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Rodriguez J, Battistini F, Learte-Aymamí S, Orozco M, Mascareñas JL. Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA. RSC Chem Biol 2023; 4:486-493. [PMID: 37415868 PMCID: PMC10320839 DOI: 10.1039/d3cb00053b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/09/2023] [Indexed: 07/08/2023] Open
Abstract
We report the modelling of the DNA complex of an artificial miniprotein composed of two zinc finger modules and an AT-hook linking peptide. The computational study provides for the first time a structural view of these types of complexes, dissecting interactions that are key to modulate their stability. The relevance of these interactions was validated experimentally. These results confirm the potential of this type of computational approach for studying peptide-DNA complexes and suggest that they could be very useful for the rational design of non-natural, DNA binding miniproteins.
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Affiliation(s)
- Jessica Rodriguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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2
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Kong L, Dong R, Huang K, Wang X, Wang D, Yue N, Wang C, Sun P, Gu J, Luo H, Liu K, Wu J, Sun H, Meng Q. Yangonin modulates lipid homeostasis, ameliorates cholestasis and cellular senescence in alcoholic liver disease via activating nuclear receptor FXR. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 90:153629. [PMID: 34304130 DOI: 10.1016/j.phymed.2021.153629] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/24/2021] [Accepted: 06/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Alcoholic liver disease (ALD) is a progressive disease beginning with simple steatosis but can progress to alcoholic steatohepatitis, fibrosis, cirrhosis, and even hepatocellular carcinoma. The morbidity of ALD is on the rise and has been a large burden on global healthcare system. It is unfortunately that there are currently no approved therapeutic drugs against ALD. Hence, it is of utmost urgency to develop the efficacious therapies. The ability of many molecular targets against ALD is under investigation. Farnesoid X receptor (FXR), a member of the ligand-activated transcription factor superfamily, has been recently demonstrated to have a crucial role in the pathogenesis and progression of ALD. PURPOSE The purpose of the study is to determine whether Yangonin (YAN), a FXR agonist previously demonstrated by us, exerts the hepatoprotective effects against ALD and further to clarify the mechanisms in vitro and in vivo. STUDY DESIGN The alcoholic liver disease model induced by Lieber-Decarli liquid diet was established with or without Yan treatment. METHODS We determined the liver to body weight ratios, the body weight, serum and hepatic biochemical indicators. The alleviation of the liver histopathological progression was evaluated by H&E and immunohistochemical staining. Western blot and quantitative real-time PCR were used to demonstrate YAN treatment-mediated alleviation mechanisms of ALD. RESULTS The data indicated that YAN existed hepatoprotective activity against ALD via FXR activation. YAN improved the lipid homeostasis by decreasing hepatic lipogenesis and increasing fatty acid β-oxidation and lipoprotein lipolysis through modulating the related protein. Also, YAN ameliorated ethanol-induced cholestasis via inhibiting bile acid uptake transporter Ntcp and inducing bile acid efflux transporter Bsep and Mrp2 expression. Besides, YAN improved bile acid homeostasis via inducing Sult2a1 expression and inhibiting Cyp7a1 and Cyp8b1 expression. Furthermore, YAN attenuated ethanol-triggered hepatocyte damage by inhibiting cellular senescence marker P16, P21 and Hmga1 expression. Also, YAN alleviated ethanol-induced inflammation by down-regulating the inflammation-related gene IL-6, IL-1β and TNF-α expression. Notably, the protective effects of YAN were cancelled by FXR siRNA in vitro and FXR antagonist GS in vivo. CONCLUSIONS YAN exerted significant hepatoprotective effects against liver injury triggered by ethanol via FXR-mediated target gene modulation.
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Affiliation(s)
- Lina Kong
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Renchao Dong
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Kai Huang
- Drug Clinical Trial Institution, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Xiaohui Wang
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Dalong Wang
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Nan Yue
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Changyuan Wang
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Pengyuan Sun
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Jiangning Gu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Haifeng Luo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Kexin Liu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Jingjing Wu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Huijun Sun
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Qiang Meng
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China.
