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Basciu A, Athar M, Kurt H, Neville C, Malloci G, Muredda FC, Bosin A, Ruggerone P, Bonvin AMJJ, Vargiu AV. Predicting binding events in very flexible, allosteric, multi-domain proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597018. [PMID: 38895346 PMCID: PMC11185556 DOI: 10.1101/2024.06.02.597018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Knowledge of the structures formed by proteins and small ligands is of fundamental importance for understanding molecular principles of chemotherapy and for designing new and more effective drugs. Due to the still high costs and to the several limitations of experimental techniques, it is most often desirable to predict these ligand-protein complexes in silico, particularly when screening for new putative drugs from databases of millions of compounds. While virtual screening based on molecular docking is widely used for this purpose, it generally fails in mimicking binding events associated with large conformational changes in the protein, particularly when the latter involve multiple domains. In this work, we describe a new methodology aimed at generating bound-like conformations of very flexible and allosteric proteins bearing multiple binding sites. Validation was performed on the enzyme adenylate kinase (ADK), a paradigmatic example of proteins that undergo very large conformational changes upon ligand binding. By only exploiting the unbound structure and the putative binding sites of the protein, we generated a significant fraction of bound-like structures, which employed in ensemble-docking calculations allowed to find native-like poses of substrates, inhibitors, and catalytically incompetent binders. Our protocol provides a general framework for the generation of bound-like conformations of flexible proteins that are suitable to host different ligands, demonstrating high sensitivity to the fine chemical details that regulate protein's activity. We foresee applications in virtual screening for difficult targets, prediction of the impact of amino acid mutations on structure and dynamics, and protein engineering.
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Affiliation(s)
- Andrea Basciu
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Mohd Athar
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Han Kurt
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Christine Neville
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Giuliano Malloci
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Fabrizio C. Muredda
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Andrea Bosin
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Alexandre M. J. J. Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Attilio V. Vargiu
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
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Masoabi M, Burger NFV, Botha AM, Le Roux ML, Vlok M, Snyman S, Van der Vyver C. Overexpression of the Small Ubiquitin-Like Modifier protease OTS1 gene enhances drought tolerance in sugarcane (Saccharum spp. hybrid). PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:1121-1141. [PMID: 37856570 DOI: 10.1111/plb.13585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Sugarcane is an economically important crop plant across the globe as it is the primary source of sugar and biofuel. Its growth and development are greatly influenced by water availability; therefore, in periods of water scarcity, yields are severely compromised. Small Ubiquitin-Like Modifier (SUMO) proteases play an important role in stress responses by regulating the SUMO-related post-translational modification of proteins. In an attempt to enhance drought tolerance in sugarcane, this crop was genetically transformed with a cysteine protease (OVERLY TOLERANT TO SALT-1; OTS1) from Arabidopsis thaliana using particle bombardment. Transgenic plants were analysed in terms of photosynthetic capacity, oxidative damage, antioxidant accumulation and the SUMO-enrich protein profile was assessed. Sugarcane transformed with the AtOTS1 gene displayed enhanced drought tolerance and delayed leaf senescence under water deficit compared to the untransformed wild type (WT). The AtOTS1 transgenic plants maintained a high relative moisture content and higher photosynthesis rate when compared to the WT. In addition, when the transgene was expressed at high levels, the transformed plants were able to maintain higher stomatal conductance and chlorophyl content under moderate stress compared to the WT. Under severe water deficit stress, the transgenic plants accumulated less malondialdehyde and maintained membrane integrity. SUMOylation of total protein and protease activity was lower in the AtOTS1 transformed plants compared to the WT, with several SUMO-enriched proteins exclusively expressed in the transgenics when exposed to water deficit stress. SUMOylation of proteins likely influenced various mechanisms contributing to enhanced drought tolerance in sugarcane.
