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Dallavalle S, Artali R, Princiotto S, Musso L, Borgonovo G, Mazzini S. Investigation of the Interaction between Aloe vera Anthraquinone Metabolites and c-Myc and C-Kit G-Quadruplex DNA Structures. Int J Mol Sci 2022; 23:ijms232416018. [PMID: 36555657 PMCID: PMC9788642 DOI: 10.3390/ijms232416018] [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: 11/12/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
G-quadruplexes are nucleotide sequences present in the promoter region of numerous oncogenes, having a key role in the suppression of gene transcription. Recently, the binding of anthraquinones from Aloe vera to G-quadruplex structures has been studied through various physico-chemical techniques. Intrigued by the reported results, we investigated the affinity of aloe emodin, aloe emodin-8-glucoside, and aloin to selected G-quadruplex nucleotide sequences by NMR spectroscopy. The structural determinants for the formation of the ligand/nucleotide complexes were elucidated and a model of the interactions between the tested compounds and C-Kit and c-Myc G-quadruplex DNA structures was built by integrated NMR and molecular modeling studies. Overall, the obtained results confirmed and implemented the previously reported findings, pointing out the complementarity of the different approaches and their contribution to a more detailed overview of the ligand/nucleotide complex formation. Furthermore, the proposed models of interaction could pave the way to the design of new nature-derived compounds endowed with increased G-quadruplex stabilizing activity.
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Affiliation(s)
- Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan (Università degli Studi di Milano), 20133 Milan, Italy
- National Institute of Fundamental Studies, Kandy 20000, Sri Lanka
| | | | - Salvatore Princiotto
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan (Università degli Studi di Milano), 20133 Milan, Italy
| | - Loana Musso
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan (Università degli Studi di Milano), 20133 Milan, Italy
| | - Gigliola Borgonovo
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan (Università degli Studi di Milano), 20133 Milan, Italy
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan (Università degli Studi di Milano), 20133 Milan, Italy
- Correspondence:
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102
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Kan Y, Jin Z, Ke Y, Lin D, Yan L, Wu L, He Y. Replicative bypass studies of l-deoxyribonucleosides in Vitro and in E. coli cell. Sci Rep 2022; 12:21183. [PMID: 36476762 PMCID: PMC9729220 DOI: 10.1038/s41598-022-24802-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
L-nucleosides were the most important antiviral lead compounds because they can inhibit viral DNA polymerase and DNA synthesis of many viruses, whereas they may lead to mutations in DNA replication and cause genomic instability. In this study, we reported the replicative bypass of L-deoxynucleosides in recombinant DNA by restriction enzyme-mediated assays to examine their impact on DNA replication in vitro and in E. coli cells. The results showed that a template L-dC inhibited Taq DNA polymerase reaction, whereas it can be bypassed by Vent (exo-) DNA polymerase as well as in cell replication, inserting correct nucleotides opposite L-dC. L-dG can be bypassed by Taq DNA polymerase and in E. coli cells, maintaining insertion of correct incoming nucleotides, and L-dG induced mutagenic replication by Vent (exo-) DNA polymerase. In contrast, L-dA can induced mutagenic replication in vitro and in E. coli cells. MD simulations were performed to investigate how DNA polymerase affected replicative bypass and mutations when D-nucleosides replaced with L-nucleosides. This study will provide a basis for the ability to assess the cytotoxic and mutagenic properties of the L-nucleoside drugs.
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Affiliation(s)
- Yuhe Kan
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.411643.50000 0004 1761 0411School of Life Sciences, Inner Mongolia University, Hohhot, 010021 Inner Mongolia People’s Republic of China ,Qilu Pharmaceutical (Inner Mongolia) CO., LTD., Hohhot, 010080 Inner Mongolia People’s Republic of China
| | - Zhaoyang Jin
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yongqi Ke
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Dao Lin
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Liang Yan
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Li Wu
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.11135.370000 0001 2256 9319State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191 People’s Republic of China
| | - Yujian He
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.11135.370000 0001 2256 9319State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191 People’s Republic of China ,grid.410726.60000 0004 1797 8419School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
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103
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The Essential Role of Prolines and Their Conformation in Allosteric Regulation of Kaiso Zinc Finger DNA-Binding Activity by the Adjacent C-Terminal Loop. Int J Mol Sci 2022; 23:ijms232415494. [PMID: 36555132 PMCID: PMC9779254 DOI: 10.3390/ijms232415494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Kaiso is a methyl-DNA-binding protein containing three C2H2 zinc fingers with a C-terminal extension that participates in DNA binding. The linker between the last zinc finger and the DNA-binding portion of the extension contains two prolines that are highly conserved in vertebrates and in cognate ZBTB4 and ZBTB38 proteins. Prolines provide chain rigidity and can exist in cis and trans conformations that can be switched by proline isomerases, affecting protein function. We found that substitution of the conserved proline P588, but not of P577, to alanine, negatively affected KaisoDNA-binding according to molecular dynamics simulation and in vitro DNA-binding assays. Molecular dynamics simulations of the Kaiso DNA-binding domain with P588 either substituted to alanine or switched to the cis-conformation revealed similar alterations in the H-bonding network and uncovered allosteric effects leading to structural rearrangements in the entire domain that resulted in the weakening of DNA-binding affinity. The substitution of proline with a large hydrophobic residue led to the same negative effects despite its ability to partially rescue the intrinsic DNA-binding activity of the C-terminal loop. Thus, the presence of the C-terminal extension and cis-conformation of proline residues are essential for efficient Kaiso-DNA binding, which likely involves intramolecular tension squeezing the DNA chain.
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104
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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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105
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Capobianco A, Landi A, Peluso A. Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations. Int J Mol Sci 2022; 23:ijms232214452. [PMID: 36430930 PMCID: PMC9697240 DOI: 10.3390/ijms232214452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/09/2022] [Accepted: 11/13/2022] [Indexed: 11/22/2022] Open
Abstract
Molecular dynamics simulations and geometry optimizations carried out at the quantum level as well as by quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations very similar to those observed in crystallographic double-stranded B-DNA, with rise coordinates close to ≈3.3 Å. In agreement with the experimental evidence, the computational results show that DNA single strands rich in adjacent purine nucleobases assume more regular arrangements than poly-thymine. The preliminary results suggest that single-stranded poly-cytosine DNA should also retain a substantial helical order in solution. A comparison of the structures of single and double helices confirms that the B-DNA motif is a favorable arrangement also for single strands. Indeed, the optimal geometry of the complementary single helices is changed to a very small extent in the formation of the duplex.
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106
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Boldinova EO, Ghodke PP, Sudhakar S, Mishra VK, Manukyan AA, Miropolskaya N, Pradeepkumar PI, Makarova AV. Translesion Synthesis across the N2-Ethyl-deoxyguanosine Adduct by Human PrimPol. ACS Chem Biol 2022; 17:3238-3250. [PMID: 36318733 DOI: 10.1021/acschembio.2c00717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Primase-DNA polymerase (PrimPol) is involved in reinitiating DNA synthesis at stalled replication forks. PrimPol also possesses DNA translesion (TLS) activity and bypasses several endogenous nonbulky DNA lesions in vitro. Little is known about the TLS activity of PrimPol across bulky carcinogenic adducts. We analyzed the DNA polymerase activity of human PrimPol on DNA templates with seven N2-dG lesions of different steric bulkiness. In the presence of Mg2+ ions, bulky N2-isobutyl-dG, N2-benzyl-dG, N2-methyl(1-naphthyl)-dG, N2-methyl(9-anthracenyl)-dG, N2-methyl(1-pyrenyl)-dG, and N2-methyl(1,3-dimethoxyanthraquinone)-dG adducts fully blocked PrimPol activity. At the same time, PrimPol incorporated complementary deoxycytidine monophosphate (dCMP) opposite N2-ethyl-dG with moderate efficiency but did not extend DNA beyond the lesion. We also demonstrated that mutation of the Arg288 residue abrogated dCMP incorporation opposite the lesion in the presence of Mn2+ ions. When Mn2+ replaced Mg2+, PrimPol carried out DNA synthesis on all DNA templates with N2-dG adducts in standing start reactions with low efficiency and accuracy, possibly utilizing a lesion "skipping" mechanism. The TLS activity of PrimPol opposite N2-ethyl-dG but not bulkier adducts was stimulated by accessory proteins, polymerase delta-interacting protein 2 (PolDIP2), and replication protein A (RPA). Molecular dynamics studies demonstrated the absence of stable interactions with deoxycytidine triphosphate (dCTP), large reactions, and C1'-C1' distances for the N2-isobutyl-dG and N2-benzyl-dG PrimPol complexes, suggesting that the size of the adduct is a limiting factor for efficient TLS across minor groove adducts by PrimPol.