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3
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Hörberg J, Moreau K, Tamás MJ, Reymer A. Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors. Nucleic Acids Res 2021; 49:9280-9293. [PMID: 34387667 PMCID: PMC8450079 DOI: 10.1093/nar/gkab691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022] Open
Abstract
Activator proteins 1 (AP-1) comprise one of the largest families of eukaryotic basic leucine zipper transcription factors. Despite advances in the characterization of AP-1 DNA-binding sites, our ability to predict new binding sites and explain how the proteins achieve different gene expression levels remains limited. Here we address the role of sequence-specific DNA flexibility for stability and specific binding of AP-1 factors, using microsecond-long molecular dynamics simulations. As a model system, we employ yeast AP-1 factor Yap1 binding to three different response elements from two genetic environments. Our data show that Yap1 actively exploits the sequence-specific flexibility of DNA within the response element to form stable protein–DNA complexes. The stability also depends on the four to six flanking nucleotides, adjacent to the response elements. The flanking sequences modulate the conformational adaptability of the response element, making it more shape-efficient to form specific contacts with the protein. Bioinformatics analysis of differential expression of the studied genes supports our conclusions: the stability of Yap1–DNA complexes, modulated by the flanking environment, influences the gene expression levels. Our results provide new insights into mechanisms of protein–DNA recognition and the biological regulation of gene expression levels in eukaryotes.
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Affiliation(s)
- Johanna Hörberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Kevin Moreau
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Anna Reymer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
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4
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Chang X, Gurung RL, Wang L, Jin A, Li Z, Wang R, Beckman KB, Adams-Haduch J, Meah WY, Sim KS, Lim WK, Davila S, Tan P, Teo JX, Yeo KK, M Y, Liu S, Lim SC, Liu J, van Dam RM, Friedlander Y, Koh WP, Yuan JM, Khor CC, Heng CK, Dorajoo R. Low frequency variants associated with leukocyte telomere length in the Singapore Chinese population. Commun Biol 2021; 4:519. [PMID: 33941849 PMCID: PMC8093266 DOI: 10.1038/s42003-021-02056-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/26/2021] [Indexed: 02/02/2023] Open
Abstract
The role of low frequency variants associated with telomere length homeostasis in chronic diseases and mortalities is relatively understudied in the East-Asian population. Here we evaluated low frequency variants, including 1,915,154 Asian specific variants, for leukocyte telomere length (LTL) associations among 25,533 Singapore Chinese samples. Three East Asian specific variants in/near POT1, TERF1 and STN1 genes are associated with LTL (Meta-analysis P 2.49×10-14-6.94×10-10). Rs79314063, a missense variant (p.Asp410His) at POT1, shows effect 5.3 fold higher and independent of a previous common index SNP. TERF1 (rs79617270) and STN1 (rs139620151) are linked to LTL-associated common index SNPs at these loci. Rs79617270 is associated with cancer mortality [HR95%CI = 1.544 (1.173, 2.032), PAdj = 0.018] and 4.76% of the association between the rs79617270 and colon cancer is mediated through LTL. Overall, genetically determined LTL is particularly associated with lung adenocarcinoma [HR95%CI = 1.123 (1.051, 1.201), Padj = 0.007]. Ethnicity-specific low frequency variants may affect LTL homeostasis and associate with certain cancers.
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Affiliation(s)
- Xuling Chang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Resham L Gurung
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Ling Wang
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Aizhen Jin
- Health Services and Systems Research, Duke-NUS Medical School Singapore, Singapore, Singapore
| | - Zheng Li
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Renwei Wang
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kenneth B Beckman
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN, USA
| | - Jennifer Adams-Haduch
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wee Yang Meah
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Kar Seng Sim
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Sonia Davila
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jing Xian Teo
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Khung Keong Yeo
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
- Department of Cardiology, National Heart Centre Singapore, Singapore, Singapore
| | - Yiamunaa M
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Sylvia Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Su Chi Lim
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
- Diabetes Centre, Admiralty Medical Centre, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yechiel Friedlander
- School of Public Health and Community Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Woon-Puay Koh
- Health Services and Systems Research, Duke-NUS Medical School Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore.
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, Singapore.
- Health Services and Systems Research, Duke-NUS Medical School Singapore, Singapore, Singapore.