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Affiliation(s)
- M Masoabi
- Institute for Plant Biotechnology, University of Stellenbosch, Stellenbosch, South Africa
| | - N F V Burger
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - A-M Botha
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - M L Le Roux
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - M Vlok
- Mass Spectrometry Unit, Central Analytic Facility, Stellenbosch University, Stellenbosch, South Africa
| | - S Snyman
- South African Sugarcane Research Institute, Mount Edgecombe, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - C Van der Vyver
- Institute for Plant Biotechnology, University of Stellenbosch, Stellenbosch, South Africa
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Zhan M, Ding Y, Huang S, Liu Y, Xiao J, Yu H, Lu L, Wang X. Lysyl oxidase-like 3 restrains mitochondrial ferroptosis to promote liver cancer chemoresistance by stabilizing dihydroorotate dehydrogenase. Nat Commun 2023; 14:3123. [PMID: 37253718 DOI: 10.1038/s41467-023-38753-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 05/11/2023] [Indexed: 06/01/2023] Open
Abstract
To overcome chemotherapy resistance, novel strategies sensitizing cancer cells to chemotherapy are required. Here, we screen the lysyl-oxidase (LOX) family to clarify its contribution to chemotherapy resistance in liver cancer. LOXL3 depletion significantly sensitizes liver cancer cells to Oxaliplatin by inducing ferroptosis. Chemotherapy-activated EGFR signaling drives LOXL3 to interact with TOM20, causing it to be hijacked into mitochondria, where LOXL3 lysyl-oxidase activity is reinforced by phosphorylation at S704. Metabolic adenylate kinase 2 (AK2) directly phosphorylates LOXL3-S704. Phosphorylated LOXL3-S704 targets dihydroorotate dehydrogenase (DHODH) and stabilizes it by preventing its ubiquitin-mediated proteasomal degradation. K344-deubiquitinated DHODH accumulates in mitochondria, in turn inhibiting chemotherapy-induced mitochondrial ferroptosis. CRISPR-Cas9-mediated site-mutation of mouse LOXL3-S704 to D704 causes a reduction in lipid peroxidation. Using an advanced liver cancer mouse model, we further reveal that low-dose Oxaliplatin in combination with the DHODH-inhibitor Leflunomide effectively inhibit liver cancer progression by inducing ferroptosis, with increased chemotherapy sensitivity and decreased chemotherapy toxicity.
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Affiliation(s)
- Meixiao Zhan
- Zhuhai Interventional Medical Center, Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital, Zhuhai Hospital affiliated with Jinan University, Zhuhai, 519000, Guangdong, China
| | - Yufeng Ding
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, 510006, Guangzhou, China.
| | - Shanzhou Huang
- Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 510080, Guangzhou, China
| | - Yuhang Liu
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, 510006, Guangzhou, China
| | - Jing Xiao
- Zhuhai Interventional Medical Center, Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital, Zhuhai Hospital affiliated with Jinan University, Zhuhai, 519000, Guangdong, China
| | - Hua Yu
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, 510006, Guangzhou, China.
| | - Ligong Lu
- Zhuhai Interventional Medical Center, Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital, Zhuhai Hospital affiliated with Jinan University, Zhuhai, 519000, Guangdong, China.
| | - Xiongjun Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, 510006, Guangzhou, China.
