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Journal articles on the topic 'SUMO SITES PREDICTION'

Author: Grafiati

Published: 11 September 2023

Last updated: 31 July 2025

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1

Sharma, Dolly, Anu Kumari, Manisha Kumari, and Ramesh C. Meena. "SUMO Sites Prediction in Human Transcription Factors Involved in Hypoxia induced Cardiac Illnesses." Defence Life Science Journal 9, no. 1 (2024): 44–54. http://dx.doi.org/10.14429/dlsj.9.19455.

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Protein SUMOylation is a reversible and well knownpost-translational modificationprocess of the cells. It may change a protein's cellular location, interactions, and possible structural shape before it develops to carry out its basic functions.Also, it decides the binding of transcription factors and DNA binding proteins tochromatin in addition to various cis and trans regulatory factors. Alterations in protein SUMOylation have been linked with a variety of disorders and developmental anomalies.Tentative approaches to identify SUMO binding sites are challenging due todynamic nature of the SUMO

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2

Zhao, Qi, Yubin Xie, Yueyuan Zheng, et al. "GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs." Nucleic Acids Research 42, W1 (2014): W325—W330. http://dx.doi.org/10.1093/nar/gku383.

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3

Ijaz, Amna. "SUMOhunt: Combining Spatial Staging between Lysine and SUMO with Random Forests to Predict SUMOylation." ISRN Bioinformatics 2013 (June 17, 2013): 1–11. http://dx.doi.org/10.1155/2013/671269.

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Modification with SUMO protein has many key roles in eukaryotic systems which renders the identification of its target proteins and sites of considerable importance. Information regarding the SUMOylation of a protein may tell us about its subcellular localization, function, and spatial orientation. This modification occurs at particular and not all lysine residues in a given protein. In competition with biochemical means of modified-site recognition, computational methods are strong contenders in the prediction of SUMOylation-undergoing sites on proteins. In this research, physicochemical prop

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4

Khan, Salman, Mukhtaj Khan, Nadeem Iqbal, Naqqash Dilshad, Maram Fahaad Almufareh, and Najah Alsubaie. "Enhancing Sumoylation Site Prediction: A Deep Neural Network with Discriminative Features." Life 13, no. 11 (2023): 2153. http://dx.doi.org/10.3390/life13112153.

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Sumoylation is a post-translation modification (PTM) mechanism that involves many critical biological processes, such as gene expression, localizing and stabilizing proteins, and replicating the genome. Moreover, sumoylation sites are associated with different diseases, including Parkinson’s and Alzheimer’s. Due to its vital role in the biological process, identifying sumoylation sites in proteins is significant for monitoring protein functions and discovering multiple diseases. Therefore, in the literature, several computational models utilizing conventional ML methods have been introduced to

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5

Lee, Choong-Eun, Tam Tran, Seol-Hee Kim, Ki-Sa Sung, and Cheol-Yong Choi. "Regulation of IL-4-induced STAT6 activation by SUMOylation (P6307)." Journal of Immunology 190, no. 1_Supplement (2013): 184.15. http://dx.doi.org/10.4049/jimmunol.190.supp.184.15.

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Abstract As a key signaling molecule in the cytokine-mediated transcriptional activation STATs are shown to undergo PTMs including phosphorylation, acetylation, methylation, ubiquitination and SUMOylation. The SUMO-modification of STAT1 has been implicated in the regulation of protein stability, nuclear translocation, and transcriptional activation, probably through the reduction of the formation and life-span of the active dimer. As a part of regulation of IL-4 signaling mechanism, we have investigated the role of SUMOylation on STAT6 activation. We have identified potential SUMOylation sites

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6

Yu, Jian, Jianping Lan, Yuanyuan Zhu, Xiaoyu Lai, and He Huang. "Sumoylation of TRF1 Is Essential for Its Recruitment to ALT-Associated PML Bodies." Blood 110, no. 11 (2007): 4169. http://dx.doi.org/10.1182/blood.v110.11.4169.4169.