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5
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Oliveira ASF, Shoemark DK, Campello HR, Wonnacott S, Gallagher T, Sessions RB, Mulholland AJ. Identification of the Initial Steps in Signal Transduction in the α4β2 Nicotinic Receptor: Insights from Equilibrium and Nonequilibrium Simulations. Structure 2019; 27:1171-1183.e3. [PMID: 31130483 DOI: 10.1016/j.str.2019.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/28/2019] [Accepted: 04/10/2019] [Indexed: 02/02/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) modulate synaptic transmission in the nervous system. These receptors have emerged as therapeutic targets in drug discovery for treating several conditions, including Alzheimer's disease, pain, and nicotine addiction. In this in silico study, we use a combination of equilibrium and nonequilibrium molecular dynamics simulations to map dynamic and structural changes induced by nicotine in the human α4β2 nAChR. They reveal a striking pattern of communication between the extracellular binding pockets and the transmembrane domains (TMDs) and show the sequence of conformational changes associated with the initial steps in this process. We propose a general mechanism for signal transduction for Cys-loop receptors: the mechanistic steps for communication proceed firstly through loop C in the principal subunit, and are subsequently transmitted, gradually and cumulatively, to loop F of the complementary subunit, and then to the TMDs through the M2-M3 linker.
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Affiliation(s)
- A Sofia F Oliveira
- School of Biochemistry, University of Bristol, Bristol BS8 1DT, UK; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Hugo Rego Campello
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Susan Wonnacott
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Timothy Gallagher
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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6
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Huggins DJ, Biggin PC, Dämgen MA, Essex JW, Harris SA, Henchman RH, Khalid S, Kuzmanic A, Laughton CA, Michel J, Mulholland AJ, Rosta E, Sansom MSP, van der Kamp MW. Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1393] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- David J. Huggins
- TCM Group, Cavendish Laboratory University of Cambridge Cambridge UK
- Unilever Centre, Department of Chemistry University of Cambridge Cambridge UK
- Department of Physiology and Biophysics Weill Cornell Medical College New York NY
| | | | - Marc A. Dämgen
- Department of Biochemistry University of Oxford Oxford UK
| | - Jonathan W. Essex
- School of Chemistry University of Southampton Southampton UK
- Institute for Life Sciences University of Southampton Southampton UK
| | - Sarah A. Harris
- School of Physics and Astronomy University of Leeds Leeds UK
- Astbury Centre for Structural and Molecular Biology University of Leeds Leeds UK
| | - Richard H. Henchman
- Manchester Institute of Biotechnology The University of Manchester Manchester UK
- School of Chemistry The University of Manchester Oxford UK
| | - Syma Khalid
- School of Chemistry University of Southampton Southampton UK
- Institute for Life Sciences University of Southampton Southampton UK
| | | | - Charles A. Laughton
- School of Pharmacy University of Nottingham Nottingham UK
- Centre for Biomolecular Sciences University of Nottingham Nottingham UK
| | - Julien Michel
- EaStCHEM school of Chemistry University of Edinburgh Edinburgh UK
| | - Adrian J. Mulholland
- Centre of Computational Chemistry, School of Chemistry University of Bristol Bristol UK
| | - Edina Rosta
- Department of Chemistry King's College London London UK
| | | | - Marc W. van der Kamp
- Centre of Computational Chemistry, School of Chemistry University of Bristol Bristol UK
- School of Biochemistry, Biomedical Sciences Building University of Bristol Bristol UK
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7
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Liu Y, Qu K, Hai Y, Zhao C. Bisphenol A (BPA) binding on full‐length architectures of estrogen receptor. J Cell Biochem 2018; 119:6784-6794. [DOI: 10.1002/jcb.26872] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 03/21/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Yaquan Liu
- School of PharmacyLanzhou UniversityLanzhouChina
| | - Kaili Qu
- School of PharmacyLanzhou UniversityLanzhouChina
| | - Ying Hai
- School of PharmacyLanzhou UniversityLanzhouChina
| | - Chunyan Zhao
- School of PharmacyLanzhou UniversityLanzhouChina
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8