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Cheng HC, Chi SC, Liang CY, Yu JY, Wang AG. Candidate Modifier Genes for the Penetrance of Leber's Hereditary Optic Neuropathy. Int J Mol Sci 2022; 23:ijms231911891. [PMID: 36233195 PMCID: PMC9569928 DOI: 10.3390/ijms231911891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Leber’s hereditary optic neuropathy (LHON) is a maternally transmitted disease caused by mitochondria DNA (mtDNA) mutation. It is characterized by acute and subacute visual loss predominantly affecting young men. The mtDNA mutation is transmitted to all maternal lineages. However, only approximately 50% of men and 10% of women harboring a pathogenic mtDNA mutation develop optic neuropathy, reflecting both the incomplete penetrance and its unexplained male prevalence, where over 80% of patients are male. Nuclear modifier genes have been presumed to affect the penetrance of LHON. With conventional genetic methods, prior studies have failed to solve the underlying pathogenesis. Whole exome sequencing (WES) is a new molecular technique for sequencing the protein-coding region of all genes in a whole genome. We performed WES from five families with 17 members. These samples were divided into the proband group (probands with acute onset of LHON, n = 7) and control group (carriers including mother and relative carriers with mtDNSA 11778 mutation, without clinical manifestation of LHON, n = 10). Through whole exome analysis, we found that many mitochondria related (MT-related) nuclear genes have high percentage of variants in either the proband group or control group. The MT genes with a difference over 0.3 of mutation percentage between the proband and control groups include AK4, NSUN4, RDH13, COQ3, and FAHD1. In addition, the pathway analysis revealed that these genes were associated with cofactor metabolism pathways. Family-based analysis showed that several candidate MT genes including METAP1D (c.41G > T), ACACB (c.1029del), ME3 (c.972G > C), NIPSNAP3B (c.280G > C, c.476C > G), and NSUN4 (c.4A > G) were involved in the penetrance of LHON. A GWAS (genome wide association study) was performed, which found that ADGRG5 (Chr16:575620A:G), POLE4 (Chr2:7495872T:G), ERMAP (Chr1:4283044A:G), PIGR (Chr1:2069357C:T;2069358G:A), CDC42BPB (Chr14:102949A:G), PROK1 (Chr1:1104562A:G), BCAN (Chr 1:1566582C:T), and NES (Chr1:1566698A:G,1566705T:C, 1566707T:C) may be involved. The incomplete penetrance and male prevalence are still the major unexplained issues in LHON. Through whole exome analysis, we found several MT genes with a high percentage of variants were involved in a family-based analysis. Pathway analysis suggested a difference in the mutation burden of MT genes underlining the biosynthesis and metabolism pathways. In addition, the GWAS analysis also revealed several candidate nuclear modifier genes. The new technology of WES contributes to provide a highly efficient candidate gene screening function in molecular genetics.
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Affiliation(s)
- Hui-Chen Cheng
- Program in Molecular Medicine, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, 201 Sec. 2, Shih-Pai Rd., Taipei 11217, Taiwan
- Department of Ophthalmology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Sheng-Chu Chi
- Department of Ophthalmology, Taipei Veterans General Hospital, 201 Sec. 2, Shih-Pai Rd., Taipei 11217, Taiwan
| | - Chiao-Ying Liang
- Department of Ophthalmology, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Jenn-Yah Yu
- Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - An-Guor Wang
- Department of Ophthalmology, Taipei Veterans General Hospital, 201 Sec. 2, Shih-Pai Rd., Taipei 11217, Taiwan
- Department of Ophthalmology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Correspondence: ; Tel.: +886-2-2875-7325; Fax: +886-2-2876-1351
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Zhang H, Kong L, Zhang Y, Wang C, Sun L. Transcriptome and proteome analysis of the antitumor activity of maslinic acid against pancreatic cancer cells. Aging (Albany NY) 2021; 13:23308-23327. [PMID: 34637398 PMCID: PMC8544341 DOI: 10.18632/aging.203623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022]
Abstract
Maslinic acid (MA) is a triterpenoid compound of natural abundance in olive plants possessing numerous biological activities. The effect and molecular mechanism of MA on pancreatic cancer cells remain elusive. Here, we explored the anti-tumor activity of MA on human pancreatic cancer cells and the potential underlying molecular mechanism. The anti-cancer effects of MA on whole-cell processes, including proliferation, migration, and invasion in pancreatic cancer cells, were systematically assessed by colony formation, transwell, and migration assays. The search for potential therapeutic targets was achieved via transcriptomics and proteomics analyses. MA was demonstrated to inhibit the proliferation, migration, and invasion of PANC-1 and Patu-8988 cells, but induced apoptosis of these cells. Several key candidate genes and proteins of functional relevance for the anti-tumor activity of MA were identified through the association analysis of transcriptomics and proteomics. To our knowledge, this is the first transcription and proteomics-based comprehensive analysis of the mechanism of MA against pancreatic cancer. The findings demonstrate that MA holds promise as a therapeutic drug for managing pancreatic cancer.