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Affiliation(s)
- Elizaveta O Boldinova
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
| | - Pratibha P Ghodke
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Vipin Kumar Mishra
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anna A Manukyan
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
| | - Nataliya Miropolskaya
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
| | | | - Alena V Makarova
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
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107
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Kumar S, Pany SPP, Sudhakar S, Singh SB, Todankar CS, Pradeepkumar PI. Targeting Parallel Topology of G-Quadruplex Structures by Indole- Fused Quindoline Scaffolds. Biochemistry 2022; 61:2546-2559. [DOI: 10.1021/acs.biochem.2c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Satendra Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | | | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Sushma B. Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Chaitra S. Todankar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
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108
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Alenaizan A. Helicene Structure between DNA and Cyanuric Acid: The Role of Noncovalent Interactions. J Phys Chem B 2022; 126:8508-8514. [PMID: 36244003 DOI: 10.1021/acs.jpcb.2c04664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The self-assembly between DNA and small organic molecules can expand the structural space of and introduce novel functionalities to DNA nanomaterials. In particular, it was demonstrated that poly(adenosine) DNA self-assembles with cyanuric acid (CA) to form a triplex helical structure. Previous molecular dynamics simulations showed that the DNA-CA assemblies adopt a novel noncovalent helicene structure that has a continuous helical hydrogen bond network. This article explores why the assemblies adopt the helicene geometry instead of an alternative planar hexameric rosette geometry. Analysis of the hydrogen bonding and stacking interaction energies indicates that constraining the system to the hexameric rosette geometry strains the hydrogen bonds without significantly improving the interaction energy. Molecular dynamics simulations for the assemblies between adenosine nucleosides and CA confirm that the formation of helicene structure is primarily driven by base-pair interactions and not because of the DNA backbone.
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Affiliation(s)
- Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran31261, Saudi Arabia
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109
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Mudedla SK, Braka A, Wu S. Quantum-based machine learning and AI models to generate force field parameters for drug-like small molecules. Front Mol Biosci 2022; 9:1002535. [PMID: 36304919 PMCID: PMC9592901 DOI: 10.3389/fmolb.2022.1002535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022] Open
Abstract
Force fields for drug-like small molecules play an essential role in molecular dynamics simulations and binding free energy calculations. In particular, the accurate generation of partial charges on small molecules is critical to understanding the interactions between proteins and drug-like molecules. However, it is a time-consuming process. Thus, we generated a force field for small molecules and employed a machine learning (ML) model to rapidly predict partial charges on molecules in less than a minute of time. We performed density functional theory (DFT) calculation for 31770 small molecules that covered the chemical space of drug-like molecules. The partial charges for the atoms in a molecule were predicted using an ML model trained on DFT-based atomic charges. The predicted values were comparable to the charges obtained from DFT calculations. The ML model showed high accuracy in the prediction of atomic charges for external test data sets. We also developed neural network (NN) models to assign atom types, phase angles and periodicities. All the models performed with high accuracy on test data sets. Our code calculated all the descriptors that were needed for the prediction of force field parameters and produced topologies for small molecules by combining results from ML and NN models. To assess the accuracy of the predicted force field parameters, we calculated solvation free energies for small molecules, and the results were in close agreement with experimental free energies. The AI-generated force field was effective in the fast and accurate generation of partial charges and other force field parameters for small drug-like molecules.
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Affiliation(s)
| | | | - Sangwook Wu
- R&D Center, PharmCADD, Busan, South Korea
- Department of Physics, Pukyong National University, Busan, South Korea
- *Correspondence: Sangwook Wu,
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110
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Bie L, Wang Y, Jiang F, Xiao Z, Zhang L, Wang J. Insights into the binding mode of AS1411 aptamer to nucleolin. Front Mol Biosci 2022; 9:1025313. [PMID: 36262475 PMCID: PMC9574071 DOI: 10.3389/fmolb.2022.1025313] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/20/2022] [Indexed: 11/23/2022] Open
Abstract
AS1411 aptamer can function as a recognition probe to detect the cell surface nucleolin overexpressed in cancer cells, however, little is known about their binding process. This study proposed a feasible binding mode for the first time and provided atomic-level descriptions for the high affinity and specific binding of AS1411. The binding pose predicted by docking was screened using knowledge-based criteria, and a microsecond molecular dynamics (MD) simulation showed the stable existence of the predicted structure in the solution. Structural analysis shows that the unique capping of the 5′ end of AS1411 provides the specific binding with RBD1, and the interactions of hydrogen bond, salt bridge, and water-mediated network between AS1411 and RBD1,2 stabilize the binding. The calculation of per-residue decomposition emphasizes the dominant contribution of van der Waals energy and critical residues are screened. Our study provides the molecular basis of this specific binding and can guide rational AS1411-based aptamers design. Further insights require tight collaborations between the experiments and in silico studies.
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Affiliation(s)
- Lihua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland
| | - Yue Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Fuze Jiang
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland
| | - Zhen Xiao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Lianjun Zhang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Jing Wang
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland
- *Correspondence: Jing Wang,
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111
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Biaggne A, Kim YC, Melinger JS, Knowlton WB, Yurke B, Li L. Molecular dynamics simulations of cyanine dimers attached to DNA Holliday junctions. RSC Adv 2022; 12:28063-28078. [PMID: 36320263 PMCID: PMC9530999 DOI: 10.1039/d2ra05045e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
Dye aggregates and their excitonic properties are of interest for their applications to organic photovoltaics, non-linear optics, and quantum information systems. DNA scaffolding has been shown to be effective at promoting the aggregation of dyes in a controllable manner. Specifically, isolated DNA Holliday junctions have been used to achieve strongly coupled cyanine dye dimers. However, the structural properties of the dimers and the DNA, as well as the role of Holliday junction isomerization are not fully understood. To study the dynamics of cyanine dimers in DNA, molecular dynamics simulations were carried out for adjacent and transverse dimers attached to Holliday junctions in two different isomers. It was found that dyes attached to adjacent strands in the junction exhibit stronger dye-DNA interactions and larger inter-dye separations compared to transversely attached dimers, as well as end-to-end arrangements. Transverse dimers exhibit lower inter-dye separations and more stacked configurations. Furthermore, differences in Holliday junction isomer are analyzed and compared to dye orientations. For transverse dyes exhibiting the smaller inter-dye separations, excitonic couplings were calculated and shown to be in agreement with experiment. Our results suggested that dye attachment locations on DNA Holliday junctions affect dye-DNA interactions, dye dynamics, and resultant dye orientations which can guide the design of DNA-templated cyanine dimers with desired properties. Molecular dynamics simulations reveal dye attachment and DNA Holliday junction isomer effects on dye dimer orientations and excitonic couplings. These simulations can guide synthesis and experiments of dye-DNA structures for excitonic applications.![]()
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Affiliation(s)
- Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA
| | - Young C. Kim
- Materials Science and Technology Division, U.S. Naval Research LaboratoryWashingtonDC20375USA
| | - Joseph. S. Melinger
- Electronics Science and Technology Division, U.S. Naval Research LaboratoryWashingtonDC20375USA
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA,Department of Electrical and Computer Engineering, Boise State UniversityBoiseID 83725USA
| | - Bernard Yurke
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA,Department of Electrical and Computer Engineering, Boise State UniversityBoiseID 83725USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA,Center for Advanced Energy StudiesIdaho FallsID 83401USA
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112
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Viviano-Posadas AO, Romero-Mendoza U, Bazany-Rodríguez IJ, Velázquez-Castillo RV, Martínez-Otero D, Bautista-Renedo JM, González-Rivas N, Galindo-Murillo R, Salomón-Flores MK, Dorazco-González A. Efficient fluorescent recognition of ATP/GTP by a water-soluble bisquinolinium pyridine-2,6-dicarboxamide compound. Crystal structures, spectroscopic studies and interaction mode with DNA. RSC Adv 2022; 12:27826-27838. [PMID: 36320280 PMCID: PMC9520314 DOI: 10.1039/d2ra05040d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/21/2022] [Indexed: 11/04/2023] Open
Abstract
The new dicationic pyridine-2,6-dicarboxamide-based compound 1 bearing two N-alkylquinolinium units was synthesized, structurally determined by single-crystal X-ray diffraction, and studied in-depth as a fluorescent receptor for nucleotides and inorganic phosphorylated anions in pure water. The addition of nucleotides to 1 at pH = 7.0 quenches its blue emission with a selective affinity towards adenosine 5'-triphosphate (ATP) and guanosine 5'-tripohosphate (GTP) over other nucleotides such CTP, UTP, ADP, AMP, dicarboxylates and inorganic anions. On the basis of the spectroscopic tools (1H, 31P NMR, UV-vis, fluorescence), MS measurements and DFT calculations, receptor 1 binds ATP with high affinity (log K = 5.04) through the simultaneous formation of strong hydrogen bonds and π-π interactions between the adenosine fragment and quinolinium ring with binding energy calculated in 8.7 kcal mol-1. High affinity for ATP/GTP is attributed to the high acidity of amides and preorganized rigid structure of 1. Receptor 1 is an order of magnitude more selective for ATP than GTP. An efficient photoinduced electron transfer quenching mechanism with simultaneous receptor-ATP complexation in both the excited and ground states is proposed. Additionally, multiple spectroscopic studies and molecular dynamics simulations showed that 1 can intercalate into DNA base pairs.