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Abstract To achieve unlimited proliferative potential, most cancer cells activate telomerase to maintain telomeres. However, some cancer cells elongate telomeres through a telomerase-independent pathway termed alternative lengthening of telomeres (ALT). These ALT cells contain a novel promyelocytic leukemia (PML) body (ALT-associated PML body, APB), which comprises telomeric DNA and a number of proteins, including PML protein, the telomere binding proteins TRF1 and TRF2, replication factor A, and recombination factors Rad51, Rad52, and the Rad50/Mre11/NBS1 complex. TRF1, as the first identifie

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7

Qian, Ying, Shasha Ye, Yu Zhang, and Jiongmin Zhang. "SUMO-Forest: A Cascade Forest based method for the prediction of SUMOylation sites on imbalanced data." Gene 741 (May 2020): 144536. http://dx.doi.org/10.1016/j.gene.2020.144536.

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8

Liu, Yan, Zhenhua Zheng, Bo Shu, et al. "SUMO Modification Stabilizes Enterovirus 71 Polymerase 3D To Facilitate Viral Replication." Journal of Virology 90, no. 23 (2016): 10472–85. http://dx.doi.org/10.1128/jvi.01756-16.

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ABSTRACT Accumulating evidence suggests that viruses hijack cellular proteins to circumvent the host immune system. Ubiquitination and SUMOylation are extensively studied posttranslational modifications (PTMs) that play critical roles in diverse biological processes. Cross talk between ubiquitination and SUMOylation of both host and viral proteins has been reported to result in distinct functional consequences. Enterovirus 71 (EV71), an RNA virus belonging to the family Picornaviridae , is a common cause of hand, foot, and mouth disease. Little is known concerning how host PTM systems interact

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9

Fang, Zhou, Yun Deng, Haihong Wang, and Jun Zhou. "SUMOylation of zebrafish transcription factor Zbtb21 affects its transcription activity." PeerJ 12 (April 22, 2024): e17234. http://dx.doi.org/10.7717/peerj.17234.

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Background Post-translational modification by Small Ubiquitin-like MOdifier (SUMO) is an important mechanism to regulate protein activity, protein stability, and localization of substrates. Zbtb21 is a zinc finger and BTB (Broad-complex, Tram-track and Bric à brac) domain-containing transcription factor. Bioinformatic prediction suggests several putative SUMOylated sites in Zbtb21 protein. Methods Two evolutionarily conserved lysine residues in Zbtb21 protein were mutated alone or in combination to disrupt the binding with SUMO molecules. Western blot and co-immunoprecipitation analyses were p

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10

Liu, Boshu, Sujun Li, Yinglin Wang, Lin Lu, Yixue Li, and Yudong Cai. "Predicting the protein SUMO modification sites based on Properties Sequential Forward Selection (PSFS)." Biochemical and Biophysical Research Communications 358, no. 1 (2007): 136–39. http://dx.doi.org/10.1016/j.bbrc.2007.04.097.

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11

Ho, Nhat‐Minh, and Jeung‐Hwan Doh. "Prediction of ultimate strength of concrete walls restrained on three sides." Structural Concrete 20, no. 3 (2019): 942–54. http://dx.doi.org/10.1002/suco.201800188.

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12

Tran, Thi-Xuan, Thi-Thu-Huong Tran, Nguyen Quoc Khanh Le, and Van Nui Nguyen. "CLW_SUMO: A hybrid deep learning model for predicting protein SUMOylation sites." Journal of Computer Science and Cybernetics 40, no. 4 (2024): 315–25. https://doi.org/10.15625/1813-9663/19626.