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Affiliation(s)
- Hewei Zhang
- Department of Surgery, Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, Zhejiang Provincial Top Key Discipline in Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Lijun Kong
- Department of Surgery, Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, Zhejiang Provincial Top Key Discipline in Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Yan Zhang
- Department of Surgery, Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, Zhejiang Provincial Top Key Discipline in Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Cheng Wang
- Department of Surgery, Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, Zhejiang Provincial Top Key Discipline in Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Linxiao Sun
- Department of Surgery, Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, Zhejiang Provincial Top Key Discipline in Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
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Feng J, Shukla D. FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution. J Phys Chem B 2020; 124:3605-3615. [PMID: 32283936 DOI: 10.1021/acs.jpcb.9b11869] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins are dynamic molecules which perform diverse molecular functions by adopting different three-dimensional structures. Recent progress in residue-residue contacts prediction opens up new avenues for the de novo protein structure prediction from sequence information. However, it is still difficult to predict more than one conformation from residue-residue contacts alone. This is due to the inability to deconvolve the complex signals of residue-residue contacts, i.e., spatial contacts relevant for protein folding, conformational diversity, and ligand binding. Here, we introduce a machine learning based method, called FingerprintContacts, for extending the capabilities of residue-residue contacts. This algorithm leverages the features of residue-residue contacts, that is, (1) a single conformation outperforms the others in the structural prediction using all the top ranking residue-residue contacts as structural constraints and (2) conformation specific contacts rank lower and constitute a small fraction of residue-residue contacts. We demonstrate the capabilities of FingerprintContacts on eight ligand binding proteins with varying conformational motions. Furthermore, FingerprintContacts identifies small clusters of residue-residue contacts which are preferentially located in the dynamically fluctuating regions. With the rapid growth in protein sequence information, we expect FingerprintContacts to be a powerful first step in structural understanding of protein functional mechanisms.
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Abstract
Adenylate kinase is a small, usually monomeric, enzyme found in every living thing due to its crucial role in energetic metabolism. This paper outlines the most relevant data about adenylate kinases isoforms, and the connection between dysregulation or mutation of human adenylate kinase and medical conditions. The following datadases were consulted: National Centre for Biotechnology Information, Protein Data Bank, and Mouse Genomic Informatics. The SmartBLAST tool, EMBOSS Needle Program, and Clustal Omega Program were used to analyze the best protein match, and to perform pairwise sequence alignment and multiple sequence alignment. Human adenylate kinase genes are located on different chromosomes, six of them being on the chromosomes 1 and 9. The adenylate kinases' intracellular localization and organ distribution explain their dysregulation in many diseases. The cytosolic isoenzyme 1 and the mitochondrial isoenzyme 2 are the main adenylate kinases that are integrated in the vast network of inflammatory modulators. The cytosolic isoenzyme 5 is correlated with limbic encephalitis and Leu673Pro mutation of the isoenzyme 7 leads to primary male infertility due to impairment of the ciliary function. The impairment of the mitochondrial isoenzymes 2 and 4 is demonstrated in neuroblastoma or glioma. The adenylate kinases are disease modifier that can assess the risk of diseases where oxidative stress plays a crucial role in pathogenesis like metabolic syndrome or neurodegenerative diseases. Because adenylate kinases has ATP as substrate, they are integrated in the global network of energetic process of any organism therefore are valid target for new pharmaceutical compounds.
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Affiliation(s)
- Mihaela Ileana Ionescu
- Department of Microbiology, Faculty of Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, 6 Louis Pasteur, Cluj-Napoca, 400349, Romania. .,County Emergency Clinical Hospital, Cluj-Napoca, Romania.
