1
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Porcelli F, Casavola AR, Grottesi A, Schiumarini D, Avaldi L. Probing the conformational dynamics of an Ago-RNA complex in water/methanol solution. Phys Chem Chem Phys 2024; 26:2497-2508. [PMID: 38170800 DOI: 10.1039/d3cp05530b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Argonaute (Ago) proteins mediate target recognition guiding miRNA to bind complementary mRNA primarily in the seed region. However, additional pairing can occur beyond the seed, forming a supplementary duplex that can contribute to the guide-target affinity. In order to shed light on the connection, between protein-RNA interactions and miRNA-mRNA seed and supplementary duplex mobility, we carried out molecular dynamics simulations at the microsecond time-scale using a different approach compared to the ones normally used. Until now, theoretical investigations with classical MD on Ago-RNA complexes have been focused primarily on pure water solvent, which mimics the natural environment of biological molecules. Here, we explored the conformational space of a human Ago2 (hAgo2) bound to the seed + supplementary miRNA-mRNA duplex, using the solvent environment as a molecular probe. MD simulations have been performed in a mixture of water/MeOH at a molar ratio of 70 : 30 as well as in pure water for comparison. Our findings revealed that the mixed solvent promotes protein RNA association, principally enhancing salt-linkages between basic amino acid side-chains and acidic phosphates of the sugar-phosphate backbone. The primary effect registered was the restriction of supplementary duplex flexibility and the stabilization of the miRNA 3' terminus. Interestingly, we observed that the influence of the solvent appears to have almost no impact on the conformation of the seed duplex.
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Affiliation(s)
- Francesco Porcelli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy.
| | - Anna Rita Casavola
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy.
| | | | - Donatella Schiumarini
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy.
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 Monterotondo Scalo, Italy.
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2
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Huang J, Chan KC, Zhou R. Novel Inhibitory Role of Fenofibric Acid by Targeting Cryptic Site on the RBD of SARS-CoV-2. Biomolecules 2023; 13:biom13020359. [PMID: 36830728 PMCID: PMC9953482 DOI: 10.3390/biom13020359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
The emergence of the recent pandemic causing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created an alarming situation worldwide. It also prompted extensive research on drug repurposing to find a potential treatment for SARS-CoV-2 infection. An active metabolite of the hyperlipidemic drug fenofibrate (also called fenofibric acid or FA) was found to destabilize the receptor-binding domain (RBD) of the viral spike protein and therefore inhibit its binding to human angiotensin-converting enzyme 2 (hACE2) receptor. Despite being considered as a potential drug candidate for SARS-CoV-2, FA's inhibitory mechanism remains to be elucidated. We used molecular dynamics (MD) simulations to investigate the binding of FA to the RBD of the SARS-CoV-2 spike protein and revealed a potential cryptic FA binding site. Free energy calculations were performed for different FA-bound RBD complexes. The results suggest that the interaction of FA with the cryptic binding site of RBD alters the conformation of the binding loop of RBD and effectively reduces its binding affinity towards ACE2. Our study provides new insights for the design of SARS-CoV-2 inhibitors targeting cryptic sites on the RBD of SARS-CoV-2.
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Affiliation(s)
- Jianxiang Huang
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Kevin C. Chan
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai 201203, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai 201203, China
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Department of Chemistry, Colombia University, New York, NY 10027, USA
- Correspondence:
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3
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Zhu L, Jiang H, Cao S, Unarta IC, Gao X, Huang X. Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex. Commun Biol 2021; 4:1345. [PMID: 34848812 PMCID: PMC8632932 DOI: 10.1038/s42003-021-02822-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/26/2021] [Indexed: 01/02/2023] Open
Abstract
Despite its functional importance, the molecular mechanism underlying target mRNA recognition by Argonaute (Ago) remains largely elusive. Based on extensive all-atom molecular dynamics simulations, we constructed quasi-Markov State Model (qMSM) to reveal the dynamics during recognition at position 6-7 in the seed region of human Argonaute 2 (hAgo2). Interestingly, we found that the slowest mode of motion therein is not the gRNA-target base-pairing, but the coordination of the target phosphate groups with a set of positively charged residues of hAgo2. Moreover, the ability of Helix-7 to approach the PIWI and MID domains was found to reduce the effective volume accessible to the target mRNA and therefore facilitate both the backbone coordination and base-pair formation. Further mutant simulations revealed that alanine mutation of the D358 residue on Helix-7 enhanced a trap state to slow down the loading of target mRNA. Similar trap state was also observed when wobble pairs were introduced in g6 and g7, indicating the role of Helix-7 in suppressing non-canonical base-paring. Our study pointed to a general mechanism for mRNA recognition by eukaryotic Agos and demonstrated the promise of qMSM in investigating complex conformational changes of biomolecular systems.
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Affiliation(s)
- Lizhe Zhu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, 518172, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hanlun Jiang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Siqin Cao
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Ilona Christy Unarta
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xin Gao
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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4
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Feng M, Bell DR, Wang Z, Zhang W. Length-Dependent Structural Transformations of Huntingtin PolyQ Domain Upon Binding to 2D-Nanomaterials. Front Chem 2020; 8:299. [PMID: 32391325 PMCID: PMC7189795 DOI: 10.3389/fchem.2020.00299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/26/2020] [Indexed: 11/13/2022] Open
Abstract
There is a strong negative correlation between the polyglutamine (polyQ) domain length (Q-length) in the intrinsically disordered Huntingtin protein (Htt) exon-1 and the age of onset of Huntington's disease (HD). PolyQ of Q-length longer than 40 has the propensity of forming very compact aggregate structures, leading to HD at full penetrance. Recent advances in nanobiotechnology provided a new platform for the development of novel diagnosis and therapeutics. Here, we explore the possibility of utilizing 2D-nanomaterials to inhibit the formation of supercompact polyQ structures through the so-called “folding-upon-binding” where the protein structure is dependent on the binding substrate. Using molecular dynamics simulations, we characterize two polyQ peptides with Q-length of 22 (Q22, normal length) and 46 (Q46, typical length causing HD) binding to both graphene and molybdenum disulfide (MoS2) nanosheets, which have been applied as antibacterial or anticancer agents. Upon binding, Q22 unfolds and elongates on both grapheme and MoS2 surfaces, regardless of its initial conformation, with graphene showing slightly stronger effect. In contrast, initially collapsed Q46 remains mostly collapsed within our simulation time on both nanosheets even though they do provide some “stretching” to Q46 as well. Further analyses indicate that the hydrophobic nature of graphene/MoS2 promotes the stretching of polyQ on nanosheets. However, there is strong competition with the intra-polyQ interactions (mainly internal hydrogen bonds) leading to the disparate folding/binding behaviors of Q22 and Q46. Our results present distinct Q-length specific behavior of the polyQ domain upon binding to two types of 2D-nanomaterials which holds clinical relevance for Huntington's disease.
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Affiliation(s)
- Mei Feng
- Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou, China
| | - David R Bell
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY, United States
| | - Zhenhua Wang
- Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou, China
| | - Wei Zhang
- School of Materials and Physics, China University of Mining and Technology, Xuzhou, China
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5
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Zhang W, Chen Y, Huynh T, Yang Y, Yang X, Zhou R. Directional extraction and penetration of phosphorene nanosheets to cell membranes. NANOSCALE 2020; 12:2810-2819. [PMID: 31961358 DOI: 10.1039/c9nr09577b] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recently, phosphorene, a novel two-dimensional nanomaterial with a puckered surface morphology, was shown to exhibit cytotoxicity, but its underlying molecular mechanisms remain unknown. Herein, using large scale molecular dynamics simulations, we show that phosphorene nanosheets can penetrate into and extract large amounts of phospholipids from the cell membranes due to the strong dispersion interaction between phosphorene and lipid molecules, which would reduce cell viability. The extracted phospholipid molecules are aligned along the wrinkle direction of the phosphorene nanosheet because of its unique puckered structure. Our results also reveal that small phosphorene nanosheets penetrate into the cell membrane in a specific direction which is determined by the size and surface topography of phosphorene and the thickness of the membrane. These findings might shed light on understanding phosphorene's cytotoxicity and would be helpful for the future potential biomedical applications of phosphorene, such as biosensors and antibacterial agents.
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Affiliation(s)
- Wei Zhang
- School of Materials and Physics, China University of Mining and Technology, Xuzhou 221116, China.
| | - Yezhe Chen
- School of Materials and Physics, China University of Mining and Technology, Xuzhou 221116, China.
| | - Tien Huynh
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA.
| | - Yunqiu Yang
- School of Materials and Physics, China University of Mining and Technology, Xuzhou 221116, China.
| | - Xianqing Yang
- School of Materials and Physics, China University of Mining and Technology, Xuzhou 221116, China.
