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Provost JJ, Cornely KA, Mertz PS, Peterson CN, Riley SG, Tarbox HJ, Narasimhan SR, Pulido AJ, Springer AL. Phosphorylation of mammalian cytosolic and mitochondrial malate dehydrogenase: insights into regulation. Essays Biochem 2024:EBC20230079. [PMID: 38864157 DOI: 10.1042/ebc20230079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/13/2024]
Abstract
Malate dehydrogenase (MDH) is a key enzyme in mammalian metabolic pathways in cytosolic and mitochondrial compartments. Regulation of MDH through phosphorylation remains an underexplored area. In this review we consolidate evidence supporting the potential role of phosphorylation in modulating the function of mammalian MDH. Parallels are drawn with the phosphorylation of lactate dehydrogenase, a homologous enzyme, to reveal its regulatory significance and to suggest a similar regulatory strategy for MDH. Comprehensive mining of phosphorylation databases, provides substantial experimental (primarily mass spectrometry) evidence of MDH phosphorylation in mammalian cells. Experimentally identified phosphorylation sites are overlaid with MDH's functional domains, offering perspective on how these modifications could influence enzyme activity. Preliminary results are presented from phosphomimetic mutations (serine/threonine residues changed to aspartate) generated in recombinant MDH proteins serving as a proof of concept for the regulatory impact of phosphorylation. We also examine and highlight several approaches to probe the structural and cellular impact of phosphorylation. This review highlights the need to explore the dynamic nature of MDH phosphorylation and calls for identifying the responsible kinases and the physiological conditions underpinning this modification. The synthesis of current evidence and experimental data aims to provide insights for future research on understanding MDH regulation, offering new avenues for therapeutic interventions in metabolic disorders and cancer.
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Affiliation(s)
- Joseph J Provost
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA, U.S.A
| | - Kathleen A Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence RI, U.S.A
| | - Pamela S Mertz
- Department of Chemistry and Biochemistry, St. Mary's College of Maryland, St. Mary's City, MD, U.S.A
| | | | - Sophie G Riley
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA, U.S.A
| | - Harrison J Tarbox
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA, U.S.A
| | - Shree R Narasimhan
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA, U.S.A
| | - Andrew J Pulido
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA, U.S.A
| | - Amy L Springer
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, U.S.A
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Bulangalire N, Claeyssen C, Douffi S, Agbulut O, Cieniewski-Bernard C. A novel 2D-electrophoresis method for the simultaneous visualization of phosphorylated and O-GlcNAcylated proteoforms of a protein. Electrophoresis 2024. [PMID: 38700120 DOI: 10.1002/elps.202400043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/16/2024] [Indexed: 05/05/2024]
Abstract
Post-translational modifications (PTMs), such as phosphorylation and O-N-acetyl-β-d-glucosaminylation (O-GlcNAcylation), are involved in the fine spatiotemporal regulation of protein functions, and their dynamic interplay is at the heart of protein language. The coexistence of phosphorylation and O-GlcNAcylation on a protein leads to the diversification of proteoforms. It is therefore essential to decipher the phosphorylation/O-GlcNAcylation interplay on protein species that orchestrates cellular processes in a specific physiological or pathophysiological context. However, simultaneous visualization of phosphorylation and O-GlcNAcylation patterns on a protein of interest remains a challenge. To map the proteoforms of a protein, we have developed an easy-to-use two-dimensional electrophoresis method with a single sample processing permitting simultaneous visualization of the phosphorylated and the O-GlcNAcylated forms of the protein of interest. This method, we termed 2D-WGA-Phos-tag-PAGE relies on proteoforms retardation by affinity gel electrophoresis. With this novel approach, we established the cartography of phospho- and glycoforms of αB-crystallin and desmin in the whole extract and the cytoskeleton protein subfraction in skeletal muscle cells. Interestingly, we have shown that the pattern of phosphorylation and O-GlcNAcylation depends of the subcellular subfraction. Moreover, we have also shown that proteotoxic stress condition increased the complexity of the pattern of PTMs on αB-crystallin.
