GPSD: a hybrid learning framework for the prediction of phosphatase-specific dephosphorylation sites.

Authors: Han, Cheng¹ (AUTHOR), Fu, Shanshan¹ (AUTHOR), Chen, Miaomiao¹ (AUTHOR), Gou, Yujie¹ (AUTHOR), Liu, Dan¹ (AUTHOR), Zhang, Chi¹ (AUTHOR), Huang, Xinhe¹ (AUTHOR), Xiao, Leming¹ (AUTHOR), Zhao, Miaoying¹ (AUTHOR), Zhang, Jiayi¹ (AUTHOR), Xiao, Qiang² (AUTHOR), Peng, Di¹ (AUTHOR), Xue, Yu¹ (AUTHOR)

Source: Briefings in Bioinformatics. Jan2025, Vol. 26 Issue 1, p1-13. 13p.

Subject Terms: *Artificial neural networks, Post-translational modification, Phosphoprotein phosphatases, Protein kinases, Blended learning

Bradykinin's carbamylation as a mechanistic link to impaired wound healing in patients with kidney dysfunction.

Authors: Kaminska, Marta^1,2 (AUTHOR) marta.kaminska@uib.no, Kałucka, Urszula^1,2 (AUTHOR) urszulakalucka@outlook.com, Babickova, Janka² (AUTHOR) janka.babickova@uib.no, Benedyk-Machaczka, Małgorzata¹ (AUTHOR) malgorzata.benedyk@uj.edu.pl, Skandalou, Eleni³ (AUTHOR) eleni.skandalou@uib.no, Grant, Melissa M.⁴ (AUTHOR) m.m.grant@bham.ac.uk, Marti, Hans-Peter^3,5 (AUTHOR) hans-peter.marti@uib.no, Mydel, Piotr^1,2 (AUTHOR) piotr.mydel@uib.no

Source: BMC Biology. 3/12/2025, Vol. 23 Issue 1, p1-13. 13p.

Subject Terms: *POST-translational modification, *LIFE sciences, *PEPTIDES, *CYTOLOGY, *BRADYKININ, *WOUND healing

Noncoding RNA-encoded peptides in cancer: biological functions, posttranslational modifications and therapeutic potential.

Authors: Tan, Shiming¹ (AUTHOR), Yang, Wenjuan¹ (AUTHOR), Ren, Zongyao^1,2 (AUTHOR), Peng, Qiu^1,2 (AUTHOR), Xu, Xuemeng^1,2 (AUTHOR), Jiang, Xianjie^1,2 (AUTHOR), Wu, Zhu^1,2 (AUTHOR), Oyang, Linda^1,2 (AUTHOR), Luo, Xia^1,2 (AUTHOR), Lin, Jinguan^1,2 (AUTHOR), Xia, Longzheng^1,2 (AUTHOR), Peng, Mingjing^1,2 (AUTHOR), Wu, Nayiyuan^1,2 (AUTHOR), Tang, Yanyan^1,2 (AUTHOR), Han, Yaqian^1,2 (AUTHOR) hanyaqian@hnca.org.cn, Liao, Qianjin³ (AUTHOR) march-on@126.com, Zhou, Yujuan^1,2 (AUTHOR) yujany_zhou@163.com

Source: Journal of Hematology & Oncology. 2/19/2025, Vol. 18 Issue 1, p1-29. 29p.

Subject Terms: *POST-translational modification, *NON-coding RNA, *CANCER invasiveness, *PEPTIDES, *MEDICAL sciences

zDHHC-Mediated S-Palmitoylation in Skin Health and Its Targeting as a Treatment Perspective.

Authors: Abdulrahman, Farah A.¹ (AUTHOR), Benford, King A.¹ (AUTHOR), Lin, Gregory T.¹ (AUTHOR), Maroun, Andrew J.¹ (AUTHOR), Sammons, Caleb¹ (AUTHOR), Shirzad, Darya N.¹ (AUTHOR), Tsai, Harrison¹ (AUTHOR), Van Brunt, Vincent L.¹ (AUTHOR), Jones, Zack¹ (AUTHOR), Marquez, Jafet E.¹ (AUTHOR), Ratkus, Evan C.¹ (AUTHOR), Shehadeh, Abdulrahman K.¹ (AUTHOR), Abasto Valle, Hugo¹ (AUTHOR), Fejzo, Dea¹ (AUTHOR), Gilbert, Ashlynn E.¹ (AUTHOR), McWee, Catherine A.¹ (AUTHOR), Underwood, Lexie F.¹ (AUTHOR), Indico, Ethny¹ (AUTHOR), Rork, Brittany B.¹ (AUTHOR), Nanjundan, Meera¹ (AUTHOR) mnanjund@usf.edu

Source: International Journal of Molecular Sciences. Feb2025, Vol. 26 Issue 4, p1673. 39p.