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA. and Department of Chemistry, Columbia University, New York, New York 10027, USA
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6
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Zou A, Lee S, Li J, Zhou R. Retained Stability of the RNA Structure in DNA Packaging Motor with a Single Mg2+ Ion Bound at the Double Mg-Clamp Structure. J Phys Chem B 2020; 124:701-707. [DOI: 10.1021/acs.jpcb.9b06428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Aodong Zou
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Sangyun Lee
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Jingyuan Li
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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7
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Gu Z, Chen SH, Ding Z, Song W, Wei W, Liu S, Ma G, Zhou R. The molecular mechanism of robust macrophage immune responses induced by PEGylated molybdenum disulfide. NANOSCALE 2019; 11:22293-22304. [PMID: 31746904 DOI: 10.1039/c9nr04358f] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molybdenum disulfide (MoS2), a representative hexagonal transition metal dichalcogenide (TMD), has been extensively exploited in biomedical applications due to its unique physicochemical properties and biocompatibility. However, the lack of adequate data regarding how MoS2 activates immunological responses of macrophages remains a key concern for its risk assessment. Here, we employ a combined theoretical and experimental approach to investigate the interactions of MoS2 and PEGylated MoS2 (MoS2-PEG) with macrophages. We first perform molecular dynamics simulations to examine the atomic-detailed interactions of MoS2 and MoS2-PEG nanoflakes with a realistic model of the macrophage membrane. We show that a small MoS2 nanoflake (edge length of 2.86 nm) is capable of penetrating the macrophage membrane independent of its concentration. We also demonstrate that when initiated with a corner point-on configuration, the surface-bound PEG chains of MoS2-PEG hinder its membrane insertion process, leading to a prolonged passage through the membrane. Moreover, when placed in a face-on arrangement initially, the MoS2-PEG exhibits a lower binding free energy than pristine MoS2 after its adsorption on the membrane surface. The PEG chains can even insert and get buried in the outer leaflet of the membrane, providing additional contact for membrane adsorption. Our flow cytometric experiments then show that the responses of macrophages to either MoS2-PEG or MoS2 are significantly higher than that of the control (no nanomaterial stimulus), with MoS2-PEG eliciting stronger cytokine secretion than the pristine MoS2. The characteristics of slower/prolonged membrane penetration and stronger membrane adsorption of MoS2-PEG compared to pristine MoS2 explain why it triggers more sustained stimulation and higher cytokine secretion in macrophages as observed in our experiments. Our findings reveal the underlying molecular mechanism of how MoS2-PEG influences the immune responses and suggest its potential applications in nanomedicine involving immune stimulation.
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Affiliation(s)
- Zonglin Gu
- Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
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8
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Perez-Aguilar JM, Kang SG, Zhang L, Zhou R. Modeling and Structural Characterization of the Sweet Taste Receptor Heterodimer. ACS Chem Neurosci 2019; 10:4579-4592. [PMID: 31553164 DOI: 10.1021/acschemneuro.9b00438] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Sweet taste receptor, a heterodimer belonging to the class C G-protein coupled receptor (GPCR) family and composed of the T1R2 and T1R3 subunits, is responsible for the perception of natural sugars, sweet proteins, various d-amino acids, as well as artificial sweeteners. Despite the critical importance of the sweet receptor not only in mediating gustation but also in its role in the food industry, the architecture of the T1R2-T1R3 complex and the mechanism by which extracellular stimuli induce conformational changes that are propagated to the intracellular milieu, i.e., the signal transduction pathway, remain largely unknown. Here, we constructed and characterized a full-length structural model of the T1R2-T1R3 receptor, including both the transmembrane (TM) and extracellular (EC) domains of the heterodimer, using comparative modeling and extensive all-atom molecular dynamics simulations. Several heterodimer interfaces were first examined for the TM domain, and conformational changes occurring at the intracellular side and associated with the receptor's activation were characterized. From the analysis on the simulated data, putative allosteric binding sites for ligands, ions, and cholesterol were proposed. Also, insights into the protein interface of the TM domain upon activation are provided. The EC domain of the heterodimer, including both the Venus flytrap and cysteine-rich domains, was also investigated. Several important intersubunit interactions located at regions responsible for the receptor's proper function were observed, which resemble those recently identified in other class C GPCR members. Integration of the results from the TM and EC domains facilitates the generation of a full-length T1R2-T1R3 receptor. These findings along with the full-length structural model of the T1R2-T1R3 receptor provide a structural framework that may assist in understanding the mechanistic details associated with the receptor activation process for the sweet T1R2-T1R3 receptor as well as other members of the same family.
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Affiliation(s)
- Jose Manuel Perez-Aguilar
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Seung-gu Kang
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Leili Zhang
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
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9
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Liu S, Yin X, Zhou H, Zhou B, Shao Q, Yang Z, Zhou R. Different platinum crystal surfaces show very distinct protein denaturation capabilities. NANOSCALE 2019; 11:19352-19361. [PMID: 31620747 DOI: 10.1039/c9nr03682b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Different platinum (Pt) surfaces of nanocrystals usually exhibit significant distinctions with regard to various biological, physical, and chemical characteristics, such as bio-recognition, surface wetting, and catalytic activities. In this study, we report for the first time that two shape-controlled Pt nanocrystals with the most common low-index surfaces, Pt(100) and Pt(111), show very dissimilar protein denaturation capabilities based on all-atom molecular dynamics simulations employing the widely used model protein, villin headpiece (HP35). We demonstrate that HP35 is well preserved on the Pt(100) crystal surface, whereas it is severely disrupted on the Pt(111) crystal surface. This surprising difference originates from the distinct water behavior in the first solvation shell (FSS) of the two Pt crystal surfaces. Within the FSS of the Pt(100) crystal surface, water molecules form a very compact and stable monolayer through a highly uniform rhombic hydrogen-bond network. This water monolayer prefers the adsorption of acidic residues (such as Glu and Asp) and acts as a shield to prevent other residues from directly coming into contact with the metal surface. On the other hand, the hydrogen bond network in the water monolayer in the FSS of the Pt(111) crystal surface is very sparse and quite defective, which makes it more vulnerable to the penetration of various residues, particularly those with planar side chains such as Phe, Trp and Arg due to strong dispersion interactions, leading to subsequent protein unfolding. The binding free energy calculations for some key amino acids on the two different crystal surfaces further uncover the molecular origin behind their distinct protein denaturation capability. Our study reveals the vital importance of interfacial water in determining the structure of proteins when binding to different metal crystal surfaces. The discovered molecular mechanisms may be helpful for the future development of a bio-assisted programmable synthetic strategy of sophisticated Pt nanostructures for biomedical applications.
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Affiliation(s)
- Shengtang Liu
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Xiuhua Yin
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Hong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Bo Zhou
- School of Electronic Engineering, Chengdu Technological University, Chengdu 611730, China
| | - Qiwen Shao
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China. and IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA and Department of Chemistry, Columbia University, New York, NY 10027, USA
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10
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Zhou H, Yang Z, Tian X, Chen L, Lee S, Huynh T, Ge C, Zhou R. Lanosterol Disrupts the Aggregation of Amyloid-β Peptides. ACS Chem Neurosci 2019; 10:4051-4060. [PMID: 31369236 DOI: 10.1021/acschemneuro.9b00285] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lanosterol, an amphipathic molecule, was discovered only very recently to effectively hinder the aggregation of lens proteins and dissolve the extremely stable fibrillar aggregates in cataracts. Here, we combined computational and experimental approaches to study how lanosterol disrupts the aggregation of another important peptide, amyloid-β (Aβ) peptide, associated with the Alzheimer's Disease (AD). Molecular dynamics simulations using the core amyloidogenic segment (KLVFFA) of Aβ peptide revealed that lanosterol exhibits at least two types of inhibition mechanism on the self-assembly of Aβ peptides. First, lanosterol entangles with peptides and forms a hydrophobic core with residues Phe-19 and Phe-20 in particular. Second, it interferes with the steric zipper interaction at the β-sheet-β-sheet interface. These simulation data suggest that lanosterol induces the unfolding of the Aβ peptide and the separation of the β-sheet layers. This predicted inhibition effect of lanosterol was then confirmed by an in vitro ThT fluorescence assay and AFM imaging. The cell toxicity assay also showed that the treatment of lanosterol indeed mitigates the cytotoxicity of the Aβ peptide in PC-12 cells. Moreover, lanosterol shows a stronger suppression effect on Aβ peptides' aggregation than cholesterol because of its higher hydrophobicity. This result establishes a foundation for the development of lanosterol-based potential therapies for AD and other protein conformational diseases.
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Affiliation(s)
- Hong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Xin Tian
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Lei Chen
- East District of Suzhou Municipal Hospital, Suzhou, Jiangsu 215001, China
| | - Sangyun Lee
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Tien Huynh
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Cuicui Ge
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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11
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Zhang L, Luan B, Zhou R. Parameterization of Molybdenum Disulfide Interacting with Water Using the Free Energy Perturbation Method. J Phys Chem B 2019; 123:7243-7252. [PMID: 31369702 DOI: 10.1021/acs.jpcb.9b02797] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Water contact angles (WCA) are often used to parametrize force field parameters of novel 2D nanomaterials, such as molybdenum disulfide (MoS2), which has emerged as a promising nanomaterial in many biomedical applications due to its unique and impressive properties. However, there is a wide range of water-MoS2 contact angles in the literature depending on the aging process on the surface of a MoS2 nanosheet and/or substrate material. In this study, we revisit and optimize existing parameters for the basal plane of MoS2 with two popular water models, TIP3P and SPC/E, using the wide range of WCAs from various experiments. We develop and deploy the free energy perturbation method for parametrizing MoS2 with experimentally determined WCAs for both fresh and aged surfaces. Energy decomposition analysis on the simulation trajectories reveals that MoS2-water interaction is dominated by van der Waals interaction, which mainly comes from the top layer of MoS2. We conclude that to describe both fresh and aged MoS2 surfaces it is convenient to only adjust the Lennard-Jones parameter εS (the depth of the potential well of a sulfur atom), which displays a surprisingly linear correlation with WCAs.