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Affiliation(s)
- Nathan Bulangalire
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
- CHU Lille, Université de Lille, F-59000, Lille, France
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005, Paris, France
| | - Charlotte Claeyssen
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
| | - Sana Douffi
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
| | - Onnik Agbulut
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005, Paris, France
| | - Caroline Cieniewski-Bernard
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
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Xie J, Quan L, Wang X, Wu H, Jin Z, Pan D, Chen T, Wu T, Lyu Q. DeepMPSF: A Deep Learning Network for Predicting General Protein Phosphorylation Sites Based on Multiple Protein Sequence Features. J Chem Inf Model 2023; 63:7258-7271. [PMID: 37931253 DOI: 10.1021/acs.jcim.3c00996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Phosphorylation, as one of the most important post-translational modifications, plays a key role in various cellular physiological processes and disease occurrences. In recent years, computer technology has been gradually applied to the prediction of protein phosphorylation sites. However, most existing methods rely on simple protein sequence features that provide limited contextual information. To overcome this limitation, we propose DeepMPSF, a phosphorylation site prediction model based on multiple protein sequence features. There are two types of features: sequence semantic features, which comprise protein residue type information and relative position information within protein sequence, and protein background biophysical features, which include global semantic information containing more comprehensive protein background information obtained from pretrained models. To extract these features, DeepMPSF employs two separate subnetworks: the S71SFE module and the BBFE module, which automatically extract high-level semantic features. Our model incorporates a learning strategy for handling imbalanced datasets through ensemble learning during training and prediction. DeepMPSF is trained and evaluated on a well-established dataset of human proteins. Comparing the analysis with other benchmark methods reveals that DeepMPSF outperforms in predicting both S/T residues and Y residues. In particular, DeepMPSF showed excellent generalization performance in cross-species blind test performance, with an average improvement of 5.63%/5.72%, 22.28%/25.94%, 20.11%/17.49%, and 26.40%/28.33% for Mus musculus/Rattus norvegicus test sets in area under curves (AUCs) of ROC curve, AUC of the PR curve, F1-score, and MCC metrics, respectively. Furthermore, it also shows excellent performance in the latest updated case of natural proteins with functional phosphorylation sites. Through an ablation study and visual analysis, we uncover that the design of different feature modules significantly contributes to the accurate classification of DeepMPSF, which provides valuable insights for predicting phosphorylation sites and offers effective support for future downstream research.
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Affiliation(s)
- Jingxin Xie
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Lijun Quan
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
- Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
| | - Xuejiao Wang
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Hongjie Wu
- Suzhou University of Science and Technology, Suzhou 215006, China
| | - Zhi Jin
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Deng Pan
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Taoning Chen
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Tingfang Wu
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
- Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
| | - Qiang Lyu
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
- Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
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Kinjo T, Ebisawa S, Nokubo T, Hashimoto M, Yamada T, Oshio M, Nakamura R, Uno K, Kuramoto N. Post-translational modifications of the apelin receptor regulate its functional expression. AIMS Neurosci 2023; 10:282-299. [PMID: 38188005 PMCID: PMC10767067 DOI: 10.3934/neuroscience.2023022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 01/09/2024] Open
Abstract
Post-translational modifications (PTMs) are protein modifications that occur after protein biosynthesis, playing a crucial role in regulating protein function. They are involved in the functional expression of G-protein-coupled receptors (GPCRs), as well as intracellular and secretory protein signaling. Here, we aimed to investigate the PTMs of the apelin receptor (APLNR), a GPCR and their potential influence on the receptor's function. In an in vitro experiment using HEK cells, we only observed glycosylation as a PTM of the APLNR and ineffective receptor signaling by the agonist, (Pyr1)-apelin-13. In contrast, when analyzing mouse spinal cord, we detected glycosylation and other PTMs, excluding isopeptidation. This suggests that additional PTMs are involved in the functional expression of the APLNR in vitro. In summary, these findings suggest that the APLNR in vivo requires multiple PTMs for functional expression. To comprehensively understand the pharmacological effects of the APLNR, it is essential to establish an in vitro system that adequately replicates the receptor's PTM profile. Nonetheless, it is crucial to overcome the challenge of heat-sensitive proteolysis in APLNR studies. By elucidating the regulation of PTMs, further research has the potential to advance the analysis and pharmacological studies of both the apelin/APLNR system and GPCR signal modulation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nobuyuki Kuramoto
- Laboratory of Molecular Pharmacology, Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka 573-0101, Japan
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Zhang B, Cai T, He H, Huang X, Chen G, Lai Y, Luo Y, Huang S, Luo J, Guo X. TRIM21 Promotes Rabies Virus Production by Degrading IRF7 through Ubiquitination. Int J Mol Sci 2023; 24:10892. [PMID: 37446070 PMCID: PMC10341556 DOI: 10.3390/ijms241310892] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Rabies, a highly fatal zoonotic disease, is a significant global public health threat. Currently, the pathogenic mechanism of rabies has not been fully elucidated, and no effective treatment for rabies is available. Increasing evidence shows that the tripartite-motif protein (TRIM) family of proteins participates in the host's regulation of viral replication. Studies have demonstrated the upregulated expression of tripartite-motif protein 21 (TRIM21) in the brain tissue of mice infected with the rabies virus. Related studies have shown that TRIM21 knockdown inhibits RABV replication, while overexpression of TRIM21 exerted the opposite effect. Knockdown of interferon-alpha and interferon-beta modulates the inhibition of RABV replication caused by TRIM21 knockdown and promotes the replication of the virus. Furthermore, our previous study revealed that TRIM21 regulates the secretion of type I interferon during RABV infection by targeting interferon regulatory factor 7 (IRF7). IRF7 knockdown reduced the inhibition of RABV replication caused by the knockdown of TRIM21 and promoted viral replication. TRIM21 regulates RABV replication via the IRF7-IFN axis. Our study identified TRIM21 as a novel host factor required by RABV for replication. Thus, TRIM21 is a potential target for rabies treatment or management.