Subject Terms: *POST-translational modification, *SMALL molecules, *ATOPIC dermatitis, *SKIN cancer, *ACYLTRANSFERASES

NEMO Family of Proteins as Polyubiquitin Receptors: Illustrating Non-Degradative Polyubiquitination's Roles in Health and Disease.

Authors: Wu, Chuan-Jin¹ (AUTHOR) wuchu@mail.nih.gov

Source: Cells (2073-4409). Feb2025, Vol. 14 Issue 4, p304. 25p.

Subject Terms: *POST-translational modification, *DNA repair, *MICROBIAL virulence, *UBIQUITIN, *PROTEIN receptors, *PROTEIN-protein interactions

Development of a reliable, sensitive, and convenient assay for the discovery of new eIF5A hypusination inhibitors.

Authors: Benaceur, Oumayma¹ (AUTHOR), Ferreira Montenegro, Paula² (AUTHOR), Kahi, Michel¹ (AUTHOR), Fontaine-Vive, Fabien² (AUTHOR), Mazure, Nathalie M.¹ (AUTHOR), Mehiri, Mohamed² (AUTHOR), Bost, Frederic¹ (AUTHOR), Peraldi, Pascal¹ (AUTHOR) pascal.peraldi@univ-cotedazur.fr

Source: PLoS ONE. 2/12/2025, Vol. 20 Issue 2, p1-19. 19p.

Subject Terms: *POST-translational modification, *CHEMICAL libraries, *RESEARCH personnel, *PROOF of concept, *SPERMIDINE

Exploration of phosphoproteomic association during epimorphic regeneration.

Authors: Banu, Sarena¹ (AUTHOR), Anusha, P V¹ (AUTHOR), Mandal, Komal¹ (AUTHOR), Idris, Mohammed M¹ (AUTHOR) idris@ccmb.res.in

Source: Scientific Reports. 2/10/2025, Vol. 15 Issue 1, p1-14. 14p.

Subject Terms: *CYTOLOGY, *POST-translational modification, *LIFE sciences, *BIOCHEMISTRY, *REGENERATION (Biology), *PROTEOMICS

"Lost in translation?" Animal research in the era of precision medicine.

Authors: Frühwein, Hamideh¹ (AUTHOR) h.mahdiani@uni-mainz.de, Paul, Norbert W.¹ (AUTHOR)

Source: Journal of Translational Medicine. 2/4/2025, Vol. 23 Issue 1, p1-12. 12p.

Subject Terms: *TRANSLATIONAL research, *INDIVIDUALIZED medicine, *ANIMAL experimentation, *LABORATORY animals, *EVIDENCE-based medicine

Targeting the PARylation-Dependent Ubiquitination Signaling Pathway for Cancer Therapies.

Authors: Huang, Daoyuan¹ (AUTHOR), Wang, Jingchao¹ (AUTHOR), Chen, Li¹ (AUTHOR), Jiang, Weiwei¹ (AUTHOR), Inuzuka, Hiroyuki¹ (AUTHOR), Simon, David K.² (AUTHOR) dsimon1@bidmc.harvard.edu, Wei, Wenyi¹ (AUTHOR) wwei2@bidmc.harvard.edu

Source: Biomolecules (2218-273X). Feb2025, Vol. 15 Issue 2, p237. 16p.

Subject Terms: *POST-translational modification, *METABOLIC regulation, *UBIQUITIN ligases, *BIOCHEMICAL substrates, *IMMUNE checkpoint proteins, *DNA repair

A Modular Customizable Ligand-Conjugate (LC) System Targeting Ghrelin O -Acyltransferase.