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Affiliation(s)
- Leili Zhang
- Computational Biology Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Binquan Luan
- Computational Biology Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Ruhong Zhou
- Computational Biology Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
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12
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Mallick B, Sharma AR, Lee SS, Chakraborty C. Understanding the molecular interaction of human argonaute-2 and miR-20a complex: A molecular dynamics approach. J Cell Biochem 2019; 120:19915-19924. [PMID: 31318096 DOI: 10.1002/jcb.29300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/18/2019] [Indexed: 12/16/2022]
Abstract
Argonaute-2 (AGO2), a member of the Argonaute family, is the only member possessing catalytic and RNA silencing activity. In here, a molecular dynamics (MDs) simulation was performed using the crystal structure of human AGO2 protein complex with miR-20a. miR-20a is involved with various kind of biological process like heart and lung development, oncogenic process, etc. In precise, MD simulation was carried out with AGO2 protein complex with wild type, two mutant sites and four mutant sites in guided microRNA (miRNA). It has been noted that root-mean-square deviation (RMSD) of atomic positions of nucleic acid for wild type and two mutant sites guided miRNA has the same pattern of fluctuations, which stabilizes around 0.27 nm after 2 ns. Cα atom of AGO2 protein in the complex shows that this complex with wild type and two mutant site mutation duplex has a stable RMSD value after 20 ns, ranging between 0.14 and 0.21 nm. From the root-mean-square fluctuation (RMSF), we observed an increased pattern of fluctuations for the atoms of four mutant complex of AGO2-miR-20a complex. This increased RMSF of non-mutated nucleic acids is contributed by U-A bond breaking at the site of the nucleotide of U2 of guided miRNA, as observed from the duplex structure taken at different time steps of the simulation. Superimposed structure of the miRNA-mRNA duplex for the three complexes depicts that the three miRNA-mRNA duplexes are stable during the simulation. Current work demonstrates the possible correlations between the conformational changes of this AGO2-miR-20a duplex structure and the interactions of different atoms.
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Affiliation(s)
- Bidyut Mallick
- Departments of Physics, Galgotias College of Engineering and Technology, Greater Noida, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do, Republic of Korea
| | - Chiranjib Chakraborty
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do, Republic of Korea.,Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India
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13
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Rigoutsos I, Londin E, Kirino Y. Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities. Curr Opin Biotechnol 2019; 58:202-210. [PMID: 31323485 DOI: 10.1016/j.copbio.2019.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/09/2019] [Accepted: 05/27/2019] [Indexed: 01/03/2023]
Abstract
We herein provide a brief review of the trajectory that the field of short RNA research followed in the last 25 years. We place emphasis on the unexpected discoveries and the ramifications of these discoveries for the field, as well as offer some thoughts about what the next 25 years may bring. Arguably, the uncovered dependence of different types of short RNAs on individual attributes such as a person's sex, population origin, race, and on tissue type, tissue state, and disease was most unexpected. This dependence has important ramifications in that it will provide a boost to our understanding of the molecular mechanisms of health disparities as well as pave the way for novel approaches to designing improved and personalized diagnostics and therapeutics.
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Affiliation(s)
- Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
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14
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Duan G, Chen L, Jing Z, De Luna P, Wen L, Zhang L, Zhao L, Xu J, Li Z, Yang Z, Zhou R. Robust Antibacterial Activity of Tungsten Oxide (WO 3-x) Nanodots. Chem Res Toxicol 2019; 32:1357-1366. [PMID: 31251039 DOI: 10.1021/acs.chemrestox.8b00399] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antibacterial agents are an important tool in the prevention of bacterial infections. Inorganic materials are attractive due to their high stability under a variety of conditions compared to organic antibacterial agents. Herein tungsten oxide nanodots (WO3-x), synthesized by a simple one-pot synthetic approach, were found to exhibit strong antibacterial capabilities. The analyses with colony-forming units (CFU) showed an excellent antibacterial activity of WO3-x against both Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus) strains. The scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images revealed clear damages to the bacterial cell membranes, which was further confirmed by molecular dynamics simulations. Additionally, exposure to simulated sunlight was found to further increase the germicidal activity of WO3-x nanodots, a 30 min exposure to sunlight combined with 50 μg/mL WO3-x nanodots showed a 70% decrease in E. coli viability compared to without exposure. Electron spin resonance spectroscopy (ESR) was used to elucidate the underlying mechanism of this photocatalytic activity through the generation of hydroxyl radical species. The cell counting kit-8 (CCK-8) and the live/dead assay were further employed to evaluate the cytotoxicity of WO3-x nanodots on eukaryotic cells, which demonstrated their general biocompatibility. In summary, our results suggest WO3-x nanodots have considerable potential in antibacterial applications, while also being biocompatible at large.
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Affiliation(s)
- Guangxin Duan
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China.,Center of Burn & Trauma , Affiliated Suzhou Hospital of Nanjing Medical University , Suzhou 215008 , China
| | - Lu Chen
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Zhifeng Jing
- IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Phil De Luna
- IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Ling Wen
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Leili Zhang
- IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Lin Zhao
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Jiaying Xu
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Zhen Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Zaixing Yang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Ruhong Zhou
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China.,IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States.,Department of Chemistry , Columbia University , New York , New York 10027 , United States
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15
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Ryan BC, Lowe K, Hanson L, Gil T, Braun L, Howard PL, Chow RL. Mapping the Pax6 3' untranslated region microRNA regulatory landscape. BMC Genomics 2018; 19:820. [PMID: 30442116 PMCID: PMC6238409 DOI: 10.1186/s12864-018-5212-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 10/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND PAX6 is a homeodomain transcription factor that acts in a highly dosage-sensitive manner to regulate the development and function of the eyes, nose, central nervous system, gut, and endocrine pancreas. Several individual microRNAs (miRNA) have been implicated in regulating PAX6 in different cellular contexts, but a more general view of how they contribute to the fine-tuning and homeostasis of PAX6 is poorly understood. RESULTS Here, a comprehensive analysis of the Pax6 3' untranslated region was performed to map potential miRNA recognition elements and served as a backdrop for miRNA expression profiling experiments to identify potential cell/tissue-specific miRNA codes. Pax6 3'UTR pull-down studies identified a cohort of miRNA interactors in pancreatic αTC1-6 cells that, based on the spacing of their recognition sites in the Pax6 3'UTR, revealed 3 clusters where cooperative miRNA regulation may occur. Some of these interacting miRNAs have been implicated in α cell function but have not previously been linked to Pax6 function and may therefore represent novel PAX6 regulators. CONCLUSIONS These findings reveal a regulatory landscape upon which miRNAs may participate in the developmental control, fine-tuning and/or homeostasis of PAX6 levels.
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Affiliation(s)
- Bridget C. Ryan
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Kieran Lowe
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Laura Hanson
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Talveen Gil
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Lauren Braun
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Perry L. Howard
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2 Canada
| | - Robert L. Chow
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
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16
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Zhou H, Liu S, Shao Q, Ma D, Yang Z, Zhou R. Mechanism by which DHA inhibits the aggregation of KLVFFA peptides: A molecular dynamics study. J Chem Phys 2018; 148:115102. [PMID: 29566504 DOI: 10.1063/1.5012032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Docosahexaenoic acid (DHA) is one of the omega-3 polyunsaturated fatty acids, which has shown promising applications in lowering Aβ peptide neurotoxicity in vitro by preventing aggregation of Aβ peptides and relieving accumulation of Aβ fibrils. Unfortunately, the underlying molecular mechanisms of how DHA interferes with the aggregation of Aβ peptides remain largely enigmatic. Herein, aggregation behaviors of amyloid-β(Aβ)16-21 peptides (KLVFFA) with or without the presence of a DHA molecule were comparatively studied using extensive all-atom molecular dynamics simulations. We found that DHA could effectively suppress the aggregation of KLVFFA peptides by redirecting peptides to unstructured oligomers. The highly hydrophobic and flexible nature of DHA made it randomly but tightly entangled with Leu-17, Phe-19, and Phe-20 residues to form unstructured but stable complexes. These lower-ordered unstructured oligomers could eventually pass through energy barriers to form ordered β-sheet structures through large conformational fluctuations. This study depicts a microscopic picture for understanding the role and mechanism of DHA in inhibition of aggregation of Aβ peptides, which is generally believed as one of the important pathogenic mechanisms of Alzheimer's disease.
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Affiliation(s)
- Hong Zhou
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Jiangsu 215123, China
| | - Shengtang Liu
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Jiangsu 215123, China
| | - Qiwen Shao
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Jiangsu 215123, China
| | - Dongfang Ma
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Jiangsu 215123, China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Jiangsu 215123, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Jiangsu 215123, China
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17
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Liu Y, Yu Z, Zhu J, Wang S, Xu D, Han W. Why Is a High Temperature Needed by Thermus thermophilus Argonaute During mRNA Silencing: A Theoretical Study. Front Chem 2018; 6:223. [PMID: 29967763 PMCID: PMC6016274 DOI: 10.3389/fchem.2018.00223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/28/2018] [Indexed: 12/26/2022] Open
Abstract
Thermus thermophiles Argonaute (TtAgo) is a complex, which is consisted of 5′-phosphorylated guide DNA and a series of target DNA with catalytic activities at high temperatures. To understand why high temperatures are needed for the catalytic activities, three molecular dynamics simulations and binding free energy calculations at 310, 324, and 338K were performed for the TtAgo-DNA complex to explore the conformational changes between 16-mer guide DNA/15-mer target DNA and TtAgo at different temperatures. The simulation results indicate that a collapse of a small β-strand (residues 507–509) at 310 K caused Glu512 to move away from the catalytic residues Asp546 and Asp478, resulting in a decrease in catalytic activity, which was not observed in the simulations at 324 and 338 K. The nucleic acid binding channel became enlarged at 324 and 338K, thereby facilitating the DNA to slide in. Binding free energy calculations and hydrogen bond occupancy indicated that the interaction between TtAgo and the DNA was more stable at 324K and 338K than at 310 K. The DNA binding pocket residues Lys575 and Asn590 became less solvent accessible at 324 and 338K than at 310 K to influence hydrophilic interaction with DNA. Our simulation studies shed some light on the mechanism of TtAgo and explained why a high temperature was needed by TtAgo during gene editing of CRISPR.