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Affiliation(s)
- Alejandro O Viviano-Posadas
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Ulises Romero-Mendoza
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Iván J Bazany-Rodríguez
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Rocío V Velázquez-Castillo
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Diego Martínez-Otero
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM km 14.5 Carrera Toluca-Atlacomulco, Campus UAEMex "El Rosedal" San Cayetano-Toluca Toluca de Lerdo 50200 Estado de México Mexico
| | - Joanatan M Bautista-Renedo
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM km 14.5 Carrera Toluca-Atlacomulco, Campus UAEMex "El Rosedal" San Cayetano-Toluca Toluca de Lerdo 50200 Estado de México Mexico
| | - Nelly González-Rivas
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM km 14.5 Carrera Toluca-Atlacomulco, Campus UAEMex "El Rosedal" San Cayetano-Toluca Toluca de Lerdo 50200 Estado de México Mexico
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah 2000 East 30 South Skaggs 306 Salt Lake City 84112 Utah USA
| | - María K Salomón-Flores
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Alejandro Dorazco-González
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
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113
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Zhang Y, Yan M, Huang T, Wang X. Understanding the Structural Elasticity of RNA and DNA: All‐Atom Molecular Dynamics. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yingtong Zhang
- Department of Physics Wenzhou University Wenzhou 325035 China
| | - Miao Yan
- Department of Physics Wenzhou University Wenzhou 325035 China
| | - Tingting Huang
- Department of Mechanical Engineering Shanghai Techanical Institute of Electronics and Information Shanghai 201411 China
| | - Xianghong Wang
- Department of Physics Wenzhou University Wenzhou 325035 China
- Department of Mechanical Engineering Shanghai Techanical Institute of Electronics and Information Shanghai 201411 China
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114
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Microsecond MD Simulations to Explore the Structural and Energetic Differences between the Human RXRα-PPARγ vs. RXRα-PPARγ-DNA. Molecules 2022; 27:molecules27185778. [PMID: 36144514 PMCID: PMC9503000 DOI: 10.3390/molecules27185778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
The heterodimeric complex between retinoic X receptor alpha (RXRα) and peroxisome proliferator-activated receptor gamma (PPARγ) is one of the most important and predominant regulatory systems, controlling lipid metabolism by binding to specific DNA promoter regions. X-ray and molecular dynamics (MD) simulations have revealed the average conformation adopted by the RXRα-PPARγ heterodimer bound to DNA, providing information about how multiple domains communicate to regulate receptor properties. However, knowledge of the energetic basis of the protein-ligand and protein-protein interactions is still lacking. Here we explore the structural and energetic mechanism of RXRα-PPARγ heterodimer bound or unbound to DNA and forming complex with co-crystallized ligands (rosiglitazone and 9-cis-retinoic acid) through microsecond MD simulations, molecular mechanics generalized Born surface area binding free energy calculations, principal component analysis, the free energy landscape, and correlated motion analysis. Our results suggest that DNA binding alters correlated motions and conformational mobility within RXRα–PPARγ system that impact the dimerization and the binding affinity on both receptors. Intradomain correlated motions denotes a stronger correlation map for RXRα-PPARγ-DNA than RXRα-PPARγ, involving residues at the ligand binding site. In addition, our results also corroborated the greater role of PPARγ in regulation of the free and bound DNA state.
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115
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Shaimardanov AR, Shulga DA, Palyulin VA. Is an Inductive Effect Explicit Account Required for Atomic Charges Aimed at Use within the Force Fields? J Phys Chem A 2022; 126:6278-6294. [PMID: 36054931 DOI: 10.1021/acs.jpca.2c02722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polarization and inductive effects are the concepts that have been widely used in qualitative and even quantitative descriptions of experimentally observed properties in chemistry. The polarization effect has proven to be important in cases of biomolecular modeling though still the vast majority of molecular simulations use the classical non-polarizable force fields. In the last few decades, a lot of effort has been put into promoting the polarization effect and incorporating it into modern force fields and charge calculation methods. In contrast, the inductive effect has not attracted such attention and is effectively absent in both classic and modern force fields. Thus, a question is whether this difference corresponds to the difference in the physical significance of the effects and their explicit account, or is an artifact that should be corrected in the next generation of force fields. The significance of the electronic effects is studied in this paper through the prism of performance of specific models for atomic charge calculation that take into explicit account a nested set of effects: the formal charge, the nearest neighbors, the inductive effect, and finally the model, which takes into account all effects, which are possible to account for using atomic charges. The specific choice for the methods is the following: formal charges, MMFF94 bond charge increments, Dynamic Electronegativity Relaxation (DENR), and RESP. We propose a special scheme for the separate estimation of each particular effect contribution. By pairwise comparing the residual molecular electrostatic potential (MEP) errors of those charge models (aimed at best reproducing the quantum chemical reference MEP), we sequentially revealed how the account of each effect contributes to the better-quality MEP reproduction. The following relative importance of effects was estimated; thus, the natural hierarchy of the effects was established. First, the account of formal charges is of primordial importance. Second, the nearest neighbors account is the next in significance. Third, the explicit account of inductive effect in empirical charge calculation schemes was shown to significantly─both qualitatively and quantitatively─improve the quality of MEP reproduction. Fourth, the contribution of polarization is indirectly assessed. Surprisingly, it is of the order of magnitude of the inductive effect even for the molecular systems, for which it is anticipated to be more significant. Finally, the relative importance of anisotropic effects in neutral molecules was additionally reviewed.
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Affiliation(s)
- Arslan R Shaimardanov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Dmitry A Shulga
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Vladimir A Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
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116
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Ai H, Sun M, Liu A, Sun Z, Liu T, Cao L, Liang L, Qu Q, Li Z, Deng Z, Tong Z, Chu G, Tian X, Deng H, Zhao S, Li JB, Lou Z, Liu L. H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity. Nat Chem Biol 2022; 18:972-980. [PMID: 35739357 DOI: 10.1038/s41589-022-01067-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/19/2022] [Indexed: 11/09/2022]
Abstract
Ubiquitination-dependent histone crosstalk plays critical roles in chromatin-associated processes and is highly associated with human diseases. Mechanism studies of the crosstalk have been of the central focus. Here our study on the crosstalk between H2BK34ub and Dot1L-catalyzed H3K79me suggests a novel mechanism of ubiquitination-induced nucleosome distortion to stimulate the activity of an enzyme. We determined the cryo-electron microscopy structures of Dot1L-H2BK34ub nucleosome complex and the H2BK34ub nucleosome alone. The structures reveal that H2BK34ub induces an almost identical orientation and binding pattern of Dot1L on nucleosome as H2BK120ub, which positions Dot1L for the productive conformation through direct ubiquitin-enzyme contacts. However, H2BK34-anchored ubiquitin does not directly interact with Dot1L as occurs in the case of H2BK120ub, but rather induces DNA and histone distortion around the modified site. Our findings establish the structural framework for understanding the H2BK34ub-H3K79me trans-crosstalk and highlight the diversity of mechanisms for histone ubiquitination to activate chromatin-modifying enzymes.
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Affiliation(s)
- Huasong Ai
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Maoshen Sun
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Aijun Liu
- MOE Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.,Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Zixian Sun
- MOE Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
| | - Tingting Liu
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Lin Cao
- MOE Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.,State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, and College of Pharmacy, Nankai University, Tianjin, China
| | - Lujun Liang
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Qian Qu
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Zichen Li
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Zhiheng Deng
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Zebin Tong
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Guochao Chu
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Xiaolin Tian
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China.
| | - Zhiyong Lou
- MOE Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.
| | - Lei Liu
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China.