Authors: Ford, Amber L.¹ (AUTHOR) alford@syr.edu, Taft, Caine W.¹ (AUTHOR) cwtaft@syr.edu, Sprague-Getsy, Andrea M.¹ (AUTHOR) anspragu@syr.edu, Carlson, Gracie C.¹ (AUTHOR) gcc44@case.edu, Mate, Nilamber A.¹ (AUTHOR) namate@syr.edu, Sieburg, Michelle A.¹ (AUTHOR) msieburg@syr.edu, Chisholm, John D.^1,2 (AUTHOR) jdchisho@syr.edu, Hougland, James L.^1,2,3 (AUTHOR) hougland@syr.edu

Source: Biomolecules (2218-273X). Feb2025, Vol. 15 Issue 2, p204. 17p.

Subject Terms: *POST-translational modification, *PEPTIDE hormones, *ENDOCRINE cells, *PEPTIDES, *HORMONE regulation, *GHRELIN receptors

GraphPhos: Predict Protein-Phosphorylation Sites Based on Graph Neural Networks.

Authors: Wang, Zeyu¹ (AUTHOR) wangzeyu21@mails.jlu.edu.cn, Yang, Xiaoli¹ (AUTHOR) xiaoliy22@mails.jlu.edu.cn, Gao, Songye¹ (AUTHOR) sygao23@mails.jlu.edu.cn, Liang, Yanchun^1,2 (AUTHOR) ycliang@jlu.edu.cn, Shi, Xiaohu¹ (AUTHOR) shixh@jlu.edu.cn

Source: International Journal of Molecular Sciences. Feb2025, Vol. 26 Issue 3, p941. 18p.

Subject Terms: *GRAPH neural networks, *POST-translational modification, *LANGUAGE models, *AMINO acid sequence, *TERTIARY structure

Key Role of Phosphorylation in Small Heat Shock Protein Regulation via Oligomeric Disaggregation and Functional Activation.

Authors: Sluzala, Zachary B.¹ (AUTHOR) zsluzala@umich.edu, Hamati, Angelina¹ (AUTHOR) hamatia@umich.edu, Fort, Patrice E.^1,2 (AUTHOR) patricef@med.umich.edu

Source: Cells (2073-4409). Jan2025, Vol. 14 Issue 2, p127. 17p.

Subject Terms: *POST-translational modification, *CELL physiology, *PHOSPHORYLATION, *DEAMINATION, *OLIGOMERS, *HEAT shock proteins

Ubiquitination Enzymes in Cancer, Cancer Immune Evasion, and Potential Therapeutic Opportunities.

Authors: Awan, Aiman B.¹ (AUTHOR) aibu38539@hbku.edu.qa, Osman, Maryiam Jama Ali^1,2 (AUTHOR) maos34113@hbku.edu.qa, Khan, Omar M.¹ (AUTHOR) okhan@hbku.edu.qa

Source: Cells (2073-4409). Jan2025, Vol. 14 Issue 2, p69. 35p.

Subject Terms: *POST-translational modification, *CYTOLOGY, *CELL cycle, *UBIQUITINATION, *METASTASIS

Unveiling the Mechanisms of a Remission in Major Depressive Disorder (MDD)-like Syndrome: The Role of Hippocampal Palmitoyltransferase Expression and Stress Susceptibility.

Authors: Schroeter, Careen A.¹ (AUTHOR) careen.schroeter@web.de, Gorlova, Anna^2,3 (AUTHOR) anna.gorlova204@gmail.com, Sicker, Michael¹ (AUTHOR), Umriukhin, Aleksei⁴ (AUTHOR) bshulgin83@gmail.com, Burova, Alisa² (AUTHOR) aliceinmsk@gmail.com, Shulgin, Boris^4,5 (AUTHOR), Morozov, Sergey² (AUTHOR), Costa-Nunes, Joao P.⁶ (AUTHOR) jpcosta.nunes@gmail.com, Strekalova, Tatyana^3,7 (AUTHOR) careen.schroeter@web.de

Source: Biomolecules (2218-273X). Jan2025, Vol. 15 Issue 1, p67. 23p.

Subject Terms: *POST-translational modification, *MENTAL depression, *SOCIAL defeat, *GENE expression, *LIPID rafts

Mapping O- and N-Glycosylation in Transmembrane and Interface Regions of Proteins: Insights from a Database Search Study.

Authors: Anghelescu, Giorgiana Diana Carmen¹ (AUTHOR) g.anghelescu20@s.bio.unibuc.ro, Mernea, Maria² (AUTHOR) dan.mihailescu@bio.unibuc.ro, Mihăilescu, Dan Florin² (AUTHOR)

Source: International Journal of Molecular Sciences. Jan2025, Vol. 26 Issue 1, p327. 18p.