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Affiliation(s)
- Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Zhengfei Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Song Wang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Dong Xu
- Department of Electric Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.,College of Computer Science and Technology, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
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18
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Clark PM, Chitnis N, Shieh M, Kamoun M, Johnson FB, Monos D. Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex. Sci Rep 2018; 8:3832. [PMID: 29497078 PMCID: PMC5832780 DOI: 10.1038/s41598-018-19427-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/23/2017] [Indexed: 02/06/2023] Open
Abstract
The MHC is recognized for its importance in human health and disease. However, many disease-associated variants throughout the region remain of unknown significance, residing predominantly within non-coding regions of the MHC. The characterization of non-coding RNA transcripts throughout the MHC is thus central to understanding the genetic contribution of these variants. Therefore, we characterize novel miRNA transcripts throughout the MHC by performing deep RNA sequencing of two B lymphoblastoid cell lines with completely characterized MHC haplotypes. Our analysis identifies 89 novel miRNA transcripts, 48 of which undergo Dicer-dependent biogenesis and are loaded onto the Argonaute silencing complex. Several of the identified mature miRNA and pre-miRNA transcripts are unique to specific MHC haplotypes and overlap common SNPs. Furthermore, 43 of the 89 identified novel miRNA transcripts lie within linkage disequilibrium blocks that contain a disease-associated SNP. These disease associated SNPs are associated with 65 unique disease phenotypes, suggesting that these transcripts may play a role in the etiology of numerous diseases associated with the MHC. Additional in silico analysis reveals the potential for thousands of putative pre-miRNA encoding loci within the MHC that may be expressed by different cell types and at different developmental stages.
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Affiliation(s)
- P M Clark
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - N Chitnis
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - M Shieh
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - M Kamoun
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - F B Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - D Monos
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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19
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Alagia A, Jorge AF, Aviñó A, Cova TFGG, Crehuet R, Grijalvo S, Pais AACC, Eritja R. Exploring PAZ/3'-overhang interaction to improve siRNA specificity. A combined experimental and modeling study. Chem Sci 2018; 9:2074-2086. [PMID: 29719684 PMCID: PMC5896489 DOI: 10.1039/c8sc00010g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/15/2018] [Indexed: 12/29/2022] Open
Abstract
The understanding of the dynamical and mechanistic aspects that lie behind siRNA-based gene regulation is a requisite to boost the performance of siRNA therapeutics. A systematic experimental and computational study on the 3'-overhang structural requirements for the design of more specific and potent siRNA molecules was carried out using nucleotide analogues differing in structural parameters, such as sugar constraint, lack of nucleobase, distance between the phosphodiester backbone and nucleobase, enantioselectivity, and steric hindrance. The results established a set of rules governing the siRNA-mediated silencing, indicating that the thermodynamic stability of the 5'-end is a crucial determinant for antisense-mediated silencing but is not sufficient to avoid sense-mediated silencing. Both theoretical and experimental approaches consistently evidence the existence of a direct connection between the PAZ/3'-overhang binding affinity and siRNA's potency and specificity. An overall description of the systems is thus achieved by atomistic simulations and free energy calculations that allow us to propose a robust and self-contained procedure for studying the factors implied in PAZ/3'-overhang siRNA interactions. A higher RNAi activity is associated with a moderate-to-strong PAZ/3'-overhang binding. Contrarily, lower binding energies compromise siRNA potency, increase specificity, and favor siRNA downregulation by Ago2-independent mechanisms. This work provides in-depth details for the design of powerful and safe synthetic nucleotide analogues for substitution at the 3'-overhang, enabling some of the intrinsic siRNA disadvantages to be overcome.
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Affiliation(s)
- Adele Alagia
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
| | - Andreia F Jorge
- CQC , Department of Chemistry , University of Coimbra , Rua Larga , 3004-535 Coimbra , Portugal .
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
| | - Tânia F G G Cova
- CQC , Department of Chemistry , University of Coimbra , Rua Larga , 3004-535 Coimbra , Portugal .
| | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
| | - Santiago Grijalvo
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
| | - Alberto A C C Pais
- CQC , Department of Chemistry , University of Coimbra , Rua Larga , 3004-535 Coimbra , Portugal .
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
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20
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Fang G, Li W, Shen X, Perez-Aguilar JM, Chong Y, Gao X, Chai Z, Chen C, Ge C, Zhou R. Differential Pd-nanocrystal facets demonstrate distinct antibacterial activity against Gram-positive and Gram-negative bacteria. Nat Commun 2018; 9:129. [PMID: 29317632 PMCID: PMC5760645 DOI: 10.1038/s41467-017-02502-3] [Citation(s) in RCA: 269] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 12/05/2017] [Indexed: 02/08/2023] Open
Abstract
Noble metal-based nanomaterials have shown promise as potential enzyme mimetics, but the facet effect and underlying molecular mechanisms are largely unknown. Herein, with a combined experimental and theoretical approach, we unveil that palladium (Pd) nanocrystals exhibit facet-dependent oxidase and peroxidase-like activities that endow them with excellent antibacterial properties via generation of reactive oxygen species. The antibacterial efficiency of Pd nanocrystals against Gram-positive bacteria is consistent with the extent of their enzyme-like activity, that is {100}-faceted Pd cubes with higher activities kill bacteria more effectively than {111}-faceted Pd octahedrons. Surprisingly, a reverse trend of antibacterial activity is observed against Gram-negative bacteria, with Pd octahedrons displaying stronger penetration into bacterial membranes than Pd nanocubes, thereby exerting higher antibacterial activity than the latter. Our findings provide a deeper understanding of facet-dependent enzyme-like activities and might advance the development of noble metal-based nanomaterials with both enhanced and targeted antibacterial activities.
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Affiliation(s)
- Ge Fang
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
| | - Weifeng Li
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
| | - Xiaomei Shen
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, China
| | | | - Yu Chong
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
| | - Xingfa Gao
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhifang Chai
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
| | - Chunying Chen
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China and Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Cuicui Ge
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China.
| | - Ruhong Zhou
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China.
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York, 10598, USA.
- Department of Chemistry, Columbia University, New York, New York, 10027, USA.
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21
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Gu Z, Song W, Yang Z, Zhou R. Metal–organic framework as an efficient filter for the removal of heavy metal cations in water. Phys Chem Chem Phys 2018; 20:30384-30391. [DOI: 10.1039/c8cp05129a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Efficient removal of heavy metal cations by a zirconium phosphonate based metal–organic framework (MOF) filter.
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Affiliation(s)
- Zonglin Gu
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University
- Suzhou 215123
- China
| | - Wei Song
- Institute of Quantitative Biology, Department of Physics, Zhejiang University
- Hangzhou 310027
- China
| | - Zaixing Yang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University
- Suzhou 215123
- China
| | - Ruhong Zhou
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University
- Suzhou 215123
- China
- IBM Thomas J. Watson Research Center
- Yorktown Heights
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22
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Park JH, Shin SY, Shin C. Non-canonical targets destabilize microRNAs in human Argonautes. Nucleic Acids Res 2017; 45:1569-1583. [PMID: 28119422 PMCID: PMC5389725 DOI: 10.1093/nar/gkx029] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/15/2017] [Indexed: 01/06/2023] Open
Abstract
Although much is known about microRNA (miRNA) biogenesis and the mechanism by which miRNAs regulate their targets, little is known about the regulation of miRNA stability. Mature miRNAs are stabilized by binding to Argonaute (Ago) proteins, the core components of the RNA-induced silencing complex (RISC). Recent studies suggest that interactions between miRNAs and their highly complementary target RNAs promote release of miRNAs from Ago proteins, and this in turn can lead to destabilization of miRNAs. However, the physiological triggers of miRNA destabilization with molecular mechanisms remain largely unknown. Here, using an in vitro system that consists of a minimal human Ago2-RISC in HEK293T cell lysates, we sought to understand how miRNAs are destabilized by their targets. Strikingly, we showed that miRNA destabilization is dramatically enhanced by an interaction with seedless, non-canonical targets. We then showed that this process entails not only unloading of miRNAs from Ago, but also 3΄ end destabilization of miRNAs occurred within Ago. Furthermore, our mutation analysis indicates that conformational changes in the hinge region of the Ago PAZ domain are likely to be the main driving force of the miRNA destabilization. Our collective results suggest that non-canonical targets may provide a stability control mechanism in the regulation of miRNAs in humans.
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Affiliation(s)
- June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang-Yoon Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
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23
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Kong R, Xu L, Piao L, Zhang D, Hou TJ, Chang S. Exploring the RNA-bound and RNA-free human Argonaute-2 by molecular dynamics simulation method. Chem Biol Drug Des 2017; 90:753-763. [PMID: 28388001 DOI: 10.1111/cbdd.12997] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 03/22/2017] [Accepted: 04/03/2017] [Indexed: 01/21/2023]
Abstract
Argonaute 2 (Ago2) protein is the major vehicle of microRNAs (miRNAs)-guided gene repression and silencing processes. Although the crystal structure of human Ago2 (hAgo2) has recently been disclosed, the information of dynamically structural character of protein-RNA recognition is still lacking. Molecular dynamics simulations were used to systematically explore hAgo2 in the presence and absence of RNA duplex. Stable direct and water-mediated hydrogen bonds were observed between guide RNA backbone atoms and hAgo2, especially for nucleotides 2-7. In addition, water-mediated hydrogen bonds are indicated to be critical in the specific recognition between hAgo2 and the conserved adenine in position 1 of target RNA. The core domains (N, PAZ, MID, and PIWI) possess rigid body movements during the simulations. The motions of N-PAZ and PIWI-MID are negatively correlated with or without RNA binding and PAZ domain is identified as the most mobile domain in both systems. The reorientation of PAZ domain not only influences the binding of helix-7 and RNA duplex, the initial pairing process, but also the shape of N-PAZ cleft, where the supplemental base pairing occurs. It is speculated that PAZ domain could be a key regulator in hAgo2-mediated miRNA-induced gene regulation.