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117
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Tian C, Liang G, Wang C, He R, Ning K, Li Z, Liu R, Ma Y, Guan S, Deng J, Zhai J. Computer simulation and design of DNA-nanoprobe for fluorescence imaging DNA repair enzyme in living cells. Biosens Bioelectron 2022; 211:114360. [DOI: 10.1016/j.bios.2022.114360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/24/2022] [Accepted: 05/08/2022] [Indexed: 11/02/2022]
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118
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Sinha S, Tam B, Wang SM. Applications of Molecular Dynamics Simulation in Protein Study. MEMBRANES 2022; 12:844. [PMID: 36135863 PMCID: PMC9505860 DOI: 10.3390/membranes12090844] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 05/29/2023]
Abstract
Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study protein function, protein stability, protein-protein interaction, enzymatic reactions and drug-protein interactions, and membrane proteins. In this review, we provide a brief review for the history of MD Simulations application and the current status of MD Simulations applications in protein studies.
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Affiliation(s)
| | | | - San Ming Wang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR, China
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119
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Alenaizan A. Structural Analysis of the Poly(thymidine)-Melamine Assembly. J Phys Chem B 2022; 126:6948-6954. [PMID: 36027577 DOI: 10.1021/acs.jpcb.2c04665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bonding between the DNA nucleobases and small organic molecules, such as melamine, is a new strategy for the design of novel DNA materials. Poly(thymidine) DNA and melamine self-assemble into a duplex structure containing two antiparallel DNA strands hydrogen bonded to central melamine units. In this Article, molecular dynamics simulations rationalize the observed antiparallel duplex structure. Alternative duplex and triplex structures with parallel and antiparallel strand orientations are shown to be unstable because of the increase in unfavorable interactions between the DNA backbones.
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Affiliation(s)
- Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia 31261
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120
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Lubecka EA, Hansmann UHE. Early Stages of RNA-Mediated Conversion of Human Prions. J Phys Chem B 2022; 126:6221-6230. [PMID: 35973105 PMCID: PMC9420815 DOI: 10.1021/acs.jpcb.2c04614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prion diseases are characterized by the conversion of prion proteins from a PrPC fold into a disease-causing PrPSC form that is self-replicating. A possible agent to trigger this conversion is polyadenosine RNA, but both mechanism and pathways of the conversion are poorly understood. Using coarse-grained molecular dynamic simulations we study the time evolution of PrPC over 600 μs. We find that both the D178N mutation and interacting with polyadenosine RNA reduce the helicity of the protein and encourage formation of segments with strand-like motifs. We conjecture that these transient β-strands nucleate the conversion of the protein to the scrapie conformation PrPSC.
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Affiliation(s)
- Emilia A Lubecka
- Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, G. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019,United States
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121
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Yusof TY, Ong EBB, Teh AH. RelEB3 toxin-antitoxin system of Salmonella Typhimurium with a ribosome-independent toxin and a mutated non-neutralising antitoxin. Int J Biol Macromol 2022; 219:1080-1086. [PMID: 36029963 DOI: 10.1016/j.ijbiomac.2022.08.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022]
Abstract
The RelEB3 toxin-antitoxin (TA) system of Salmonella enterica subsp. enterica serovar Typhimurium consists of a RelE3 toxin which suppresses bacterial growth, but its RelB3 antitoxin does not neutralise the toxin. The relEB3 operon is widespread in Proteobacteria and is related to higBA2 from Vibrio cholerae. In contrast to the ribosome-dependent HigB2 toxin, however, the RelE3 toxin degraded free RNA independently of the ribosome. A basic loop possibly involved in HigB2's binding to the ribosome is shortened in RelE3, which instead contains a uniquely conserved R51 important for RelE3's toxicity. The RelB3 antitoxin, meanwhile, specifically recognised the CACCTGGTG palindromic motif in the promoter site. RelB3 contains P14 which is conserved as Ala in most homologues, and mutating P14 to Ala enabled the antitoxin to bind to RelE3 and restored bacterial growth. The P14 RelB3 variant, which most likely arose by a point mutation in a recent ancestor of S. Typhimurium and closely related serovars, could have possibly provided the bacteria with a faster response to stress, and might have spread to other serovars through homologous recombination.
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Affiliation(s)
- Tengku Yasmin Yusof
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia; University Hospital Development Centre, Universiti Sultan Zainal Abidin, Terengganu, Malaysia
| | - Eugene Boon Beng Ong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia.
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122
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Abstract
Generalized force fields (FFs) act as extensions to biomolecular FFs to provide a wide coverage of organic molecules. However, their precise application to an arbitrary molecule presents a separate challenge. We show that MATCH assigns different atom types and bonded and nonbonded parameters than CGenFF, and the AM1-BCC charge model, commonly used with GAFF/GAFF2, does not exactly reproduce the performance of the RESP charge model. The results indicate the need for caution when employing FFs to ensure their integrity with respect to their implementation and validation.
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Affiliation(s)
- Asuka A. Orr
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Suliman Sharif
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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123
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Panczyk T, Nieszporek K, Wolski P. Stability and Existence of Noncanonical I-motif DNA Structures in Computer Simulations Based on Atomistic and Coarse-Grained Force Fields. Molecules 2022; 27:molecules27154915. [PMID: 35956863 PMCID: PMC9370271 DOI: 10.3390/molecules27154915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/13/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022] Open
Abstract
Cytosine-rich DNA sequences are able to fold into noncanonical structures, in which semi-protonated cytosine pairs develop extra hydrogen bonds, and these bonds are responsible for the overall stability of a structure called the i-motif. The i-motif can be formed in many regions of the genome, but the most representative is the telomeric region in which the CCCTAA sequences are repeated thousands of times. The ability to reverse folding/unfolding in response to pH change makes the above sequence and i-motif very promising components of nanomachines, extended DNA structures, and drug carriers. Molecular dynamics analysis of such structures is highly beneficial due to direct insights into the microscopic structure of the considered systems. We show that Amber force fields for DNA predict the stability of the i-motif over a long timescale; however, these force fields are not able to predict folding of the cytosine-rich sequences into the i-motif. The reason is the kinetic partitioning of the folding process, which makes the transitions between various intermediates too time-consuming in atomistic force field representation. Application of coarse-grained force fields usually highly accelerates complex structural transitions. We, however, found that three of the most popular coarse-grained force fields for DNA (oxDNA, 3SPN, and Martini) were not able to predict the stability of the i-motif structure. Obviously, they were not able to accelerate the folding of unfolded states into an i-motif. This observation must be strongly highlighted, and the need to develop suitable extensions of coarse-grained force fields for DNA is pointed out. However, it will take a great deal of effort to successfully solve these problems.
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Affiliation(s)
- Tomasz Panczyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30239 Cracow, Poland;
- Correspondence:
| | - Krzysztof Nieszporek
- Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University in Lublin pl. Maria Curie-Sklodowska 3, 20031 Lublin, Poland;
| | - Pawel Wolski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30239 Cracow, Poland;
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124
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Exploring the Interaction of G-quadruplex Binders with a (3 + 1) Hybrid G-quadruplex Forming Sequence within the PARP1 Gene Promoter Region. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154792. [PMID: 35897968 PMCID: PMC9369712 DOI: 10.3390/molecules27154792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
Abstract
The enzyme PARP1 is an attractive target for cancer therapy, as it is involved in DNA repair processes. Several PARP1 inhibitors have been approved for clinical treatments. However, the rapid outbreak of resistance is seriously threatening the efficacy of these compounds, and alternative strategies are required to selectively regulate PARP1 activity. A noncanonical G-quadruplex-forming sequence within the PARP1 promoter was recently identified. In this study, we explore the interaction of known G-quadruplex binders with the G-quadruplex structure found in the PARP gene promoter region. The results obtained by NMR, CD, and fluorescence titration, also confirmed by molecular modeling studies, demonstrate a variety of different binding modes with small stabilization of the G-quadruplex sequence located at the PARP1 promoter. Surprisingly, only pyridostatin produces a strong stabilization of the G-quadruplex-forming sequence. This evidence makes the identification of a proper (3+1) stabilizing ligand a challenging goal for further investigation.