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AK4 Promotes the Progression of HER2-Positive Breast Cancer by Facilitating Cell Proliferation and Invasion. DISEASE MARKERS 2019; 2019:8186091. [PMID: 31827645 PMCID: PMC6886328 DOI: 10.1155/2019/8186091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/23/2019] [Accepted: 10/05/2019] [Indexed: 12/31/2022]
Abstract
Breast cancer (BC) is a type of malignant tumor originating from the epithelial tissue of the mammary gland, and about 20% of breast cancers are human epidermal growth factor receptor 2 positive (HER2+), which is a subtype with more aggression. Recently, HER2-positive breast cancer is often accompanied by poor prognosis of patients, and targeted therapy showed a promising prospect. To combat this disease, novel therapeutic targets are still needed. Adenylate kinase 4 (AK4) is a member of the adenylate kinase family and is expressed in the mitochondrial matrix. AK4 is involved in multiple cellular functions such as energy metabolism homeostasis. Interestingly, AK4 was observed highly expressed in several tumor tissues, and the involvement of AK4 in cancer development was generally revealed. However, the possible role of AK4 on the growth and development of breast cancer is still unclear. Here, we investigated the possible functions of AK4 on the progression of HER2-positive breast cancer. We found the high expression of AK4 in HER2-positive breast cancer tissues from patients who received surgical treatment. Additionally, AK4 expression levels were obviously correlated with clinical-pathological features, including pTNM stage (P = 0.017) and lymph node metastasis (P = 0.046). We mechanically confirmed that AK4 depletion showed the obvious impairment of cell proliferation and invasion in MCF7 and MDA-MB-231 cells. AK4 also facilitates tumor growth and metastasis of HER2-positive breast cancer in vivo. In conclusion, we identified and mechanically confirmed that AK4 is a novel therapeutic target of HER2-positive breast cancer.
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Zhong F, Liang S, Zhong Z. Emerging Role of Mitochondrial DNA as a Major Driver of Inflammation and Disease Progression. Trends Immunol 2019; 40:1120-1133. [PMID: 31744765 DOI: 10.1016/j.it.2019.10.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 12/13/2022]
Abstract
Inflammation benefits the host by promoting the elimination of invading pathogens and clearance of cellular debris after tissue injury. Inflammation also stimulates tissue repair and regeneration to restore homeostasis and organismal health. Emerging evidence suggests that mitochondrial DNA (mtDNA), the only form of non-nuclear DNA in eukaryotic cells, is a major activator of inflammation when leaked out from stressed mitochondria. Here, we review the current understanding on the role of mtDNA in innate immunity, discussing how dysregulated mtDNA metabolism can promote chronic inflammation and disease progression.
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Affiliation(s)
- Fei Zhong
- Laboratory of Molecular Virology and Immunology, College of Animal Science and Technology and College of Veterinary Medicine, Agricultural University of Hebei, Baoding, Hebei 071000, China
| | - Shuang Liang
- Department of Immunology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Zhenyu Zhong
- Department of Immunology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.
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Ionescu MI, Oniga O. Molecular Docking Evaluation of ( E)-5-arylidene-2-thioxothiazolidin-4-one Derivatives as Selective Bacterial Adenylate Kinase Inhibitors. Molecules 2018; 23:molecules23051076. [PMID: 29751552 PMCID: PMC6102543 DOI: 10.3390/molecules23051076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/27/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
Multi-drug resistant microorganism infections with emerging problems that require not only a prevention strategy, but also the development of new inhibitory compounds. Six previously synthesized 5-arylidene-2-thioxothiazolidin-4-one derivatives 1a–f, were screened for inhibitory activity on adenylate kinases of different origins by molecular docking. The compounds 1c and 1d were the most efficient inhibitors of bacterial and some archean adenylate kinases. Hydrogen bond interactions were observed with the residues belonging to the ATP binding site. Moreover human adenylate kinases are poor targets, suggesting that this selectivity offers promising prospectives for refining the structure of our compounds.
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Affiliation(s)
- Mihaela Ileana Ionescu
- Department of Microbiology, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania.
- Department of Microbiology, County Emergency Clinical Hospital, 400006 Cluj-Napoca, Romania.
| | - Ovidiu Oniga
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania.