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Affiliation(s)
- Ren Kong
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Lei Xu
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Lianhua Piao
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Dawei Zhang
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Ting-Jun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shan Chang
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
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24
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Zhang L, Kang H, Vázquez FX, Toledo-Sherman L, Luan B, Zhou R. Molecular Mechanism of Stabilizing the Helical Structure of Huntingtin N17 in a Micellar Environment. J Phys Chem B 2017; 121:4713-4721. [DOI: 10.1021/acs.jpcb.7b01476] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leili Zhang
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | - Hongsuk Kang
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | - Francisco X. Vázquez
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | | | - Binquan Luan
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | - Ruhong Zhou
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
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25
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Harikrishna S, Pradeepkumar PI. Probing the Binding Interactions between Chemically Modified siRNAs and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations. J Chem Inf Model 2017; 57:883-896. [DOI: 10.1021/acs.jcim.6b00773] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- S. Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai−400076, India
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai−400076, India
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26
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Duan G, Zhang Y, Luan B, Weber JK, Zhou RW, Yang Z, Zhao L, Xu J, Luo J, Zhou R. Graphene-Induced Pore Formation on Cell Membranes. Sci Rep 2017; 7:42767. [PMID: 28218295 PMCID: PMC5317030 DOI: 10.1038/srep42767] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/13/2017] [Indexed: 01/21/2023] Open
Abstract
Examining interactions between nanomaterials and cell membranes can expose underlying mechanisms of nanomaterial cytotoxicity and guide the design of safer nanomedical technologies. Recently, graphene has been shown to exhibit potential toxicity to cells; however, the molecular processes driving its lethal properties have yet to be fully characterized. We here demonstrate that graphene nanosheets (both pristine and oxidized) can produce holes (pores) in the membranes of A549 and Raw264.7 cells, substantially reducing cell viability. Electron micrographs offer clear evidence of pores created on cell membranes. Our molecular dynamics simulations reveal that multiple graphene nanosheets can cooperate to extract large numbers of phospholipids from the membrane bilayer. Strong dispersion interactions between graphene and lipid-tail carbons result in greatly depleted lipid density within confined regions of the membrane, ultimately leading to the formation of water-permeable pores. This cooperative lipid extraction mechanism for membrane perforation represents another distinct process that contributes to the molecular basis of graphene cytotoxicity.
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Affiliation(s)
- Guangxin Duan
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Yuanzhao Zhang
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Binquan Luan
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Jeffrey K Weber
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Royce W Zhou
- Department of Oncology, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, 213003, China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Lin Zhao
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Jiaying Xu
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Judong Luo
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.,Department of Oncology, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, 213003, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.,IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA.,Department of Chemistry, Columbia University, New York, NY 10027, USA
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27
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Liu X, Duan G, Li W, Zhou Z, Zhou R. Membrane destruction-mediated antibacterial activity of tungsten disulfide (WS2). RSC Adv 2017. [DOI: 10.1039/c7ra06442j] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tungsten disulfide (WS2) demonstrates clear antibacterial activity through inducing mechanical damage to the bacteria membrane integrity.
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Affiliation(s)
- Xu Liu
- Institute of Quantitative Biology and Medicine
- SRMP and RAD-X
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou 215123
| | - Guangxin Duan
- Institute of Quantitative Biology and Medicine
- SRMP and RAD-X
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou 215123
| | - Weifeng Li
- Institute of Quantitative Biology and Medicine
- SRMP and RAD-X
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou 215123
| | - Zhufa Zhou
- College of Chemistry
- Chemical Engineering and Material Science
- Soochow University
- Suzhou 215123
- China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine
- SRMP and RAD-X
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou 215123
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28
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Gu Z, De Luna P, Yang Z, Zhou R. Structural influence of proteins upon adsorption to MoS2 nanomaterials: comparison of MoS2 force field parameters. Phys Chem Chem Phys 2017; 19:3039-3045. [DOI: 10.1039/c6cp05260f] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molybdenum disulfide (MoS2) has recently emerged as a promising nanomaterial in a wide range of applications due to its unique and impressive properties.
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Affiliation(s)
- Zonglin Gu
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
| | - Phil De Luna
- Computational Biological Center
- IBM Thomas J. Watson Research Center
- Yorktown Heights
- USA
| | - Zaixing Yang
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
| | - Ruhong Zhou
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
- Computational Biological Center
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29
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Zhu L, Jiang H, Sheong FK, Cui X, Wang Y, Gao X, Huang X. Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 128:39-46. [PMID: 27697475 DOI: 10.1016/j.pbiomolbio.2016.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 09/04/2016] [Accepted: 09/26/2016] [Indexed: 12/14/2022]
Abstract
At the core of RNA interference, the Argonaute proteins (Ago) load and utilize small guide nucleic acids to silence mRNAs or cleave foreign nucleic acids in a sequence specific manner. In recent years, based on extensive structural studies of Ago and its interaction with the nucleic acids, considerable progress has been made to reveal the dynamic aspects of various Ago-mediated processes. Here we review these novel insights into the guide-strand loading, duplex unwinding, and effects of seed mismatch, with a focus on two representative Agos, the human Ago 2 (hAgo2) and the bacterial Thermus thermophilus Ago (TtAgo). In particular, comprehensive molecular simulation studies revealed that although sharing similar overall structures, the two Agos have vastly different conformational landscapes and guide-strand loading mechanisms because of the distinct rigidity of their L1-PAZ hinge. Given the central role of the PAZ motions in regulating the exposure of the nucleic acid binding channel, these findings exemplify the importance of protein motions in distinguishing the overlapping, yet distinct, mechanisms of Ago-mediated processes in different organisms.
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Affiliation(s)
- Lizhe Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hanlun Jiang
- Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Fu Kit Sheong
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuefeng Cui
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, 23955, Saudi Arabia
| | - Yanli Wang
- Laboratory of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, 23955, Saudi Arabia
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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30
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Mogilyansky E, Clark P, Quann K, Zhou H, Londin E, Jing Y, Rigoutsos I. Post-transcriptional Regulation of BRCA2 through Interactions with miR-19a and miR-19b. Front Genet 2016; 7:143. [PMID: 27630665 PMCID: PMC5005319 DOI: 10.3389/fgene.2016.00143] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/21/2016] [Indexed: 12/31/2022] Open
Abstract
Breast cancer type 2, early onset susceptibility gene (BRCA2) is a major component of the homologous recombination DNA repair pathway. It acts as a tumor suppressor whose function is often lost in cancers. Patients with specific mutations in the BRCA2 gene often display discrete clinical, histopathological, and molecular features. However, a subset of sporadic cancers has wild type BRCA2 and display defects in the homology-directed repair pathway, which is the hallmark of ‘BRCAness.’ The mechanisms by which BRCAness arises are not well understood but post-transcriptional regulation of BRCA2 gene expression by microRNAs (miRNAs) may contribute to this phenotype. Here, we examine the post-transcriptional effects that some members of the six-miRNA cluster known as the miR-17/92 cluster have on the abundance of BRCA2’s messenger RNA (mRNA) and protein. We discuss two interactions involving the miR-19a and miR-19b members of the cluster and the 3′UTR of BRCA2’s mRNA. We investigated these miRNA:mRNA interactions in 15 cell lines derived from pancreatic, breast, colon, and kidney tissue. We show that over-expression of these two miRNAs results in a concomitant decrease of BRCA2’s mRNA and protein expression in a subset of the tested cell lines. Additionally, using luciferase reporter assays we identified direct interactions between miR-19a/miR-19b and a miRNA response element (MRE) in BRCA2’s 3′UTR. Our results suggest that BRCA2 is subject to a complex post-transcriptional regulatory program that has specific dependencies on the genetic and phenotypic background of cell types.
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Affiliation(s)
- Elena Mogilyansky
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
| | - Peter Clark
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia PA, USA
| | - Kevin Quann
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
| | - Honglei Zhou
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
| | - Yi Jing
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
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31
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Robust Denaturation of Villin Headpiece by MoS2 Nanosheet: Potential Molecular Origin of the Nanotoxicity. Sci Rep 2016; 6:28252. [PMID: 27312409 PMCID: PMC4911589 DOI: 10.1038/srep28252] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/02/2016] [Indexed: 12/13/2022] Open
Abstract
MoS2 nanosheet, a new two-dimensional transition metal dichalcogenides nanomaterial, has attracted significant attentions lately due to many potential promising biomedical applications. Meanwhile, there is also a growing concern on its biocompatibility, with little known on its interactions with various biomolecules such as proteins. In this study, we use all-atom molecular dynamics simulations to investigate the interaction of a MoS2 nanosheet with Villin Headpiece (HP35), a model protein widely used in protein folding studies. We find that MoS2 exhibits robust denaturing capability to HP35, with its secondary structures severely destroyed within hundreds of nanosecond simulations. Both aromatic and basic residues are critical for the protein anchoring onto MoS2 surface, which then triggers the successive protein unfolding process. The main driving force behind the adsorption process is the dispersion interaction between protein and MoS2 monolayer. Moreover, water molecules at the interface between some key hydrophobic residues (e.g. Trp-64) and MoS2 surface also help to accelerate the process driven by nanoscale drying, which provides a strong hydrophobic force. These findings might have shed new light on the potential nanotoxicity of MoS2 to proteins with atomic details, which should be helpful in guiding future biomedical applications of MoS2 with its nanotoxicity mitigated.