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Protein SUMOylation is one of the most important post-translational modifications in Eukaryotes species and plays significant roles in many biological processes. The mechanism underlined the SUMOylation process will be an important cause leading to many common serious diseases, such as breast cancer, cardiac, Parkinson’s, Alzheimer’s disease, etc. Due to the very important roles regulated by SUMOylation, the demand for an in-depth understanding of SUMOylation and its mechanism is currently a hot topic that interests many scientists. In this study, we propose a novel approach, called CLW-SUMO,

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13

Kawai, Toru, Mohammad Kholid Ridwan, and Manabu Kanda. "Evaluation of the Simple Urban Energy Balance Model Using Selected Data from 1-yr Flux Observations at Two Cities." Journal of Applied Meteorology and Climatology 48, no. 4 (2009): 693–715. http://dx.doi.org/10.1175/2008jamc1891.1.

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Abstract The authors’ objective was to apply the Simple Urban Energy Balance Model for Mesoscale Simulation (SUMM) to cities. Data were selected from 1-yr flux observations conducted at three sites in two cities: one site in Kugahara, Japan (Ku), and two sites in Basel, Switzerland (U1 and U2). A simple vegetation scheme was implemented in SUMM to apply the model to vegetated cities, and the surface energy balance and radiative temperature TR were evaluated. SUMM generally reproduced seasonal and diurnal trends of surface energy balance and TR at Ku and U2, whereas relatively large errors were

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14

Hipólito-Romero, Enrique, Eliezer Cocoletzi-Vásquez, José M. Ramos-Prado, Cesar Espinoza, Magdiel Torres-de la Cruz, and Jorge Ricaño-Rodríguez. "Breve aproximación a la naturaleza genómica de Moniliophthora roreri CPMRT01 aislado de cacao en Tabasco, México//Brief approach to the genomic nature of Moniliophthora roreri CPMRT01 isolated from cocoa in Tabasco, Mexico." Biotecnia 22, no. 2 (2020): 39–49. http://dx.doi.org/10.18633/biotecnia.v22i2.1244.

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Moniliophthora roreri es un hongo de suma importancia agroeconómica principalmente en el continente americano, ya que es el agente causal de la moniliasis de al menos cuatro especies de cacao. El genoma de este hongo consta de aproximadamente 52,3 Mpb, cuyos genes de interés se reagrupan dependiendo de su naturaleza (e.g. hemibiotróficos, biotróficos y fitopatogénicos). Por otro lado, Moniliophthora es capaz de metabolizar proteínas involucradas en procesos de infección, regulación metabólica y mecanismos de defensa. El objetivo principal de este trabajo fue caracterizar un fragmento del genom

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15

Gou, Yujie, Dan Liu, Miaomiao Chen, et al. "GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs." Nucleic Acids Research, May 6, 2024. http://dx.doi.org/10.1093/nar/gkae346.

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Abstract Small ubiquitin-like modifiers (SUMOs) are tiny but important protein regulators involved in orchestrating a broad spectrum of biological processes, either by covalently modifying protein substrates or by noncovalently interacting with other proteins. Here, we report an updated server, GPS-SUMO 2.0, for the prediction of SUMOylation sites and SUMO-interacting motifs (SIMs). For predictor training, we adopted three machine learning algorithms, penalized logistic regression (PLR), a deep neural network (DNN), and a transformer, and used 52 404 nonredundant SUMOylation sites in 8262 prot

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16

Zhao, Yi-Wei, Shihua Zhang, and Hui Ding. "Recent development of machine learning methods in sumoylation sites prediction." Current Medicinal Chemistry 28 (September 15, 2021). http://dx.doi.org/10.2174/0929867328666210915112030.

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: Sumoylation of proteins is an important reversible post-translational modification of proteins and mediates a variety of cellular processes. Sumo-modified proteins can change their subcellular localization, activity and stability. In addition, it also plays an important role in various cellular processes such as transcriptional regulation and signal transduction. The abnormal sumoylation is involved in many diseases, including neurodegeneration and immune-related diseases, as well as the development of cancer. Therefore, identification of the sumoylation site (SUMO site) is fundamental to un

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17

Khan, Salman, Salman A. AlQahtani, Sumaiya Noor, and Nijad Ahmad. "PSSM-Sumo: deep learning based intelligent model for prediction of sumoylation sites using discriminative features." BMC Bioinformatics 25, no. 1 (2024). http://dx.doi.org/10.1186/s12859-024-05917-0.