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Peng H, Zhu Y, Yeh F, Cole SA, Best LG, Lin J, Blackburn E, Devereux RB, Roman MJ, Lee ET, Howard BV, Zhao J. Impact of biological aging on arterial aging in American Indians: findings from the Strong Heart Family Study. Aging (Albany NY) 2017; 8:1583-92. [PMID: 27540694 PMCID: PMC5032684 DOI: 10.18632/aging.101013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/28/2016] [Indexed: 11/25/2022]
Abstract
Telomere length, a marker of biological aging, has been associated with cardiovascular disease (CVD). Increased arterial stiffness, an indicator of arterial aging, predicts adverse CVD outcomes. However, the relationship between telomere length and arterial stiffness is less well studied. Here we examined the cross-sectional association between leukocyte telomere length (LTL) and arterial stiffness in 2,165 American Indians in the Strong Heart Family Study (SHFS). LTL was measured by qPCR. Arterial stiffness was assessed by stiffness index β. The association between LTL and arterial stiffness was assessed by generalized estimating equation model, adjusting for sociodemographics (age, sex, education level), study site, metabolic factors (fasting glucose, lipids, systolic blood pressure, and kidney function), lifestyle (BMI, smoking, drinking, and physical activity), and prevalent CVD. Results showed that longer LTL was significantly associated with a decreased arterial stiffness (β=-0.070, P=0.007). This association did not attenuate after further adjustment for hsCRP (β=-0.071, P=0.005) or excluding participants with overt CVD (β=-0.068, P=0.012), diabetes (β=-0.070, P=0.005), or chronic kidney disease (β=-0.090, P=0.001). In summary, shorter LTL was significantly associated with an increased arterial stiffness, independent of known risk factors. This finding may shed light on the potential role of biological aging in arterial aging in American Indians.
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Affiliation(s)
- Hao Peng
- Department of Epidemiology, Tulane University School of Public Health, New Orleans, LA 70112, USA
| | - Yun Zhu
- Department of Epidemiology, Tulane University School of Public Health, New Orleans, LA 70112, USA
| | - Fawn Yeh
- Center for American Indian Health Research, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
| | - Shelley A Cole
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Lyle G Best
- Missouri Breaks Industries Research Inc, Timber Lake, SD 57656, USA
| | - Jue Lin
- Department of Biochemistry and Biophysics at the University of California, San Francisco, CA 94143, USA
| | - Elizabeth Blackburn
- Department of Biochemistry and Biophysics at the University of California, San Francisco, CA 94143, USA
| | - Richard B Devereux
- Greenberg Division of Cardiology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Mary J Roman
- Greenberg Division of Cardiology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Elisa T Lee
- Center for American Indian Health Research, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
| | | | - Jinying Zhao
- Department of Epidemiology, Tulane University School of Public Health, New Orleans, LA 70112, USA
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9
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Kumar S, Sharma G, Chakraborty C, Sharma AR, Kim J. Regulatory functional territory of PLK-1 and their substrates beyond mitosis. Oncotarget 2017; 8:37942-37962. [PMID: 28415805 PMCID: PMC5514964 DOI: 10.18632/oncotarget.16290] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/03/2017] [Indexed: 12/04/2022] Open
Abstract
Polo-like kinase 1 (PLK-1) is a well-known (Ser/Thr) mitotic protein kinase and is considered as a proto-oncogene. As hyper-activation of PLK-1 is broadly associated with poor prognosis and cancer progression, it is one of the most extensively studied mitotic kinases. During mitosis, PLK-1 regulates various cell cycle events, such as spindle pole maturation, chromosome segregation and cytokinesis. However, studies have demonstrated that the role of PLK-1 is not only restricted to mitosis, but PLK-1 can also regulate other vital events beyond mitosis, including transcription, translation, ciliogenesis, checkpoint adaptation and recovery, apoptosis, chromosomes dynamics etc. Recent reviews have tried to define the regulatory role of PLK-1 during mitosis progression and tumorigenesis, but its' functional role beyond mitosis is still largely unexplored. PLK-1 can regulate the activity of many proteins that work outside of its conventional territory. The dysregulation of these proteins can cause diseases such as Alzheimer's disease, tumorigenesis etc. and may also lead to drug resistance. Thus, in this review, we discussed the versatile role of PLK-1 and tried to collect data to validate its' functional role in cell cycle regulation apart from mitosis.