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Monzon AM, Rohr CO, Fornasari MS, Parisi G. CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw038. [PMID: 27022160 PMCID: PMC4809262 DOI: 10.1093/database/baw038] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/02/2016] [Indexed: 01/01/2023]
Abstract
CoDNaS (conformational diversity of the native state) is a protein conformational diversity database. Conformational diversity describes structural differences between conformers that define the native state of proteins. It is a key concept to understand protein function and biological processes related to protein functions. CoDNaS offers a well curated database that is experimentally driven, thoroughly linked, and annotated. CoDNaS facilitates the extraction of key information on small structural differences based on protein movements. CoDNaS enables users to easily relate the degree of conformational diversity with physical, chemical and biological properties derived from experiments on protein structure and biological characteristics. The new version of CoDNaS includes ∼70% of all available protein structures, and new tools have been added that run sequence searches, display structural flexibility profiles and allow users to browse the database for different structural classes. These tools facilitate the exploration of protein conformational diversity and its role in protein function. Database URL:http://ufq.unq.edu.ar/codnas
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Affiliation(s)
| | - Cristian Oscar Rohr
- Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA)-Laboratorio de Genómica Médica y Evolución, Universidad Nacional de Buenos Aires, Argentina
| | | | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
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12
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Vihinen M. Types and effects of protein variations. Hum Genet 2015; 134:405-21. [DOI: 10.1007/s00439-015-1529-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/09/2015] [Indexed: 12/12/2022]
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13
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RNA mimicry by the fap7 adenylate kinase in ribosome biogenesis. PLoS Biol 2014; 12:e1001860. [PMID: 24823650 PMCID: PMC4019466 DOI: 10.1371/journal.pbio.1001860] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 04/04/2014] [Indexed: 11/22/2022] Open
Abstract
The structure of a ribosome assembly factor in complex bound to a ribosomal protein uncovers a chaperoning function that uses RNA mimicry and is regulated by ATP hydrolysis. During biogenesis of the 40S and 60S ribosomal subunits, the pre-40S particles are exported to the cytoplasm prior to final cleavage of the 20S pre-rRNA to mature 18S rRNA. Amongst the factors involved in this maturation step, Fap7 is unusual, as it both interacts with ribosomal protein Rps14 and harbors adenylate kinase activity, a function not usually associated with ribonucleoprotein assembly. Human hFap7 also regulates Cajal body assembly and cell cycle progression via the p53–MDM2 pathway. This work presents the functional and structural characterization of the Fap7–Rps14 complex. We report that Fap7 association blocks the RNA binding surface of Rps14 and, conversely, Rps14 binding inhibits adenylate kinase activity of Fap7. In addition, the affinity of Fap7 for Rps14 is higher with bound ADP, whereas ATP hydrolysis dissociates the complex. These results suggest that Fap7 chaperones Rps14 assembly into pre-40S particles via RNA mimicry in an ATP-dependent manner. Incorporation of Rps14 by Fap7 leads to a structural rearrangement of the platform domain necessary for the pre-rRNA to acquire a cleavage competent conformation. Ribosomes are the cellular machines responsible for all protein synthesis. In eukaryotes, the assembly of ribosomes from their protein and RNA components is extremely complicated and involves more than 200 nonribosomal factors—three times the number of proteins in the mature complex. Among these factors, the Fap7 protein is particularly intriguing because it interacts with the small subunit ribosomal protein Rps14 and it exhibits adenylate kinase activity—a molecular function more commonly associated with regulating ATP/ADP levels than assembling protein–RNA complexes. Combining structural and biochemical analysis of the Rps14–Fap7 complex, we show that Fap7 uses protein side chains to mimic RNA contacts, rendering the interaction of Rps14 with ribosomal RNA or with Fap7 competitive and mutually exclusive. Once bound, Rps14 blocks the substrate-binding cavity of Fap7, and ATP hydrolysis will then break the Fap7–Rps14 complex apart. At the same time, the ribosome structure at the location where Rps14 binds is disrupted when the Fap7/Rps14 complex is formed, and this process is regulated by ATP binding and hydrolysis. Our model is thus that Fap7 temporarily removes Rps14 from the ribosome to enable a conformational change of the ribosomal RNA that is needed for the final maturation step of the small ribosomal subunit.
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Mikoulinskaia GV, Taran SA, Skoblov YS, Feofanov SA. The study of the bacteriophage T5 deoxynucleoside monophosphate kinase active site by site-directed mutagenesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013. [DOI: 10.1134/s1068162013060071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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