1
|
Španinger E, Potočnik U, Bren U. Molecular Dynamics Simulations Predict That rSNP Located in the HNF‑1α Gene Promotor Region Linked with MODY3 and Hepatocellular Carcinoma Promotes Stronger Binding of the HNF‑4α Transcription Factor. Biomolecules 2020; 10:biom10121700. [PMID: 33371430 PMCID: PMC7767403 DOI: 10.3390/biom10121700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/06/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
Our study aims to investigate the impact of the Maturity-onset diabetes of the young 3 disease-linked rSNP rs35126805 located in the HNF-1α gene promotor on the binding of the transcription factor HNF-4α and consequently on the regulation of HNF-1α gene expression. Our focus is to calculate the change in the binding affinity of the transcription factor HNF-4α to the DNA, caused by the regulatory single nucleotide polymorphism (rSNP) through molecular dynamics simulations and thermodynamic analysis of acquired results. Both root-mean-square difference (RMSD) and the relative binding free energy ΔΔGbind reveal that the HNF-4α binds slightly more strongly to the DNA containing the mutation (rSNP) making the complex more stable/rigid, and thereby influencing the expression of the HNF-1α gene. The resulting disruption of the HNF-4α/HNF-1α pathway is also linked to hepatocellular carcinoma metastasis and enhanced apoptosis in pancreatic cancer cells. To the best of our knowledge, this represents the first study where thermodynamic analysis of the results obtained from molecular dynamics simulations is performed to uncover the influence of rSNP on the protein binding to DNA. Therefore, our approach can be generally applied for studying the impact of regulatory single nucleotide polymorphisms on the binding of transcription factors to the DNA.
Collapse
Affiliation(s)
- Eva Španinger
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia; (E.Š.); (U.P.)
| | - Uroš Potočnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia; (E.Š.); (U.P.)
- Faculty of Medicine, University of Maribor, Taborska 8, SI-2000 Maribor, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia; (E.Š.); (U.P.)
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
- Correspondence: ; Tel.: +386-2-2294-421
| |
Collapse
|
2
|
Lv WL, Arnesano F, Carloni P, Natile G, Rossetti G. Effect of in vivo post-translational modifications of the HMGB1 protein upon binding to platinated DNA: a molecular simulation study. Nucleic Acids Res 2019; 46:11687-11697. [PMID: 30407547 PMCID: PMC6294504 DOI: 10.1093/nar/gky1082] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/19/2018] [Indexed: 12/26/2022] Open
Abstract
Cisplatin is one of the most widely used anticancer drugs. Its efficiency is unfortunately severely hampered by resistance. The High Mobility Group Box (HMGB) proteins may sensitize tumor cells to cisplatin by specifically binding to platinated DNA (PtDNA) lesions. In vivo, the HMGB/PtDNA binding is regulated by multisite post-translational modifications (PTMs). The impact of PTMs on the HMGB/PtDNA complex at atomistic level is here investigated by enhanced sampling molecular simulations. The PTMs turn out to affect the structure of the complex, the mobility of several regions (including the platinated site), and the nature of the protein/PtDNA non-covalent interactions. Overall, the multisite PTMs increase significantly the apparent synchrony of all the contacts between the protein and PtDNA. Consequently, the hydrophobic anchoring of the side chain of F37 between the two cross-linked guanines at the platinated site-a key element of the complexes formation - is more stable than in the complex without PTM. These differences can account for the experimentally measured greater affinity for PtDNA of the protein isoforms with PTMs. The collective behavior of multisite PTMs, as revealed here by the synchrony of contacts, may have a general significance for the modulation of intermolecular recognitions occurring in vivo.
Collapse
Affiliation(s)
- Wenping Lyu Lv
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany.,Faculty of Mathematics, Computer Science and Natural Sciences, RWTH-Aachen University, 52056 Aachen, Germany.,Computation-Based Science and Technology Research Center, Cyprus Institute, 2121 Aglantzia, Nicosia, Cyprus
| | - Fabio Arnesano
- Department of Chemistry, University of Bari "A. Moro", via Edoardo Orabona 4, 70125 Bari, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Giovanni Natile
- Department of Chemistry, University of Bari "A. Moro", via Edoardo Orabona 4, 70125 Bari, Italy
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany.,Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, 52062 Aachen, Germany.,Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, 52425 Jülich, Germany
| |
Collapse
|
3
|
Tu Z, Xiong J, Xiao R, Shao L, Yang X, Zhou L, Yuan W, Wang M, Yin Q, Wu Y, Pan S, Leng J, Jiang D, He C, Zhang Q. Loss of miR-146b-5p promotes T cell acute lymphoblastic leukemia migration and invasion via the IL-17A pathway. J Cell Biochem 2018; 120:5936-5948. [PMID: 30362152 DOI: 10.1002/jcb.27882] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/21/2018] [Indexed: 12/25/2022]
Abstract
Metastatic disease remains the primary cause of death for individuals with T cell acute lymphoblastic leukemia (T-ALL). microRNAs (miRNAs) play important roles in the pathogenesis of T-ALL by inhibiting gene expression at posttranscriptional levels. The goal of the current project is to identify any significant miRNAs in T-ALL metastasis. We observed miR-146b-5p to be downregulated in T-ALL patients and cell lines, and bioinformatics analysis implicated miR-146b-5p in the hematopoietic system. miR-146b-5p inhibited the migration and invasion in T-ALL cells. Interleukin-17A (IL-17A) was predicted to be a target of miR-146b-5p; this was confirmed by luciferase assays. Interestingly, T-ALL patients and cell lines secreted IL-17A and expressed the IL-17A receptor (IL-17RA). IL-17A/IL-17RA interactions promoted strong T-ALL cell migration and invasion responses. Gene set enrichment analysis (GSEA) and quantitative polymerase chain reaction (qPCR) analysis indicated that matrix metallopeptidase-9 (MMP9), was a potential downstream effector of IL-17A activation, and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling was also implicated in this process. Moreover, IL-17A activation promoted T-ALL cell metastasis to the liver in IL17A -/- mouse models. These results indicate that reduced miR-146b-5p expression in T-ALL may lead to the upregulation of IL-17A, which then promotes T-ALL cell migration and invasion by upregulating MMP9 via NF-κB signaling.
Collapse
Affiliation(s)
- Zhenbo Tu
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jie Xiong
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Ruijing Xiao
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Liang Shao
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiangyong Yang
- Department of Bioengineering, Hubei University of Technology Engineering and Technology College, Wuhan, China
| | - Lu Zhou
- Department of Hematology, Taihe Hospital, Shiyan, China
| | - Wen Yuan
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Meng Wang
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Qian Yin
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yingjie Wu
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Shan Pan
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jun Leng
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Daozi Jiang
- Department of Hematology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chunjiang He
- Department of Medical Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Qiuping Zhang
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan University, Wuhan, China
| |
Collapse
|
4
|
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
| |
Collapse
|