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125
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Galindo-Murillo R, Cheatham TE. Transient Hoogsteen Base Pairs Observed in Unbiased Molecular Dynamics Simulations of DNA. J Phys Chem Lett 2022; 13:6283-6287. [PMID: 35775742 PMCID: PMC9466961 DOI: 10.1021/acs.jpclett.2c01348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Duplex DNA is modeled as canonical B-DNA displaying the characteristic Watson-Crick base pairs. A less common and short-lived pairing of the nucleobases is the Hoogsteen (HG) conformation. The low population of the HG base pairs (<1%) necessitates extended sampling times in order to analyze through unbiased molecular dynamics (MD) simulations. We have discovered that with extended sampling times using multiple independent copies of an 18-mer sequence, the MD trajectories reproduce the expected and transient HG base pairing. Consistent with experiment, the percentage of the HG events are within the range of ∼0.1-1.0% over the combined aggregate sampling time of more than 3.6 ms. We present the reliability of the current AMBER set of nucleic acid force fields and tools to accurately simulate naturally occurring base-pairing and opening events without any bias or restraints. The mechanism consists of base pair fraying, flipping of the purine, and reformation with HG base pairs.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
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126
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Cervantes-Salguero K, Biaggne A, Youngsman JM, Ward BM, Kim YC, Li L, Hall JA, Knowlton WB, Graugnard E, Kuang W. Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching. Int J Mol Sci 2022; 23:7690. [PMID: 35887059 PMCID: PMC9323263 DOI: 10.3390/ijms23147690] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 11/18/2022] Open
Abstract
Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5's orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - John M. Youngsman
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - Brett M. Ward
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - Young C. Kim
- Materials Science and Technology Division, U.S. Naval Research Laboratory, Code 6300, Washington, DC 20375, USA;
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - John A. Hall
- Division of Research and Economic Development, Boise State University, Boise, ID 83725, USA;
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Elton Graugnard
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Wan Kuang
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
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127
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Zirbel CL, Auffinger P. Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey. Molecules 2022; 27:molecules27144365. [PMID: 35889236 PMCID: PMC9323530 DOI: 10.3390/molecules27144365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 02/04/2023] Open
Abstract
Z-DNA and Z-RNA have long appeared as oddities to nucleic acid scientists. However, their Z-step constituents are recurrently observed in all types of nucleic acid systems including ribosomes. Z-steps are NpN steps that are isostructural to Z-DNA CpG steps. Among their structural features, Z-steps are characterized by the presence of a lone pair…π contact that involves the stacking of the ribose O4′ atom of the first nucleotide with the 3′-face of the second nucleotide. Recently, it has been documented that the CpG step of the ubiquitous r(UNCG) tetraloops is a Z-step. Accordingly, such r(UNCG) conformations were called Z-turns. It has also been recognized that an r(GAAA) tetraloop in appropriate conditions can shapeshift to an unusual Z-turn conformation embedding an ApA Z-step. In this report, we explore the multiplicity of RNA motifs based on Z-steps by using the WebFR3D tool to which we added functionalities to be able to retrieve motifs containing lone pair…π contacts. Many examples that underscore the diversity and universality of these motifs are provided as well as tutorial guidance on using WebFR3D. In addition, this study provides an extensive survey of crystallographic, cryo-EM, NMR, and molecular dynamics studies on r(UNCG) tetraloops with a critical view on how to conduct database searches and exploit their results.
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Affiliation(s)
- Craig L. Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA;
| | - Pascal Auffinger
- Architecture et Réactivité de l’ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 67084 Strasbourg, France
- Correspondence: ; Tel.: +33-3-8841-7049; Fax: +33-3-8860-2218
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128
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Sun S, Wang X, Lin R, Wang K. Deciphering the functional mechanism of zinc ions of PARP1 binding with single strand breaks and double strand breaks. RSC Adv 2022; 12:19029-19039. [PMID: 35865614 PMCID: PMC9240923 DOI: 10.1039/d2ra02683j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/23/2022] [Indexed: 11/21/2022] Open
Abstract
Poly(ADP-ribose)polymerase 1 (PARP1) is a key target for the treatment of cancer-related diseases, and plays an important role in biological processes such as DNA repair, regulating a variety of metabolic and signal transduction processes. Understanding the dynamic binding mechanisms between each domain of PARP1 and DNA is of great significance to deepen the understanding on the function of PARP1 and to facilitate the design of inhibitors. Herein, strategies such as classical molecular dynamics simulation, conformational analysis, binding free energy calculation and energy decomposition were used to shed light on the binding mechanisms of different DNA binding domains (DBDs, including ZnF1, ZnF2 and ZnF3) in PARP1 with DNA and on the influences of zinc ions on the binding process. On one hand, during binding with DNA, ZnF2 tends to expand its space to identify the DNA damage sites and ZnF1/ZnF2 recognizes the interfaces on both sides of DNA damage rather than one side during the process of DNA repair. More importantly, the stable secondary structure of L2 of ZnF2 (PRO146 to MET153) is the key conformational change for ZnF1 and ZnF2 to recognize DNA damage. Meanwhile, ZnF3 has little effect on the binding mechanisms of PARP1. On the other hand, for the structural differences of DBD domains, zinc ions in ZnF1 and ZnF2 (Zn1 and Zn2) have an impact not only on the conformational changes of PARP1, but also on the conformational changes brought by the interaction of double strand breaks (DSB) and single strand breaks (SSB). And meanwhile, Zn3 also has little effect on ZnF3 for the system of ZnF3/DSB. The findings presented in this work deepen the understanding on the functional mechanism of PARP1 and provide a theoretical basis for further study on the interaction between different inhibitors and DBD domains to design more potential inhibitors. Poly(ADP-ribose)polymerase 1 (PARP1) is a key target for treatment of cancer-related diseases. Detailed structural changes DBD in PARP1 during the binding process with DNA were investigated and the dynamic conformational differences of DBD caused by zinc ions were revealed.![]()
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Affiliation(s)
- Shuya Sun
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine No. 232, Waihuan East Road Guangzhou 510006 China
| | - Xin Wang
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering Guangzhou 510000 P. R. China
| | - Rongfeng Lin
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine No. 232, Waihuan East Road Guangzhou 510006 China
| | - Kai Wang
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering Guangzhou 510000 P. R. China .,Abinitio Technology Company, Ltd Guangzhou 510640 P. R. China
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129
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Jana J, Vianney YM, Schröder N, Weisz K. Guiding the folding of G-quadruplexes through loop residue interactions. Nucleic Acids Res 2022; 50:7161-7175. [PMID: 35758626 PMCID: PMC9262619 DOI: 10.1093/nar/gkac549] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/25/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
A G-rich sequence was designed to allow folding into either a stable parallel or hybrid-type topology. With the parent sequence featuring coexisting species, various related sequences with single and double mutations and with a shortened central propeller loop affected the topological equilibrium. Two simple modifications, likewise introduced separately to all sequences, were employed to lock folds into one of the topologies without noticeable structural alterations. The unique combination of sequence mutations, high-resolution NMR structural information, and the thermodynamic stability for both topological competitors identified critical loop residue interactions. In contrast to first loop residues, which are mostly disordered and exposed to solvent in both propeller and lateral loops bridging a narrow groove, the last loop residue in a lateral three-nucleotide loop is engaged in stabilizing stacking interactions. The propensity of single-nucleotide loops to favor all-parallel topologies by enforcing a propeller-like conformation of an additional longer loop is shown to result from their preference in linking two outer tetrads of the same tetrad polarity. Taken together, the present studies contribute to a better structural and thermodynamic understanding of delicate loop interactions in genomic and artificially designed quadruplexes, e.g. when employed as therapeutics or in other biotechnological applications.
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Affiliation(s)
- Jagannath Jana
- Institute of Biochemistry, Universität Greifswald, D-17489 Greifswald, Germany
| | | | - Nina Schröder
- Institute of Biochemistry, Universität Greifswald, D-17489 Greifswald, Germany
| | - Klaus Weisz
- To whom correspondence should be addressed. Tel: +49 3834 420 4426; Fax: +49 3834 420 4427;
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130
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Tucker MR, Piana S, Tan D, LeVine MV, Shaw DE. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes. J Phys Chem B 2022; 126:4442-4457. [PMID: 35694853 PMCID: PMC9234960 DOI: 10.1021/acs.jpcb.1c10971] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Although molecular
dynamics (MD) simulations have been used extensively
to study the structural dynamics of proteins, the role of MD simulation
in studies of nucleic acid based systems has been more limited. One
contributing factor to this disparity is the historically lower level
of accuracy of the physical models used in such simulations to describe
interactions involving nucleic acids. By modifying nonbonded and torsion
parameters of a force field from the Amber family of models, we recently
developed force field parameters for RNA that achieve a level of accuracy
comparable to that of state-of-the-art protein force fields. Here
we report force field parameters for DNA, which we developed by transferring
nonbonded parameters from our recently reported RNA force field and
making subsequent adjustments to torsion parameters. We have also
modified the backbone charges in both the RNA and DNA parameter sets
to make the treatment of electrostatics compatible with our recently
developed variant of the Amber protein and ion force field. We name
the force field resulting from the union of these three parameter
sets (the new DNA parameters, the revised RNA parameters, and the
existing protein and ion parameters) DES-Amber. Extensive
testing of DES-Amber indicates that it can describe the thermal stability
and conformational flexibility of single- and double-stranded DNA
systems with a level of accuracy comparable to or, especially for
disordered systems, exceeding that of state-of-the-art nucleic acid
force fields. Finally, we show that, in certain favorable cases, DES-Amber
can be used for long-timescale simulations of protein–nucleic
acid complexes.