Subject Terms: *MEMBRANE proteins, *POST-translational modification, *PROTEIN folding, *DATABASE searching, *GLYCOSYLATION

S6K2 in Focus: Signaling Pathways, Post-Translational Modifications, and Computational Analysis.

Authors: Khalil, Mahmoud I.^1,2 (AUTHOR) m.khalil@bau.edu.lb, Helal, Mohamed^3,4 (AUTHOR) mhelal@biology.sdu.dk, El-Sayed, Ahmed F.^5,6 (AUTHOR) ahmedfikry.nrc@gmail.com, El Hajj, Rana¹ (AUTHOR), Holail, Jasmine^7,8 (AUTHOR) rb22182@bristol.ac.uk, Houssein, Marwa⁹ (AUTHOR) housseinmarwa@gmail.com, Waraky, Ahmed^10,11,12 (AUTHOR) ahmed.waraky@gu.se, Pardo, Olivier E.¹³ (AUTHOR) m.khalil@bau.edu.lb

Source: International Journal of Molecular Sciences. Jan2025, Vol. 26 Issue 1, p176. 31p.

Subject Terms: *POST-translational modification, *POLLUTANTS, *MOLECULAR docking, *BINDING sites, *MOLECULAR dynamics

The Role of Vimentin Peptide Citrullination in the Structure and Dynamics of HLA-DRB1 Rheumatoid Arthritis Risk-Associated Alleles.

Authors: Alves, Cinthia C.¹ (AUTHOR) cinthiacalves@alumni.usp.br, Lewis, Jaila² (AUTHOR), Antunes, Dinler A.² (AUTHOR) dinler@uh.edu, Donadi, Eduardo A.¹ (AUTHOR)

Source: International Journal of Molecular Sciences. Jan2025, Vol. 26 Issue 1, p34. 17p.

Subject Terms: *PEPTIDES, *POST-translational modification, *BANKING industry, *CHEMICAL bonds, *HYDROGEN bonding

Novel post-translational modifications in cancer.

Authors: Li, Dongling¹ (AUTHOR), Cai, Qinrui¹ (AUTHOR), Li, Li^1,2 (AUTHOR), Chen, Yao^1,2 (AUTHOR), Lin, Ling¹ (AUTHOR), Zhou, Xiaoya^1,2 (AUTHOR), Lin, Jianshan^1,2 (AUTHOR), Yang, Fan^1,2 (AUTHOR) yangfanbio@cqu.edu.cn

Source: Oncologie (De Gruyter). Jan2025, Vol. 27 Issue 1, p3-14. 12p.

Subject Terms: *POST-translational modification, *TUMOR proteins, *CANCER invasiveness, *CARCINOGENESIS, *CELLULAR signal transduction

Influence of Site Effects on Scaling Relation Between Rotational and Translational Signals Produced by Anthropogenic Seismicity.

Authors: Nawrocki, Dariusz¹, dariusz.nawrocki@us.edu.pl, Mendecki, Maciej J.¹, maciej.mendecki@us.edu.pl, Mutke, Grzegorz², g.mutke@gig.eu, Teper, Lesław¹, leslaw.teper@us.edu.pl

Source: Applied Sciences (2076-3417); Jan2025, Vol. 15 Issue 1, p102, 19p

Current computational tools for protein lysine acylation site prediction.

Authors: Qin, Zhaohui¹ (AUTHOR), Ren, Haoran¹ (AUTHOR), Zhao, Pei² (AUTHOR), Wang, Kaiyuan¹ (AUTHOR), Liu, Huixia¹ (AUTHOR), Miao, Chunbo¹ (AUTHOR), Du, Yanxiu¹ (AUTHOR), Li, Junzhou¹ (AUTHOR) chenzhen-win2009@163.com, Wu, Liuji³ (AUTHOR) chenzhen-win2009@163.com, Chen, Zhen¹ (AUTHOR) chenzhen-win2009@163.com

Source: Briefings in Bioinformatics. Nov2024, Vol. 25 Issue 6, p1-17. 17p.

Subject Terms: Language transfer (Language learning), Post-translational modification, Protein models, Deep learning, Classification algorithms