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Affiliation(s)
- Boyue Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Ting Cai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Hongling He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Xuezhe Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Guie Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Yanqin Lai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Yongwen Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Shile Huang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130-3932, USA;
- Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA 71130-3932, USA
| | - Jun Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Xiaofeng Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
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Imidazole-amino acids. Conformational switch under tautomer and pH change. Amino Acids 2023; 55:33-49. [PMID: 36319875 PMCID: PMC9877100 DOI: 10.1007/s00726-022-03201-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/16/2022] [Indexed: 01/26/2023]
Abstract
Replacement of the main chain peptide bond by imidazole ring seems to be a promising tool for the peptide-based drug design, due to the specific prototropic tautomeric as well as amphoteric properties. In this study, we present that both tautomer and pH change can cause a conformational switch of the studied residues of alanine (1-4) and dehydroalanine (5-8) with the C-terminal peptide group replaced by imidazole. The DFT methods are applied and an environment of increasing polarity is simulated. The conformational maps (Ramachandram diagrams) are presented and the stability of possible conformations is discussed. The neutral forms, tautomers τ (1) and π (2), adapt the conformations αRτ (φ, ψ = - 75°, - 114°) and C7eq (φ, ψ = - 75°, 66°), respectively. Their torsion angles ψ differ by about 180°, which results in a considerable impact on the peptide chain conformation. The cation form (3) adapts both these conformations, whereas the anion analogue (4) prefers the conformations C5 (φ, ψ = - 165°, - 178°) and β2 (φ, ψ ~ - 165°, - 3°). Dehydroamino acid analogues, the tautomers τ (5) and π (6) as well as the anion form (8), have a strong tendency toward the conformations β2 (φ, ψ = - 179°, 0°) and C5 (φ, ψ = - 180°, 180°). The preferences of the protonated imidazolium form (7) depend on the environment. The imidazole ring, acting as a donor or acceptor of the hydrogen bonds created within the studied residues, has a profound effect on the type of conformation.
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Implications of Post-Translational Modifications in Autoimmunity with Emphasis on Citrullination, Homocitrullination and Acetylation for the Pathogenesis, Diagnosis and Prognosis of Rheumatoid Arthritis. Int J Mol Sci 2022; 23:ijms232415803. [PMID: 36555449 PMCID: PMC9781636 DOI: 10.3390/ijms232415803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 12/15/2022] Open
Abstract
Post-translational modifications (PTMs) influence cellular processes and consequently, their dysregulation is related to the etiologies of numerous diseases. It is widely known that a variety of autoimmune responses in human diseases depend on PTMs of self-proteins. In this review we summarize the latest findings about the role of PTMs in the generation of autoimmunity and, specifically, we address the most relevant PTMs in rheumatic diseases that occur in synovial tissue. Citrullination, homocitrullination (carbamylation) and acetylation are responsible for the generation of Anti-Modified Protein/Peptide Antibodies (AMPAs family), autoantibodies which have been implicated in the etiopathogenesis, diagnosis and prognosis of rheumatoid arthritis (RA). Synthetic peptides provide complete control over the exact epitopes presented as well as the specific positions in their sequence where post-translationally modified amino acids are located and are key to advancing the detection of serological RA biomarkers that could be useful to stratify RA patients in order to pursue a personalized rheumatology. In this review we specifically address the latest findings regarding synthetic peptides post-translationally modified for the specific detection of autoantibodies in RA patients.
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Inhibition mechanism of baicalein against alcohol dehydrogenase in vitro via biological techniques, spectroscopy and computer simulation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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