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Affiliation(s)
| | - Stefano Piana
- D. E. Shaw Research, New York, New York 10036, United States
| | - Dazhi Tan
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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131
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Cruz-León S, Vanderlinden W, Müller P, Forster T, Staudt G, Lin YY, Lipfert J, Schwierz N. Twisting DNA by salt. Nucleic Acids Res 2022; 50:5726-5738. [PMID: 35640616 PMCID: PMC9177979 DOI: 10.1093/nar/gkac445] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/11/2022] Open
Abstract
The structure and properties of DNA depend on the environment, in particular the ion atmosphere. Here, we investigate how DNA twist -one of the central properties of DNA- changes with concentration and identity of the surrounding ions. To resolve how cations influence the twist, we combine single-molecule magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases monotonously with increasing concentration for all ions investigated. Second, for a given salt concentration, DNA twist strongly depends on cation identity. At 100 mM concentration, DNA twist increases as Na+ < K+ < Rb+ < Ba2+ < Li+ ≈ Cs+ < Sr2+ < Mg2+ < Ca2+. Our molecular dynamics simulations reveal that preferential binding of the cations to the DNA backbone or the nucleobases has opposing effects on DNA twist and provides the microscopic explanation of the observed ion specificity. However, the simulations also reveal shortcomings of existing force field parameters for Cs+ and Sr2+. The comprehensive view gained from our combined approach provides a foundation for understanding and predicting cation-induced structural changes both in nature and in DNA nanotechnology.
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Affiliation(s)
- Sergio Cruz-León
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Willem Vanderlinden
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Peter Müller
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Tobias Forster
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Georgina Staudt
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Yi-Yun Lin
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Jan Lipfert
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
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132
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Castelli M, Doria F, Freccero M, Colombo G, Moroni E. Studying the Dynamics of a Complex G-Quadruplex System: Insights into the Comparison of MD and NMR Data. J Chem Theory Comput 2022; 18:4515-4528. [PMID: 35666124 PMCID: PMC9281369 DOI: 10.1021/acs.jctc.2c00291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Molecular dynamics
(MD) simulations are coming of age in the study
of nucleic acids, including specific tertiary structures such as G-quadruplexes.
While being precious for providing structural and dynamic information
inaccessible to experiments at the atomistic level of resolution,
MD simulations in this field may still be limited by several factors.
These include the force fields used, different models for ion parameters,
ionic strengths, and water models. We address various aspects of this
problem by analyzing and comparing microsecond-long atomistic simulations
of the G-quadruplex structure formed by the human immunodeficiency
virus long terminal repeat (HIV LTR)-III sequence for which nuclear
magnetic resonance (NMR) structures are available. The system is studied
in different conditions, systematically varying the ionic strengths,
ion numbers, and water models. We comparatively analyze the dynamic
behavior of the G-quadruplex motif in various conditions and assess
the ability of each simulation to satisfy the nuclear magnetic resonance
(NMR)-derived experimental constraints and structural parameters.
The conditions taking into account K+-ions to neutralize
the system charge, mimicking the intracellular ionic strength, and
using the four-atom water model are found to be the best in reproducing
the experimental NMR constraints and data. Our analysis also reveals
that in all of the simulated environments residues belonging to the
duplex moiety of HIV LTR-III exhibit the highest flexibility.
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Affiliation(s)
- Matteo Castelli
- Department of Chemistry, University of Pavia, V.le Taramelli 12, 27100 Pavia, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, V.le Taramelli 12, 27100 Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, V.le Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, V.le Taramelli 12, 27100 Pavia, Italy.,Institute of Chemical Sciences and Technologies SCITEC-CNR, Via Mario Bianco, 9, 20131 Milano, Italy
| | - Elisabetta Moroni
- Institute of Chemical Sciences and Technologies SCITEC-CNR, Via Mario Bianco, 9, 20131 Milano, Italy
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133
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Transformation characteristics of A-DNA in salt solution revealed through molecular dynamics simulations. Biophys Chem 2022; 288:106845. [DOI: 10.1016/j.bpc.2022.106845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/25/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022]
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134
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Biaggne A, Spear L, Barcenas G, Ketteridge M, Kim YC, Melinger JS, Knowlton WB, Yurke B, Li L. Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates. Molecules 2022; 27:3456. [PMID: 35684394 PMCID: PMC9182218 DOI: 10.3390/molecules27113456] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M−1cm−1) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules for desirable properties (i.e., large ε and μ), a computational workflow was established using machine learning (ML), DFT, time-dependent (TD-) DFT, and molecular dynamics (MD). ML models were developed through training and validation on a dataset of 8802 dyes using structural features. A Classifier was developed with an accuracy of 97% and a Regressor was constructed with an R2 of above 0.9, comparing between experiment and ML prediction. Using the Regressor, the ε values of over 18,000 dyes were predicted. The top 100 dyes were further screened using DFT and TD-DFT to identify 15 dyes with a μ relative to a reference dye, pentamethine indocyanine dye Cy5. Two benchmark MD simulations were performed on Cy5 and Cy5.5 dimers, and it was found that MD could accurately capture experimental results. The results of this study exhibit that our computational workflow for identifying dyes with a large μ for excitonic applications is effective and can be used as a tool to develop new dyes for excitonic applications.
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Affiliation(s)
- Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (L.S.); (G.B.); (M.K.); (W.B.K.); (B.Y.)
| | - Lawrence Spear
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (L.S.); (G.B.); (M.K.); (W.B.K.); (B.Y.)
| | - German Barcenas
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (L.S.); (G.B.); (M.K.); (W.B.K.); (B.Y.)
| | - Maia Ketteridge
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (L.S.); (G.B.); (M.K.); (W.B.K.); (B.Y.)
| | - Young C. Kim
- Materials Science and Technology Division, U.S. Naval Research Laboratory, Washington, DC 20375, USA;
| | - Joseph S. Melinger
- Electronics Science and Technology Division, U.S. Naval Research Laboratory, Washington, DC 20375, USA;
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (L.S.); (G.B.); (M.K.); (W.B.K.); (B.Y.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Bernard Yurke
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (L.S.); (G.B.); (M.K.); (W.B.K.); (B.Y.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (L.S.); (G.B.); (M.K.); (W.B.K.); (B.Y.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
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135
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Dusek CO, Dash RC, McPherson KS, Calhoun JT, Bezsonova I, Korzhnev DM, Hadden MK. DNA Sequence Specificity Reveals a Role of the HLTF HIRAN Domain in the Recognition of Trinucleotide Repeats. Biochemistry 2022; 61:10.1021/acs.biochem.2c00027. [PMID: 35608245 PMCID: PMC9684356 DOI: 10.1021/acs.biochem.2c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA damage tolerance (DDT) pathways enable cells to cope with a variety of replication blocks that threaten their ability to complete DNA replication. Helicase-like transcription factor (HLTF) plays a central role in the error-free DDT pathway, template switching (TS), by serving as a ubiquitin ligase to polyubiquitinate the DNA sliding clamp PCNA, which promotes TS initiation. HLTF also serves as an ATP-dependent DNA translocase facilitating replication fork remodeling. The HIP116, Rad5p N-terminal (HIRAN) domain of HLTF specifically recognizes the unmodified 3'-end of single-stranded DNA (ssDNA) at stalled replication forks to promote fork regression. Several crystal structures of the HIRAN domain in complex with ssDNA have been reported; however, optimal ssDNA sequences for high-affinity binding with the domain have not been described. Here we elucidated DNA sequence preferences of HLTF HIRAN through systematic studies of its binding to ssDNA substrates using fluorescence polarization assays and a computational analysis of the ssDNA:HIRAN interaction. These studies reveal that the HLTF HIRAN domain preferentially recognizes a (T/C)TG sequence at the 3'-hydroxyl ssDNA end, which occurs in the CTG trinucleotide repeat (TNR) regions that are susceptible to expansion and deletion mutations identified in neuromuscular and neurodegenerative disorders. These findings support a role for HLTF in maintaining the stability of difficult to replicate TNR microsatellite regions.
