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Nikolsky KS, Kulikova LI, Petrovskiy DV, Rudnev VR, Malsagova KA, Kaysheva AL. Analysis of Structural Changes in the Protein near the Phosphorylation Site. Biomolecules 2023; 13:1564. [PMID: 38002246 PMCID: PMC10668964 DOI: 10.3390/biom13111564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 11/26/2023] Open
Abstract
Modification of the protein after synthesis (PTM) often affects protein function as supported by numerous studies. However, there is no consensus about the degree of structural protein changes after modification. For phosphorylation of serine, threonine, and tyrosine, which is a common PTM in the biology of living organisms, we consider topical issues related to changes in the geometric parameters of a protein (Rg, RMSD, Cα displacement, SASA). The effect of phosphorylation on protein geometry was studied both for the whole protein and at the local level (i.e., in different neighborhoods of the modification site). Heterogeneity in the degree of protein structural changes after phosphorylation was revealed, which allowed for us to isolate a group of proteins having pronounced local structural changes in the neighborhoods of up to 15 amino acid residues from the modification site. This is a comparative study of protein structural changes in neighborhoods of 3-15 amino acid residues from the modified site. Amino acid phosphorylation in proteins with pronounced local changes caused switching from the inactive functional state to the active one.
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Affiliation(s)
| | | | | | | | - Kristina A. Malsagova
- Institute of Biomedical Chemistry, Biobanking Group, Pogodinskaya, 10, 119121 Moscow, Russia; (K.S.N.); (L.I.K.); (D.V.P.); (V.R.R.); (A.L.K.)
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Yin X, Zhang H, Wei Z, Wang Y, Han S, Zhou M, Xu W, Han W. Large-Scale Identification of Lysine Crotonylation Reveals Its Potential Role in Oral Squamous Cell Carcinoma. Cancer Manag Res 2023; 15:1165-1179. [PMID: 37868687 PMCID: PMC10590141 DOI: 10.2147/cmar.s424422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023] Open
Abstract
Purpose Lysine crotonylation, an emerging posttranslational modification, has been implicated in the regulation of diverse biological processes. However, its involvement in oral squamous cell carcinoma (OSCC) remains elusive. This study aims to reveal the global crotonylome in OSCC under hypoxic conditions and explore the potential regulatory mechanism of crotonylation in OSCC. Methods Liquid-chromatography fractionation, affinity enrichment of crotonylated peptides, and high-resolution mass spectrometry were employed to detect differential crotonylation in CAL27 cells cultured under hypoxia. The obtained data were further subjected to bioinformatics analysis to uncover the involved biological processes and pathways of the dysregulated crotonylated proteins. A site-mutated plasmid was utilized to investigate the effect of crotonylation on Heat Shock Protein 90 Alpha Family Class B Member 1 (HAP90AB1) function. Results A large-scale crotonylome analysis revealed 1563 crotonylated modification sites on 605 proteins in CAL27 cells under hypoxia. Bioinformatics analysis revealed a significant decrease in histone crotonylation levels, while up-regulated crotonylated proteins were mainly concentrated in non-histone proteins. Notably, glycolysis-related proteins exhibited prominent up-regulation among the identified crotonylated proteins, with HSP90AB1 displaying the most significant changes. Subsequent experimental findings confirmed that mutating lysine 265 of HSP90AB1 into a silent arginine impaired its function in promoting glycolysis. Conclusion Our study provides insights into the crotonylation modification of proteins in OSCC under hypoxic conditions and elucidates the associated biological processes and pathways. Crotonylation of HSP90AB1 in hypoxic conditions may enhance the glycolysis regulation ability in OSCC, offering novel perspectives on the regulatory mechanism of crotonylation in hypoxic OSCC and potential therapeutic targets for OSCC treatment.
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Affiliation(s)
- Xiteng Yin
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Hongbo Zhang
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Zheng Wei
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Pediatric Dentistry, Nanjing Stomatology Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Yufeng Wang
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Shengwei Han
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Meng Zhou
- Department of Oral and Maxillofacial Surgery, the Affiliated Stomatological Hospital of Xuzhou Medical University, Xuzhou, People’s Republic of China
| | - Wenguang Xu
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Wei Han
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
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Smith BJ, Carregari VC. Post-Translational Modifications During Brain Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:29-38. [DOI: 10.1007/978-3-031-05460-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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