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32
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Zhu L, Jiang H, Sheong FK, Cui X, Gao X, Wang Y, Huang X. A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus thermophilus. J Phys Chem B 2016; 120:2709-20. [PMID: 26908081 DOI: 10.1021/acs.jpcb.5b12426] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Argonaute proteins (Ago) are core components of the RNA Induced Silencing Complex (RISC) that load and utilize small guide nucleic acids to silence mRNAs or cleave foreign DNAs. Despite the essential role of Ago in gene regulation and defense against virus, the molecular mechanism of guide-strand loading into Ago remains unclear. We explore such a mechanism in the bacterium Thermus thermophilus Ago (TtAgo), via a computational approach combining molecular dynamics, bias-exchange metadynamics, and protein-DNA docking. We show that apo TtAgo adopts multiple closed states that are unable to accommodate guide-DNA. Conformations able to accommodate the guide are beyond the reach of thermal fluctuations from the closed states. These results suggest an induced-fit dominant mechanism for guide-strand loading in TtAgo, drastically different from the two-step mechanism for human Ago 2 (hAgo2) identified in our previous study. Such a difference between TtAgo and hAgo2 is found to mainly originate from the distinct rigidity of their L1-PAZ hinge. Further comparison among known Ago structures from various species indicates that the L1-PAZ hinge may be flexible in general for prokaryotic Ago's but rigid for eukaryotic Ago's.
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Affiliation(s)
| | | | | | - Xuefeng Cui
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology , Thuwal 23955-6900, Saudi Arabia
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology , Thuwal 23955-6900, Saudi Arabia
| | - Yanli Wang
- Laboratory of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
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33
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Leoni G, Tramontano A. A structural view of microRNA-target recognition. Nucleic Acids Res 2016; 44:e82. [PMID: 26825463 PMCID: PMC4872079 DOI: 10.1093/nar/gkw043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 01/14/2016] [Indexed: 11/14/2022] Open
Abstract
It is well established that the correct identification of the messenger RNA targeted by a given microRNA (miRNA) is a difficult problem, and that available methods all suffer from low specificity. We hypothesize that the correct identification of the pairing should take into account the effect of the Argonaute protein (AGO), an essential catalyst of the recognition process. Therefore, we developed a strategy named MiREN for building and scoring three-dimensional models of the ternary complex formed by AGO, a miRNA and 22 nt of a target mRNA that putatively interacts with it. We show here that MiREN can be used to assess the likelihood that an RNA molecule is the target of a given miRNA and that this approach is more accurate than other existing methods, usually based on sequence or sequence-related features. Our results also suggest that AGO plays a relevant role in the selection of the miRNA targets. Our method can represent an additional step for refining predictions made by faster but less accurate classical methods for the identification of miRNA targets.
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Affiliation(s)
- Guido Leoni
- Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy
| | - Anna Tramontano
- Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy Istituto Pasteur-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy
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34
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Jin YY, Andrade J, Wickstrom E. Non-Specific Blocking of miR-17-5p Guide Strand in Triple Negative Breast Cancer Cells by Amplifying Passenger Strand Activity. PLoS One 2015; 10:e0142574. [PMID: 26629823 PMCID: PMC4667903 DOI: 10.1371/journal.pone.0142574] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/24/2015] [Indexed: 12/18/2022] Open
Abstract
Conventional wisdom holds that only one of the two strands in a micro ribonucleic acid (miRNA) precursor duplex is selected as the active miRNA guide strand. The complementary miRNA passenger strand, however, is thought to be inactive. High levels of the oncogenic miRNA (oncomiR) guide strand called miR-17-5p is overexpressed in triple negative breast cancer (TNBC) and can inhibit ribosomal translation of tumor suppressor gene mRNAs, such as programmed cell death 4 (PDCD4) or phosphatase and tensin homolog (PTEN). We hypothesized that knocking down the oncogenic microRNA (oncomiR) miR-17-5p might restore the expression levels of PDCD4 and PTEN tumor suppressor proteins, illustrating a route to oligonucleotide therapy of TNBC. Contrary to conventional wisdom, antisense knockdown of oncomiR miR-17-5p guide strand reduced PDCD4 and PTEN proteins by 1.8±0.3 fold in human TNBC cells instead of raising them. Bioinformatics analysis and folding energy calculations revealed that mRNA targets of miR-17-5p guide strand, such as PDCD4 and PTEN, could also be regulated by miR-17-3p passenger strand. Due to high sequence homology between the antisense molecules and miR-17-3p passenger strand, as well as the excess binding sites for the passenger strand on the 3’UTR of PDCD4 and PTEN mRNAs, introducing a miR-17-3p DNA-LNA mimic to knock down miR-17-5p reduced PDCD4 and PTEN protein expression instead of raising them. Our results imply that therapeutic antisense sequences against miRNAs should be designed to target the miRNA strand with the greatest number of putative binding sites in the target mRNAs, while minimizing affinity for the minor strand.
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Affiliation(s)
- Yuan-Yuan Jin
- Biochemistry & Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Jade Andrade
- Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Eric Wickstrom
- Biochemistry & Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
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35
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Dysregulated co-stimulatory molecule expression in a Sjögren's syndrome mouse model with potential implications by microRNA-146a. Mol Immunol 2015; 68:606-16. [PMID: 26505653 DOI: 10.1016/j.molimm.2015.09.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 01/04/2023]
Abstract
Sjögren's syndrome (SjS) is an autoimmune condition that primarily affects salivary and lacrimal glands, causing loss of secretion. We have previously shown that microRNA-146a (miR-146a) is over-expressed in the salivary glands and peripheral blood mononuclear cells (PBMC) of SjS-prone mice (C57BL/6.NOD-Aec1Aec2, B6DC) and in PBMC of SjS patients. The purpose of this research was to identify a target molecule of miR-146a and identify subpopulations of cells affected by altered miR-146a in the salivary glands of SjS-prone mice. In silico analyses identified costimulatory molecule CD80 as a potential target of miR-146a. Luciferase assay of the human CD80 3'untranslated region demonstrated miR-146a directly inhibited CD80 protein expression as indicated by reduced luciferase reporter expression and an examination of B6DC salivary glands revealed a reduction in CD80 protein. More interestingly, the specific reduction in CD80 protein was detected from the salivary gland epithelial cell population and in interstitial dendritic cells in the glands as well. The reduction in CD80 protein levels in salivary gland epithelial cells were negatively associated with elevated miR-146a expression. Therefore, this study provides the first indication that salivary gland epithelial cells may be critically involved in SjS progression by altering CD86:CD80 protein ratio in response to miR-146a upregulation.
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36
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Telonis AG, Loher P, Jing Y, Londin E, Rigoutsos I. Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity. Nucleic Acids Res 2015; 43:9158-75. [PMID: 26400174 PMCID: PMC4627084 DOI: 10.1093/nar/gkv922] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 09/04/2015] [Indexed: 12/21/2022] Open
Abstract
Here we describe our study of miRNA isoforms (isomiRs) in breast cancer (BRCA) and normal breast data sets from the Cancer Genome Atlas (TCGA) repository. We report that the full isomiR profiles, from both known and novel human-specific miRNA loci, are particularly rich in information and can distinguish tumor from normal tissue much better than the archetype miRNAs. IsomiR expression is also dependent on the patient's race, exemplified by miR-183-5p, several isomiRs of which are upregulated in triple negative BRCA in white but not black women. Additionally, we find that an isomiR's 5′ endpoint and length, but not the genomic origin, are key determinants of the regulation of its expression. Overexpression of distinct miR-183-5p isomiRs in MDA-MB-231 cells followed by microarray analysis revealed that each isomiR has a distinct impact on the cellular transcriptome. Parallel integrative analysis of mRNA expression from BRCA data sets of the TCGA repository demonstrated that isomiRs can distinguish between the luminal A and luminal B subtypes and explain in more depth the molecular differences between them than the archetype molecules. In conclusion, our findings provide evidence that post-transcriptional studies of BRCA will benefit from transcending the one-locus-one-miRNA paradigm and taking into account all isoforms from each miRNA locus as well as the patient's race.
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Affiliation(s)
- Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Yi Jing
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
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Jiang H, Sheong FK, Zhu L, Gao X, Bernauer J, Huang X. Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement. PLoS Comput Biol 2015; 11:e1004404. [PMID: 26181723 PMCID: PMC4504477 DOI: 10.1371/journal.pcbi.1004404] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/16/2015] [Indexed: 01/17/2023] Open
Abstract
Argonaute (Ago) proteins and microRNAs (miRNAs) are central components in RNA interference, which is a key cellular mechanism for sequence-specific gene silencing. Despite intensive studies, molecular mechanisms of how Ago recognizes miRNA remain largely elusive. In this study, we propose a two-step mechanism for this molecular recognition: selective binding followed by structural re-arrangement. Our model is based on the results of a combination of Markov State Models (MSMs), large-scale protein-RNA docking, and molecular dynamics (MD) simulations. Using MSMs, we identify an open state of apo human Ago-2 in fast equilibrium with partially open and closed states. Conformations in this open state are distinguished by their largely exposed binding grooves that can geometrically accommodate miRNA as indicated in our protein-RNA docking studies. miRNA may then selectively bind to these open conformations. Upon the initial binding, the complex may perform further structural re-arrangement as shown in our MD simulations and eventually reach the stable binary complex structure. Our results provide novel insights in Ago-miRNA recognition mechanisms and our methodology holds great potential to be widely applied in the studies of other important molecular recognition systems. In RNA interference, Argonaute proteins and microRNAs together form the functional core that regulates the gene expression with high sequence specificity. Elucidating the detailed mechanism of molecular recognition between Argonaute proteins and microRNAs is thus important not only for the fundamental understanding of RNA interference, but also for the further development of microRNA-based therapeutic application. In this work, we propose a two-step model to understand the mechanism of microRNA loading into human Argonaute-2: selective binding followed by structural re-arrangement. Our model is based on the results from a combined approach of molecular dynamics simulations, Markov State Models and protein-RNA docking. In particular, we identify a metastable open state of apo hAgo2 in rapid equilibrium with other states. Some of conformations in this open state have largely exposed RNA binding groove that can accommodate microRNA. We further show that the initial Argonaute-microRNA binding complex undergoes structural re-arrangement to reach stable binary crystal structure. These results provide novel insights into the underlying mechanism of Argonaute-microRNA recognition. In addition, our method is readily applicable to the investigation of other complex molecular recognition events such as protein-protein interactions and protein-ligand binding.