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Affiliation(s)
- Christopher O Dusek
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
| | - Radha Charan Dash
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
| | - Kerry S McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Jackson T Calhoun
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
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136
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Fakharzadeh A, Zhang J, Roland C, Sagui C. Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats. Nucleic Acids Res 2022; 50:4860-4876. [PMID: 35536254 PMCID: PMC9122592 DOI: 10.1093/nar/gkac339] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/19/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022] Open
Abstract
The expansion of d(CGG) trinucleotide repeats (TRs) lies behind several important neurodegenerative diseases. Atypical DNA secondary structures have been shown to trigger TR expansion: their characterization is important for a molecular understanding of TR disease. CD spectroscopy experiments in the last decade have unequivocally demonstrated that CGG runs adopt a left-handed Z-DNA conformation, whose features remain uncertain because it entails accommodating GG mismatches. In order to find this missing motif, we have carried out molecular dynamics (MD) simulations to explore all the possible Z-DNA helices that potentially form after the transition from B- to Z-DNA. Such helices combine either CpG or GpC Watson-Crick steps in Z-DNA form with GG-mismatch conformations set as either intrahelical or extrahelical; and participating in BZ or ZZ junctions or in alternately extruded conformations. Characterization of the stability and structural features (especially overall left-handedness, higher-temperature and steered MD simulations) identified two novel Z-DNA helices: the most stable one displays alternately extruded Gs, and is followed by a helix with symmetrically extruded ZZ junctions. The G-extrusion favors a seamless stacking of the Watson-Crick base pairs; extruded Gs favor syn conformations and display hydrogen-bonding and stacking interactions. Such conformations could have the potential to hijack the MMR complex, thus triggering further expansion.
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Affiliation(s)
- Ashkan Fakharzadeh
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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137
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Miclot T, Hognon C, Bignon E, Terenzi A, Grandemange S, Barone G, Monari A. Never Cared for What They Do: High Structural Stability of Guanine-Quadruplexes in the Presence of Strand-Break Damage. Molecules 2022; 27:3256. [PMID: 35630732 PMCID: PMC9146567 DOI: 10.3390/molecules27103256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
DNA integrity is an important factor that assures genome stability and, more generally, the viability of cells and organisms. In the presence of DNA damage, the normal cell cycle is perturbed when cells activate their repair processes. Although efficient, the repair system is not always able to ensure complete restoration of gene integrity. In these cases, mutations not only may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold that induces apoptosis and programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiation are the most toxic due to the inherent difficultly of repair, which may lead to genomic instability. In this article we show, by using classical molecular simulation techniques, that compared to canonical double-helical B-DNA, guanine-quadruplex (G4) arrangements show remarkable structural stability, even in the presence of two strand breaks. Since G4-DNA is recognized for its regulatory roles in cell senescence and gene expression, including oncogenes, this stability may be related to an evolutionary cellular response aimed at minimizing the effects of ionizing radiation.
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Affiliation(s)
- Tom Miclot
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, viale delle Scienze, Ed. 17, 90128 Palermo, Italy; (T.M.); (A.T.)
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France; (C.H.); (E.B.)
| | - Cécilia Hognon
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France; (C.H.); (E.B.)
| | - Emmanuelle Bignon
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France; (C.H.); (E.B.)
| | - Alessio Terenzi
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, viale delle Scienze, Ed. 17, 90128 Palermo, Italy; (T.M.); (A.T.)
| | | | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, viale delle Scienze, Ed. 17, 90128 Palermo, Italy; (T.M.); (A.T.)
| | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS, F-75006 Paris, France
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138
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Assenza S, Pérez R. Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA. J Chem Theory Comput 2022; 18:3239-3256. [PMID: 35394775 PMCID: PMC9097290 DOI: 10.1021/acs.jctc.2c00138] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
We introduce MADna,
a sequence-dependent coarse-grained model of
double-stranded DNA (dsDNA), where each nucleotide is described by
three beads localized at the sugar, at the base moiety, and at the
phosphate group, respectively. The sequence dependence is included
by considering a step-dependent parametrization of the bonded interactions,
which are tuned in order to reproduce the values of key observables
obtained from exhaustive atomistic simulations from the literature.
The predictions of the model are benchmarked against an independent
set of all-atom simulations, showing that it captures with high fidelity
the sequence dependence of conformational and elastic features beyond
the single step considered in its formulation. A remarkably good agreement
with experiments is found for both sequence-averaged and sequence-dependent
conformational and elastic features, including the stretching and
torsion moduli, the twist–stretch and twist–bend couplings,
the persistence length, and the helical pitch. Overall, for the inspected
quantities, the model has a precision comparable to atomistic simulations,
hence providing a reliable coarse-grained description for the rationalization
of single-molecule experiments and the study of cellular processes
involving dsDNA. Owing to the simplicity of its formulation, MADna
can be straightforwardly included in common simulation engines. Particularly,
an implementation of the model in LAMMPS is made available on an online
repository to ease its usage within the DNA research community.
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139
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Chhetri KB, Dasgupta C, Maiti PK. Diameter Dependent Melting and Softening of dsDNA Under Cylindrical Confinement. Front Chem 2022; 10:879746. [PMID: 35586267 PMCID: PMC9108266 DOI: 10.3389/fchem.2022.879746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Carbon nanotubes (CNTs) are considered promising candidates for biomolecular confinement, including DNA encapsulation for gene delivery. Threshold values of diameters have been reported for double-stranded DNA (dsDNA) encapsulation inside CNTs. We have performed all-atom molecular dynamics (MD) simulations of dsDNAs confined inside single-walled CNTs (SWCNTs) at the physiologically relevant temperature of 300 K. We found that the dsDNA can be confined without being denatured only when the diameter of the SWCNT exceeds a threshold value. Below this threshold diameter, the dsDNA gets denatured and melts even at the temperature of 300 K. Our simulations using SWCNTs with chirality indices (20,20) to (30,30) at 300 K found the critical diameter to be 3.25 nm (corresponding to (24,24) chirality). Analyses of the hydrogen bonds (H-bonds), Van der Walls (VdW) energy, and other inter-base interactions show drastic reduction in the number of H-bonds, VdW energy, and electrostatic energies between the bases of dsDNA when it is confined in narrower SWCNTs (up to diameter of 3.12 nm). On the other hand, the higher interaction energy between the dsDNA and the SWCNT surface in narrower SWCNTs assists in the melting of the dsDNA. Electrostatic mapping and hydration status analyses show that the dsDNA is not adequately hydrated and the counter ion distribution is not uniform below the critical diameter of the SWCNT. As properly hydrated counter ions provide stability to the dsDNA, we infer that the inappropriate hydration of counter ions and their non-uniform distribution around the dsDNA cause the melting of the dsDNA inside SWCNTs of diameter below the critical value of 3.25 nm. For confined dsDNAs that do not get denatured, we computed their elastic properties. The persistence length of dsDNA was found to increase by a factor of about two and the torsional stiffness by a factor of 1.5 for confinement inside SWCNTs of diameters up to 3.79 nm, the stretch modulus also following nearly the same trend. Interestingly, for higher diameters of SWCNT, 3.79 nm and above, the dsDNA becomes more flexible, demonstrating that the mechanical properties of the dsDNA under cylindrical confinement depend non-monotonically on the confinement diameter.
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Affiliation(s)
- Khadka B. Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Pokhara, Nepal
| | - Chandan Dasgupta
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
| | - Prabal K. Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
- *Correspondence: Prabal K. Maiti,
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140
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Discovery, Topo I inhibitory activity and mechanism evaluation of two novel cytisine-type alkaloid dimers from the seeds of Sophora alopecuroides L. Bioorg Med Chem 2022; 61:116723. [PMID: 35396127 DOI: 10.1016/j.bmc.2022.116723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/21/2022]
Abstract
Alopecurosines A and B (CMs 1 and 2, respectively) are two novel cytisine-type alkaloid dimers first isolated from the aerial parts of Sophora alopecuroides L. CMs 1 and 2 are new dimeric alkaloids whose piperidine matrine ring is cleaved and connected via the N'-1 bond. Their chemical structures have been confirmed by IR, UV, HR-ESI-MS, and NMR. Preliminary screening shows that they have topoisomerase I (Topo I)-based anti-tumor activity. Their Topo I inhibitory activities and mechanism have been evaluated by agarose gel electrophoresis assay and a molecular docking study. The results show that the inhibition rate of CM 1 is 82.26% at 1 mM concentration and that it exhibits significantly Topo I inhibitory activity. Further research has illustrated that CMs 1 and 2 exert inhibitory activity by stabilising the Topo I-DNA cleavage complex, implying that they have the potential to be developed as novel Topo I inhibitors.
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141
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Schneider AL, Albrecht AV, Huang K, Germann MW, Poon GMK. Self-Consistent Parameterization of DNA Residues for the Non-Polarizable AMBER Force Fields. Life (Basel) 2022; 12:life12050666. [PMID: 35629334 PMCID: PMC9143812 DOI: 10.3390/life12050666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/22/2022] Open
Abstract
Fixed-charge (non-polarizable) forcefields are accurate and computationally efficient tools for modeling the molecular dynamics of nucleic acid polymers, particularly DNA, well into the µs timescale. The continued utility of these forcefields depends in part on expanding the residue set in step with advancing nucleic acid chemistry and biology. A key step in parameterizing new residues is charge derivation which is self-consistent with the existing residues. As atomic charges are derived by fitting against molecular electrostatic potentials, appropriate structural models are critical. Benchmarking against the existing charge set used in current AMBER nucleic acid forcefields, we report that quantum mechanical models of deoxynucleosides, even at a high level of theory, are not optimal structures for charge derivation. Instead, structures from molecular mechanics minimization yield charges with up to 6-fold lower RMS deviation from the published values, due to the choice of such an approach in the derivation of the original charge set. We present a contemporary protocol for rendering self-consistent charges as well as optimized charges for a panel of nine non-canonical residues that will permit comparison with literature as well as studying the dynamics of novel DNA polymers.