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18

Han, Yegi. "The localization to PML nuclear bodies and stability of TRAIP/RNF206 are controlled by SUMOylation." FASEB Journal 31, S1 (2017). http://dx.doi.org/10.1096/fasebj.31.1_supplement.602.1.

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TRAIP (TNF Receptor Associated factor Interacting Protein), also known as RNF206 (RING Finger protein 206), is an E3‐ubiquitin‐ligase protein participated in DNA damage signaling, DNA repair pathway and cell cycle progression. Post‐translational modifications of protein are important for stability control, subcellular localization and protein‐protein interaction. SUMO (Small‐ubiquitin‐like modifier) is one of the post‐translational protein modifiers and SUMOylation regulates diverse cellular processes including protein stability control, nuclear‐cytosolic transport transcriptional regulation,

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19

Palacios, Andrew Vargas, Pujan Acharya, Anthony Stephen Peidl, et al. "SumoPred-PLM: human SUMOylation and SUMO2/3 sites Prediction using Pre-trained Protein Language Model." NAR Genomics and Bioinformatics 6, no. 1 (2024). http://dx.doi.org/10.1093/nargab/lqae011.

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Abstract SUMOylation is an essential post-translational modification system with the ability to regulate nearly all aspects of cellular physiology. Three major paralogues SUMO1, SUMO2 and SUMO3 form a covalent bond between the small ubiquitin-like modifier with lysine residues at consensus sites in protein substrates. Biochemical studies continue to identify unique biological functions for protein targets conjugated to SUMO1 versus the highly homologous SUMO2 and SUMO3 paralogues. Yet, the field has failed to harness contemporary AI approaches including pre-trained protein language models to f

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20

Ho, Cheng-Hsun, Yen-Wei Chu, Lan-Ying Huang, and Chi-Wei Chen. "SUMO-LMNet: Lossless Mapping Network for Predicting SUMOylation Sites in SUMO1 and SUMO2 using High-Dimensional Features." Computational and Structural Biotechnology Journal, March 2025. https://doi.org/10.1016/j.csbj.2025.03.005.

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21

Metzger, Konrad, Frank Liebisch, Herrera Juan M., Thomas Guillaume, Florian Walder, and Luca Bragazza. "The use of visible and near- infrared spectroscopy for in- situ characterization of agricultural soil fertility: A proposition of best practice by comparing scanning positions and spectrometers." July 26, 2023. https://doi.org/10.1111/sum.12952.

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The application of visible and near-infrared (vis–NIR) spectroscopy to characterize soil samples has gained growing interest as a fast and cost-effective methodology for soil fertility assessment. In order to profit from the full potential of vis–NIR spectroscopy, the acquisition of soil spectra directly in-situ would increase the possibility to obtain data rapidly and at a high spatial and temporal resolution. In the present study, we test and propose the best practice to characterize a set of fertility-related parameters (i.e. texture, organic carbon, pH, cation exchange capacity

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22

Floris, Andrea, Swati Chandla, Youngyi Lim, et al. "Sumoylation of methionine adenosyltransferase alpha 1 promotes mitochondrial dysfunction in alcohol-associated liver disease." Hepatology, December 15, 2023. http://dx.doi.org/10.1097/hep.0000000000000717.

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Background & Aims: Methionine adenosyltransferase alpha1 (MATα1) is responsible for the biosynthesis of S-adenosylmethionine (SAMe) in normal liver. Alcohol consumption enhances MATα1 interaction with peptidylprolyl cis-trans isomerase NIMA-interacting 1 (PIN1), which blocks MATα1 mitochondrial targeting, resulting in lower mitochondrial MATα1 content and mitochondrial dysfunction in alcohol-associated liver disease (ALD) in part through up-regulation of cytochrome P450 2E1 (CYP2E1). Conversely, alcohol intake enhances SUMOylation, which enhances CYP2E1 expression. MATα1 has potential SUMO

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