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Affiliation(s)
- Hanlun Jiang
- Bioengineering Graduate Program, Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- The HKUST Shenzhen Research Institute, Shenzhen, China
| | - Fu Kit Sheong
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Lizhe Zhu
- The HKUST Shenzhen Research Institute, Shenzhen, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Julie Bernauer
- Inria Saclay-Île de France, Bâtiment Alan Turing, Campus de l’École Polytechnique, Palaiseau, France
- Laboratoire d’Informatique de l’École Polytechnique (LIX), CNRS UMR 7161, École Polytechnique, Palaiseau, France
- * E-mail: (JB); (XH)
| | - Xuhui Huang
- Bioengineering Graduate Program, Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- The HKUST Shenzhen Research Institute, Shenzhen, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- * E-mail: (JB); (XH)
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Lamontagne J, Steel LF, Bouchard MJ. Hepatitis B virus and microRNAs: Complex interactions affecting hepatitis B virus replication and hepatitis B virus-associated diseases. World J Gastroenterol 2015; 21:7375-7399. [PMID: 26139985 PMCID: PMC4481434 DOI: 10.3748/wjg.v21.i24.7375] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/25/2015] [Accepted: 05/21/2015] [Indexed: 02/06/2023] Open
Abstract
Chronic infection with the hepatitis B virus (HBV) is the leading risk factor for the development of hepatocellular carcinoma (HCC). With nearly 750000 deaths yearly, hepatocellular carcinoma is the second highest cause of cancer-related death in the world. Unfortunately, the molecular mechanisms that contribute to the development of HBV-associated HCC remain incompletely understood. Recently, microRNAs (miRNAs), a family of small non-coding RNAs that play a role primarily in post-transcriptional gene regulation, have been recognized as important regulators of cellular homeostasis, and altered regulation of miRNA expression has been suggested to play a significant role in virus-associated diseases and the development of many cancers. With this in mind, many groups have begun to investigate the relationship between miRNAs and HBV replication and HBV-associated disease. Multiple findings suggest that some miRNAs, such as miR-122, and miR-125 and miR-199 family members, are playing a role in HBV replication and HBV-associated disease, including the development of HBV-associated HCC. In this review, we discuss the current state of our understanding of the relationship between HBV and miRNAs, including how HBV affects cellular miRNAs, how these miRNAs impact HBV replication, and the relationship between HBV-mediated miRNA regulation and HCC development. We also address the impact of challenges in studying HBV, such as the lack of an effective model system for infectivity and a reliance on transformed cell lines, on our understanding of the relationship between HBV and miRNAs, and propose potential applications of miRNA-related techniques that could enhance our understanding of the role miRNAs play in HBV replication and HBV-associated disease, ultimately leading to new therapeutic options and improved patient outcomes.
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MESH Headings
- Animals
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/therapy
- Carcinoma, Hepatocellular/virology
- Cell Transformation, Viral
- Gene Expression Regulation, Neoplastic
- Genetic Therapy
- Hepatitis B virus/genetics
- Hepatitis B virus/growth & development
- Hepatitis B virus/metabolism
- Hepatitis B, Chronic/complications
- Hepatitis B, Chronic/therapy
- Hepatitis B, Chronic/virology
- Host-Pathogen Interactions
- Humans
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Liver Neoplasms/therapy
- Liver Neoplasms/virology
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Virus Replication
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Pliatsika V, Rigoutsos I. "Off-Spotter": very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs. Biol Direct 2015; 10:4. [PMID: 25630343 PMCID: PMC4326336 DOI: 10.1186/s13062-015-0035-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 01/09/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated nucleases) is a powerful component of the prokaryotic immune system that has been adapted for targeted genetic engineering in higher organisms. A key element of CRISPR/Cas is the "guide" RNA (gRNA) that is ~20 nucleotides (nts) in length and designed to be complementary to the intended target site. An integral requirement of the CRISPR/Cas system is that the target site be followed by a protospacer adjacent motif (PAM). Care needs to be exercised during gRNA design to avoid unintended ("off-target") interactions. RESULTS We designed and implemented the Off-Spotter algorithm to assist with the design of optimal gRNAs. When presented with a candidate gRNA sequence and a PAM, Off-Spotter quickly and exhaustively identifies all genomic sites that satisfy the PAM constraint and are identical or nearly-identical to the provided gRNA. Off-Spotter achieves its extreme performance through purely algorithmic means and not through hardware accelerators such as graphical processing units (GPUs). Off-Spotter also allows the user to identify on-the-fly how many and which nucleotides of the gRNA comprise the "seed". Off-Spotter's output includes a histogram showing the number of potential off-targets as a function of the number of mismatches. The output also includes for each potential off-target the site's genomic location, a human genome browser hyperlink to the corresponding location, genomic annotation in the vicinity of the off-target, GC content, etc. CONCLUSION Off-Spotter is very fast and flexible and can help in the design of optimal gRNAs by providing several PAM choices, a run-time definition of the seed and of the allowed number of mismatches, and a flexible output interface that allows sorting of the results, optional viewing/hiding of columns, etc. A key element of Off-Spotter is that it does not have a rigid definition of the seed: instead, the user can declare both the seed's location and extent on-the-fly. We expect that this flexibility in combination with Off-Spotter's speed and richly annotated output will enable experimenters to interactively and quickly explore different scenarios and gRNA possibilities.
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Affiliation(s)
- Venetia Pliatsika
- Computational Medicine Center, Jefferson Alumni Hall, #M81, Sidney Kimmel Medical College at Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107 USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Jefferson Alumni Hall, #M81, Sidney Kimmel Medical College at Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107 USA
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miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nat Chem Biol 2014; 11:107-14. [PMID: 25531890 DOI: 10.1038/nchembio.1713] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 10/29/2014] [Indexed: 12/19/2022]
Abstract
Identifying the interaction partners of noncoding RNAs is essential for elucidating their functions. We have developed an approach, termed microRNA crosslinking and immunoprecipitation (miR-CLIP), using pre-miRNAs modified with psoralen and biotin to capture their targets in cells. Photo-crosslinking and Argonaute 2 immunopurification followed by streptavidin affinity purification of probe-linked RNAs provided selectivity in the capture of targets, which were identified by deep sequencing. miR-CLIP with pre-miR-106a, a miR-17-5p family member, identified hundreds of putative targets in HeLa cells, many carrying conserved sequences complementary to the miRNA seed but also many that were not predicted computationally. miR-106a overexpression experiments confirmed that miR-CLIP captured functional targets, including H19, a long noncoding RNA that is expressed during skeletal muscle cell differentiation. We showed that miR-17-5p family members bind H19 in HeLa cells and myoblasts. During myoblast differentiation, levels of H19, miR-17-5p family members and mRNA targets changed in a manner suggesting that H19 acts as a 'sponge' for these miRNAs.
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41
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Zhou H, Rigoutsos I. MiR-103a-3p targets the 5' UTR of GPRC5A in pancreatic cells. RNA (NEW YORK, N.Y.) 2014; 20:1431-9. [PMID: 24984703 PMCID: PMC4138326 DOI: 10.1261/rna.045757.114] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/28/2014] [Indexed: 05/22/2023]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that regulate the expression of their targets in a sequence-dependent manner. For protein-coding transcripts, miRNAs regulate expression levels through binding sites in either the 3' untranslated region (3' UTR) or the amino acid coding sequence (CDS) of the targeted messenger RNA (mRNA). Currently, for the 5' untranslated region (5' UTR) of mRNAs, very few naturally occurring examples exist whereby the targeting miRNA down-regulates the expression of the corresponding mRNA in a seed-dependent manner. Here we describe and characterize two miR-103a-3p target sites in the 5' UTR of GPRC5A, a gene that acts as a tumor suppressor in some cancer contexts and as an ongocene in other cancer contexts. In particular, we show that the interaction of miR-103a-3p with each of these two 5' UTR targets reduces the expression levels of both GPRC5A mRNA and GPRC5A protein in one normal epithelial and two pancreatic cancer cell lines. By ectopically expressing "sponges" that contain instances of the wild-type 5' UTR targets we also show that we can reduce miR-103a-3p levels and increase GPRC5A mRNA and protein levels. These findings provide some first knowledge on the post-transcriptional regulation of this tumor suppressor/oncogene and present additional evidence for the participation of 5' UTRs in miRNA driven post-transcriptional regulatory control.