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Affiliation(s)
- Shiv Kumar
- Department of Biochemistry, Institute of Cell Differentiation and Aging, Hallym University, College of Medicine, Chucheonsi, Gangwondo, Republic of Korea
| | - Garima Sharma
- Institute For Skeletal Aging & Orthopedic Surgery, Hallym University, College of Medicine, Chucheonsi, Gangwondo, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Bio-informatics, School of Computer and Information Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India
| | - Ashish Ranjan Sharma
- Institute For Skeletal Aging & Orthopedic Surgery, Hallym University, College of Medicine, Chucheonsi, Gangwondo, Republic of Korea
| | - Jaebong Kim
- Department of Biochemistry, Institute of Cell Differentiation and Aging, Hallym University, College of Medicine, Chucheonsi, Gangwondo, Republic of Korea
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10
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Patel TN, Vasan R, Gupta D, Patel J, Trivedi M. Shelterin proteins and cancer. Asian Pac J Cancer Prev 2016; 16:3085-90. [PMID: 25921101 DOI: 10.7314/apjcp.2015.16.8.3085] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The telomeric end structures of the DNA are known to contain tandem repeats of TTAGGG sequence bound with specialised protein complex called the "shelterin complex". It comprises six proteins, namely TRF1, TRF2, TIN2, POT1, TPP1 and RAP1. All of these assemble together to form a complex with double strand and single strand DNA repeats at the telomere. Such an association contributes to telomere stability and its protection from undesirable DNA damage control-specific responses. However, any alteration in the structure and function of any of these proteins may lead to undesirable DNA damage responses and thus cellular senescence and death. In our review, we throw light on how mutations in the proteins belonging to the shelterin complex may lead to various malfunctions and ultimately have a role in tumorigenesis and cancer progression.
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Affiliation(s)
- Trupti Nv Patel
- Department of Medical Biotechnology, Vellore Institute of Technology, Vellore, Tamilnadu, India E-mail : ,
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11
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Etheve L, Martin J, Lavery R. Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction. Nucleic Acids Res 2015; 44:1440-8. [PMID: 26721385 PMCID: PMC4756839 DOI: 10.1093/nar/gkv1511] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/15/2015] [Indexed: 11/13/2022] Open
Abstract
Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1 bound to its cognate DNA site show that the protein–DNA interface undergoes significant dynamics on the microsecond timescale. A detailed analysis of the simulation shows that movements of two key arginine side chains between the major groove and the backbone of DNA generate distinct conformational sub-states that each recognize only part of the consensus binding sequence of SKN-1, while the experimentally observed binding specificity results from a time-averaged view of the dynamic recognition occurring within this complex.
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Affiliation(s)
- Loïc Etheve
- BMSSI UMR 5086 CNRS/Univ. Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Juliette Martin
- BMSSI UMR 5086 CNRS/Univ. Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Richard Lavery
- BMSSI UMR 5086 CNRS/Univ. Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
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Zhitnikova MY, Boryskina OP, Shestopalova AV. Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein-DNA recognition. J Biomol Struct Dyn 2013; 32:1670-85. [PMID: 23998351 DOI: 10.1080/07391102.2013.830579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Variations of the shape and polarity of the DNA grooves caused by changes of the DNA conformation play an important role in the DNA readout. Despite the fact that non-canonical trans and gauche- conformations of the DNA backbone angle γ (O5'-C5'-C4'-C3') are frequently found in the DNA crystal structures, their possible role in the DNA recognition has not been studied systematically. In order to fill in this gap, we analyze the available high-resolution crystal structures of the naked and complexed DNA. The analysis shows that the non-canonical γ angle conformations are present both in the naked and bound DNA, more often in the bound vs. naked DNA, and in the nucleotides with the A-like vs. the B-like sugar pucker. The alternative angle γ torsions are more frequently observed in the purines with the A-like sugar pucker and in the pyrimidines with the B-like sugar conformation. The minor groove of the nucleotides with non-canonical γ angle conformation is more polar, while the major groove is more hydrophobic than in the nucleotides with the classical γ torsions due to variations in exposure of the polar and hydrophobic groups of the DNA backbone. The propensity of the nucleotides with different γ angle conformations to participate in the protein-nucleic acid contacts in the minor and major grooves is connected with their sugar pucker and sequence-specific. Our findings imply that the angle γ transitions contribute to the process of the protein-DNA recognition due to modification of the polar/hydrophobic profile of the DNA grooves.
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Affiliation(s)
- Mariia Yu Zhitnikova
- a O. Ya. Usikov Institute for Radiophysics and Electronics of the National Academy of Sciences of Ukraine , Acad. Proskura Street, 12, Kharkiv , 61085 , Ukraine
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