simulations identifying the mechanism of holoenzyme formation by O-GlcNAc transferase and active p38α

Literature Information

Publication Date 2023-02-17
DOI 10.1039/D2CP05968A
Impact Factor 3.676
Authors

Yu Wang, Zhiyang Zhang, Xiaoyuan Liu, Nianhang Chen, Yuan Zhao, Chaojie Wang


View Original

Abstract

O-N-Acetylglucosamine transferase (OGT) can catalyze the O-GlcNAc modification of thousands of proteins. The holoenzyme formation of OGT and adaptor protein is the precondition for further recognition and glycosylation of the target protein, while the corresponding mechanism is still open. Here, static and dynamic schemes based on statistics can successfully screen the feasible identifying, approaching, and binding mechanism of OGT and its typical adaptor protein p38α. The most favorable interface, energy contribution of hotspots, and conformational changes of fragments were discovered. The hydrogen bond interactions were verified as the main driving force for the whole process. The distinct characteristic of active and inactive p38α is explored and demonstrates that the phosphorylated tyrosine and threonine will form strong ion–pair interactions with Lys714, playing a key role in the dynamic identification stage. Multiple method combinations from different points of view may be helpful for exploring other systems of the protein–protein interactions.

Related Literature

Solvatochromism in perylene diimides; experiment and theory

C. A. Fuller, C. E. Finlayson

2017-11-16 Paper

DOI: 10.1039/C7CP05039A

UV-Vis spectrophotometry of quinone flow battery electrolyte for in situ monitoring and improved electrochemical modeling of potential and quinhydrone formation

Liuchuan Tong, Qing Chen, Andrew A. Wong, Rafael Gómez-Bombarelli, Alán Aspuru-Guzik, Roy G. Gordon, Michael J. Aziz

2017-11-15 Paper

DOI: 10.1039/C7CP05881K

Theoretical aspects of femtosecond double-pump single-molecule spectroscopy. I. Weak-field regime

Elisa Palacino-González, Maxim F. Gelin, Wolfgang Domcke

2017-11-20 Paper

DOI: 10.1039/C7CP04809B

Debye ring diffraction elucidation of 2D photonic crystal self-assembly and ordering at the air–water interface

N. L. Smith, A. Coukouma, S. Dubnik, S. A. Asher

2017-11-15 Paper

DOI: 10.1039/C7CP07130B

Ultrafast dynamics of ionic liquids in colloidal dispersion

Zhe Ren, Jordan Kelly, C. Prasad Gunathilaka, Thomas Brinzer, Samrat Dutta, Clinton A. Johnson, Sunayana Mitra, Sean Garrett-Roe

2017-11-03 Paper

DOI: 10.1039/C7CP04441K

A new scaling for the rotational diffusion of molecular probes in polymer solutions

Jing Qing, Anpu Chen, Nanrong Zhao

2017-11-07 Paper

DOI: 10.1039/C7CP07047K

Role of halogen⋯halogen interactions in the 2D crystallization of n-semiconductors at the liquid–solid interface

Zongxia Guo, Ping Yu, Kai Sun, Shengbin Lei, Yuanping Yi, Zhibo Li

2017-09-25 Communication

DOI: 10.1039/C7CP06027K

Back cover

Cover

DOI: 10.1039/C7CP90281F

Controlling the H to T′ structural phase transition via chalcogen substitution in MoTe2 monolayers

Joshua Young, Thomas L. Reinecke

2017-11-16 Paper

DOI: 10.1039/C7CP05634F

Infrared spectroscopy of hydrated polycyclic aromatic hydrocarbon cations: naphthalene+–water

Kuntal Chatterjee, Otto Dopfer

2017-11-22 Paper

DOI: 10.1039/C7CP06893J

You might also like

Compound Q&A

What are the main uses of 1H-Indazole-6-carbonitrile (CAS: 141290-59-7)?

1H-Indazole-6-carbonitrile finds applications in pharmaceuticals, where it serve...

141290-59-71H-Indazole-6-carbon...
Compound Q&A

How should waste containing Dioctyl (2E)-2-butenedioate (CAS: 2997-85-5) be handled?

Waste containing Dioctyl (2E)-2-butenedioate (CAS: 2997-85-5) should be collecte...

2997-85-5Dioctyl (2E)-2-buten...
Compound Q&A

What industries use Sodium [(1,2-benzoxazol-3-ylmethyl)sulfonyl]azanide (CAS: 68291-98-5)?

Sodium [(1,2-benzoxazol-3-ylmethyl)sulfonyl]azanide is primarily used in pharmac...

68291-98-5Sodium [(1,2-benzoxa...
Compound Q&A

Are there alternatives to Dimethyl 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2,6-pyridinedicarboxylate (CAS: 741709-66-0) in synthesis?

Dimethyl 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2,6-pyridinedicarboxyla...

741709-66-0Dimethyl 4-(4,4,5,5-...
Compound Q&A

How should waste containing 2-Fluoro-6-hydrazinopyridine (CAS: 80714-39-2) be handled?

Waste containing 2-Fluoro-6-hydrazinopyridine (CAS: 80714-39-2) should be manage...

80714-39-22-Fluoro-6-hydrazino...
Compound Q&A

What is 6-Formyl-2-pyridinecarboxylic acid (CAS: 499214-11-8)?

6-Formyl-2-pyridinecarboxylic acid is an organic compound with the molecular for...

499214-11-86-Formyl-2-pyridinec...
900874-91-13-(3,4-dimethoxyphen...
Compound Q&A

How is 9H-Tribenzo[b,d,f]azepine (CAS: 29875-73-8) typically synthesized?

9H-Tribenzo[b,d,f]azepine is typically synthesized via a multi-step process invo...

29875-73-89H-Tribenzo[b,d,f]az...
Compound Q&A

How is 1-Cyclopropyl-7-ethoxy-6-fluoro-8-methoxy-4-oxo-1,4-dihydro-3-quinolinecarboxylic acid (CAS: 1797982-51-4) typically synthesized?

1-Cyclopropyl-7-ethoxy-6-fluoro-8-methoxy-4-oxo-1,4-dihydro-3-quinolinecarboxyli...

1797982-51-41-Cyclopropyl-7-etho...
Compound Q&A

How should waste containing Methyl 3-oxo-1,2,3,4-tetrahydro-6-quinoxalinecarboxylate (CAS: 671820-52-3) be handled?

Waste containing Methyl 3-oxo-1,2,3,4-tetrahydro-6-quinoxalinecarboxylate (CAS: ...

671820-52-3Methyl 3-oxo-1,2,3,4...

Source Journal

Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
Articles per Year: 3036

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

Recommended Compounds

Recommended Suppliers

Disclaimer
This page provides academic journal information for reference and research purposes only. We are not affiliated with any journal publishers and do not handle publication submissions. For publication-related inquiries, please contact the respective journal publishers directly.
If you notice any inaccuracies in the information displayed, please contact us at support@chemtradehub.com. We will promptly review and address your concerns.