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Affiliation(s)
- Honglei Zhou
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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42
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Kakrana A, Hammond R, Patel P, Nakano M, Meyers BC. sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software. Nucleic Acids Res 2014; 42:e139. [PMID: 25120269 PMCID: PMC4191380 DOI: 10.1093/nar/gku693] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Parallel analysis of RNA ends (PARE) is a technique utilizing high-throughput sequencing to profile uncapped, mRNA cleavage or decay products on a genome-wide basis. Tools currently available to validate miRNA targets using PARE data employ only annotated genes, whereas important targets may be found in unannotated genomic regions. To handle such cases and to scale to the growing availability of PARE data and genomes, we developed a new tool, 'sPARTA' (small RNA-PARE target analyzer) that utilizes a built-in, plant-focused target prediction module (aka 'miRferno'). sPARTA not only exhibits an unprecedented gain in speed but also it shows greater predictive power by validating more targets, compared to a popular alternative. In addition, the novel 'seed-free' mode, optimized to find targets irrespective of complementarity in the seed-region, identifies novel intergenic targets. To fully capitalize on the novelty and strengths of sPARTA, we developed a web resource, 'comPARE', for plant miRNA target analysis; this facilitates the systematic identification and analysis of miRNA-target interactions across multiple species, integrated with visualization tools. This collation of high-throughput small RNA and PARE datasets from different genomes further facilitates re-evaluation of existing miRNA annotations, resulting in a 'cleaner' set of microRNAs.
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Affiliation(s)
- Atul Kakrana
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19714, USA Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA
| | - Reza Hammond
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19714, USA Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA
| | - Parth Patel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19714, USA Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA
| | - Mayumi Nakano
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Blake C Meyers
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
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Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types. Sci Rep 2014; 4:5947. [PMID: 25103560 PMCID: PMC4894423 DOI: 10.1038/srep05947] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/09/2014] [Indexed: 01/08/2023] Open
Abstract
To date, analyses of individual targets have provided evidence of a miRNA targetome that extends beyond the boundaries of messenger RNAs (mRNAs) and can involve non-Watson-Crick base pairing in the miRNA seed region. Here we report our findings from analyzing 34 Argonaute HITS-CLIP datasets from several human and mouse cell types. Investigation of the architectural (i.e. bulge vs. contiguous pairs) and sequence (Watson-Crick vs. G:U pairs) preferences for human and mouse miRNAs revealed that many heteroduplexes are “non-canonical” i.e. their seed region comprises G:U and bulge combinations. The genomic distribution of miRNA targets differed distinctly across cell types but remained congruent across biological replicates of the same cell type. For some cell types intergenic and intronic targets were more frequent whereas in other cell types mRNA targets prevailed. The findings suggest an expanded model of miRNA targeting that is more frequent than the standard model currently in use. Lastly, our analyses of data from different cell types and laboratories revealed consistent Ago-loaded miRNA profiles across replicates whereas, unexpectedly, the Ago-loaded targets exhibited a much more dynamic behavior across biological replicates.
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44
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Sequencing of Captive Target Transcripts Identifies the Network of Regulated Genes and Functions of Primate-Specific miR-522. Cell Rep 2014; 8:1225-39. [DOI: 10.1016/j.celrep.2014.07.023] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 05/07/2014] [Accepted: 07/16/2014] [Indexed: 11/22/2022] Open
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Mogilyansky E, Rigoutsos I. The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease. Cell Death Differ 2014; 20:1603-14. [PMID: 24212931 PMCID: PMC3824591 DOI: 10.1038/cdd.2013.125] [Citation(s) in RCA: 635] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/15/2013] [Accepted: 07/19/2013] [Indexed: 12/11/2022] Open
Abstract
The miR-17/92 cluster is among the best-studied microRNA clusters. Interest in the cluster and its members has been increasing steadily and the number of publications has grown exponentially since its discovery with more than 1000 articles published in 2012 alone. Originally found to be involved in tumorigenesis, research work in recent years has uncovered unexpected roles for its members in a wide variety of settings that include normal development, immune diseases, cardiovascular diseases, neurodegenerative diseases and aging. In light of its ever-increasing importance and ever-widening regulatory roles, we review here the latest body of knowledge on the cluster's involvement in health and disease as well as provide a novel perspective on the full spectrum of protein-coding and non-coding transcripts that are likely regulated by its members.
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Affiliation(s)
- E Mogilyansky
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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Chi M, Bhagwat B, Lane WD, Tang G, Su Y, Sun R, Oomah BD, Wiersma PA, Xiang Y. Reduced polyphenol oxidase gene expression and enzymatic browning in potato (Solanum tuberosum L.) with artificial microRNAs. BMC PLANT BIOLOGY 2014; 14:62. [PMID: 24618103 PMCID: PMC4007649 DOI: 10.1186/1471-2229-14-62] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 03/04/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Polyphenol oxidase (PPO), often encoded by a multi-gene family, causes oxidative browning, a significant problem in many food products. Low-browning potatoes were produced previously through suppression of PPO gene expression, but the contribution of individual PPO gene isoform to the oxidative browning process was unknown. Here we investigated the contributions of different PPO genes to total PPO protein activity, and the correlations between PPO protein level, PPO activity and tuber tissue browning potential by suppression of all previously characterized potato PPO genes, both individually and in combination using artificial microRNAs (amiRNAs) technology. RESULTS Survey of the potato genome database revealed 9 PPO-like gene models, named StuPPO1 to StuPPO9 in this report. StuPPO1, StuPPO2, StuPPO3 and StuPPO4 are allelic to the characterized POTP1/P2, POT32, POT33 and POT72, respectively. Fewer ESTs were found to support the transcriptions of StuPPO5 to StuPPO8. StuPPO9 related ESTs were expressed at significant higher levels in pathogen-infected potato tissues. A series of browning phenotypes were obtained by suppressing StuPPO1 to StuPPO4 genes alone and in combination. Down-regulation of one or several of the PPO genes did not usually cause up-regulation of the other PPO genes in the transgenic potato tubers, but resulted in reduced PPO protein levels. The different PPO genes did not contribute equally to the total PPO protein content in the tuber tissues, with StuPPO2 accounting for ~ 55% as the major contributor, followed by StuPPO1, ~ 25-30% and StuPPO3 and StuPPO4 together with less than 15%. Strongly positive correlations between PPO protein level, PPO activity and browning potential were demonstrated in our analysis. Low PPO activity and low-browning potatoes were produced by simultaneous down-regulation of StuPPO2 to StuPPO4, but the greatest reduction occurred when StuPPO1 to StuPPO4 were all suppressed. CONCLUSION StuPPO1 to StuPPO4 genes contributed to browning reactions in tuber tissues but their effect was not equal. Different PPO genes may be regulated independently reflecting their diversified functions. Our results show that amiRNAs can be used to suppress closely related members of highly conserved multi-gene family. This approach also suggests a new strategy for breeding low-browning crops using small DNA inserts.
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Affiliation(s)
- Ming Chi
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Basdeo Bhagwat
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - W David Lane
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Yinquan Su
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - Runcang Sun
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - B Dave Oomah
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Paul A Wiersma
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Yu Xiang
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
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47
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Xia Z, Huynh T, Ren P, Zhou R. Large domain motions in Ago protein controlled by the guide DNA-strand seed region determine the Ago-DNA-mRNA complex recognition process. PLoS One 2013; 8:e54620. [PMID: 23382927 PMCID: PMC3558513 DOI: 10.1371/journal.pone.0054620] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 12/13/2012] [Indexed: 11/27/2022] Open
Abstract
The recognition mechanism and cleavage activity of argonaute (Ago), miRNA, and mRNA complexes are the core processes to the small non-coding RNA world. The 5′ nucleation at the ‘seed’ region (position 2–8) of miRNA was believed to play a significant role in guiding the recognition of target mRNAs to the given miRNA family. In this paper, we have performed all-atom molecular dynamics simulations of the related and recently revealed Ago-DNA:mRNA ternary complexes to study the dynamics of the guide-target recognition and the effect of mutations by introducing “damaging” C·C mismatches at different positions in the seed region of the DNA-RNA duplex. Our simulations show that the A-form-like helix duplex gradually distorts as the number of seed mismatches increases and the complex can survive no more than two such mismatches. Severe distortions of the guide-target heteroduplex are observed in the ruinous 4-sites mismatch mutant, which give rise to a bending motion of the PAZ domain along the L1/L2 “hinge-like” connection segment, resulting in the opening of the nucleic-acid-binding channel. These long-range interactions between the seed region and PAZ domain, moderated by the L1/L2 segments, reveal the central role of the seed region in the guide-target strands recognition: it not only determines the guide-target heteroduplex’s nucleation and propagation, but also regulates the dynamic motions of Ago domains around the nucleic-acid-binding channel.
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Affiliation(s)
- Zhen Xia
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York, New York, United States of America
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
| | - Tien Huynh
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York, New York, United States of America
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York, New York, United States of America
- Department of Chemistry, Columbia University, New York, New York, United States of America
- * E-mail:
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48
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Hibio N, Hino K, Shimizu E, Nagata Y, Ui-Tei K. Stability of miRNA 5'terminal and seed regions is correlated with experimentally observed miRNA-mediated silencing efficacy. Sci Rep 2012; 2:996. [PMID: 23251782 PMCID: PMC3524778 DOI: 10.1038/srep00996] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 11/30/2012] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are key regulators of sequence-specific gene silencing. However, crucial
factors that determine the efficacy of miRNA-mediated target gene silencing are poorly
understood. Here we mathematized base-pairing stability and showed that miRNAs with an
unstable 5′ terminal duplex and stable seed-target duplex exhibit strong silencing activity.
The results are consistent with the previous findings that an RNA strand with unstable 5′
terminal in miRNA duplex easily loads onto the RNA-induced silencing complex (RISC), and
miRNA recognizes target mRNAs with seed-complementary sequences to direct
posttranscriptional repression. Our results suggested that both the unwinding and target
recognition processes of miRNAs could be proficiently controlled by the thermodynamics of
base-pairing in protein-free condition. Interestingly, such thermodynamic parameters might
be evolutionarily well adapted to the body temperatures of various species.
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Affiliation(s)
- Naoki Hibio
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo , 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba-ken 277-8561, Japan
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