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Affiliation(s)
- Amelia L. Schneider
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Amanda V. Albrecht
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Kenneth Huang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Markus W. Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.W.G.); (G.M.K.P.)
| | - Gregory M. K. Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.W.G.); (G.M.K.P.)
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142
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Nicy, Chakraborty D, Wales DJ. Energy Landscapes for Base-Flipping in a Model DNA Duplex. J Phys Chem B 2022; 126:3012-3028. [PMID: 35427136 PMCID: PMC9098180 DOI: 10.1021/acs.jpcb.2c00340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/24/2022] [Indexed: 12/31/2022]
Abstract
We explore the process of base-flipping for four central bases, adenine, guanine, cytosine, and thymine, in a deoxyribonucleic acid (DNA) duplex using the energy landscape perspective. NMR imino-proton exchange and fluorescence correlation spectroscopy studies have been used in previous experiments to obtain lifetimes for bases in paired and extrahelical states. However, the difference of almost 4 orders of magnitude in the base-flipping rates obtained by the two methods implies that they are exploring different pathways and possibly different open states. Our results support the previous suggestion that minor groove opening may be favored by distortions in the DNA backbone and reveal links between sequence effects and the direction of opening, i.e., whether the base flips toward the major or the minor groove side. In particular, base flipping along the minor groove pathway was found to align toward the 5' side of the backbone. We find that bases align toward the 3' side of the backbone when flipping along the major groove pathway. However, in some cases for cytosine and thymine, the base flipping along the major groove pathway also aligns toward the 5' side. The sequence effect may be caused by the polar interactions between the flipping-base and its neighboring bases on either of the strands. For guanine flipping toward the minor groove side, we find that the equilibrium constant for opening is large compared to flipping via the major groove. We find that the estimated rates of base opening, and hence the lifetimes of the closed state, obtained for thymine flipping through small and large angles along the major groove differ by 6 orders of magnitude, whereas for thymine flipping through small angles along the minor groove and large angles along the major groove, the rates differ by 3 orders of magnitude.
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Affiliation(s)
- Nicy
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
| | - Debayan Chakraborty
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
| | - David J. Wales
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
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143
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Silva BM, Santos LH, de Almeida JPP, de Magalhães MTQ. Rad5 HIRAN domain: Structural insights into its interaction with ssDNA through molecular modeling approaches. J Biomol Struct Dyn 2022; 41:3062-3075. [PMID: 35249470 DOI: 10.1080/07391102.2022.2045222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Rad5 protein is an SWI/SNF family ubiquitin ligase that contains an N-terminal HIRAN domain and a RING C3HC4 motif. The HIRAN domain is critical for recognition of the stalled replication fork during the replication process and acts as a sensor to initiate the damaged DNA checkpoint. It is a conserved domain widely distributed in eukaryotic organisms and is present in several DNA-binding proteins from all kingdoms. Here we showed that distant species have important differences in key residues that affect affinity for ssDNA. Based on these findings, we hypothesized that different HIRAN domains might affect fork reversal and translesion synthesis through different metabolic processes. To address this question, we predicted the tertiary structure of both yeast and human HIRAN domains using molecular modeling. Structural dynamics experiments showed that the yeast HIRAN domain exhibited higher structural denaturation than its human homolog, although both domains became stable in the presence of ssDNA. Analysis of atomic contacts revealed that a greater number of interactions between the ssDNA nucleotides and the Rad5 domain are electrostatic. Taken together, these results provide new insights into the molecular mechanism of the HIRAN domain of Rad5 and may guide us to further elucidate differences in the ancient eukaryotes HIRAN sequences and their DNA affinity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bruno M Silva
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Macromolecular Biophysics Laboratory (LBM), Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Lucianna H Santos
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Molecular Modeling and Drug Planning Laboratory, Department of Biochemistry and Immunology, Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - João Paulo P de Almeida
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Mariana T Q de Magalhães
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Macromolecular Biophysics Laboratory (LBM), Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
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144
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Grotz KK, Schwierz N. Magnesium Force Fields for OPC Water with Accurate Solvation, Ion-Binding, and Water-Exchange Properties: Successful Transfer from SPC/E. J Chem Phys 2022; 156:114501. [DOI: 10.1063/5.0087292] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Magnesium plays a vital role in a large variety of biological processes. To model such processes by molecular dynamics simulations, researchers rely on accurate force field parameters for Mg2+ and water. OPC is one of the most promising water models yielding an improved description of biomolecules in water. The aim of this work is to provide force field parameters for Mg2+ that lead to accurate simulation results in combination with OPC water. Using twelve different Mg2+ parameter sets, that were previously optimized with different water models, we systematically assess the transferability to OPC based on a large variety of experimental properties. The results show that the Mg2+ parameters for SPC/E are transferable to OPC and closely reproduce the experimental solvation free energy, radius of the first hydration shell, coordination number, activity derivative, and binding affinity toward the phosphate oxygens on RNA. Two optimal parameter sets are presented: MicroMg yields water exchange in OPC on the microsecond timescale in agreement with experiments. NanoMg yields accelerated exchange on the nanosecond timescale and facilitates the direct observation of ion binding events for enhanced sampling purposes.
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Affiliation(s)
- Kara K. Grotz
- Theoretical Biophysics, Max Planck Institute of Biophysics, Germany
| | - Nadine Schwierz
- Theoretical Biophysics, Max Planck Institute of Biophysics, Germany
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145
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Côté S, Bouilly D, Mousseau N. The molecular origin of the electrostatic gating of single-molecule field-effect biosensors investigated by molecular dynamics simulations. Phys Chem Chem Phys 2022; 24:4174-4186. [PMID: 35113103 DOI: 10.1039/d1cp04626h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Field-effect biosensors (bioFETs) offer a novel way to measure the kinetics of biomolecular events such as protein function and DNA hybridization at the single-molecule level on a wide range of time scales. These devices generate an electrical current whose fluctuations are correlated to the kinetics of the biomolecule under study. BioFETs are indeed highly sensitive to changes in the electrostatic potential (ESP) generated by the biomolecule. Here, using all-atom solvent explicit molecular dynamics simulations, we further investigate the molecular origin of the variation of this ESP for two prototypical cases of proteins or nucleic acids attached to a carbon nanotube bioFET: the function of the lysozyme protein and the hybridization of a 10-nt DNA sequence, as previously done experimentally. Our results show that the ESP changes significantly on the surface of the carbon nanotube as the state of these two biomolecules changes. More precisely, the ESP distributions calculated for these molecular states explain well the magnitude of the conductance fluctuations measured experimentally. The dependence of the ESP with salt concentration is found to agree with the reduced conductance fluctuations observed experimentally for the lysozyme, but to differ for the case of DNA, suggesting that other mechanisms might be at play in this case. Furthermore, we show that the carbon nanotube does not impact significantly the structural stability of the lysozyme, corroborating that the kinetic rates measured using bioFETs are similar to those measured by other techniques. For DNA, we find that the structural ensemble of the single-stranded DNA is significantly impacted by the presence of the nanotube, which, combined with the ESP analysis, suggests a stronger DNA-device interplay. Overall, our simulations strengthen the comprehension of the inner working of field-effect biosensors used for single-molecule kinetics measurements on proteins and nucleic acids.
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Affiliation(s)
- Sébastien Côté
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal, Canada. .,Département de Physique, Cégep de Saint-Jérôme, Saint-Jérôme, Canada
| | - Delphine Bouilly
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal, Canada. .,Institut de recherche en immunologie et cancérologie (IRIC), Université de Montréal, Montréal, Canada.
| | - Normand Mousseau
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal, Canada.
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146
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Li S, Peng Y, Landsman D, Panchenko AR. DNA methylation cues in nucleosome geometry, stability and unwrapping. Nucleic Acids Res 2022; 50:1864-1874. [PMID: 35166834 DOI: 10.1093/nar/gkac097] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 01/04/2023] Open
Abstract
Cytosine methylation at the 5-carbon position is an essential DNA epigenetic mark in many eukaryotic organisms. Although countless structural and functional studies of cytosine methylation have been reported, our understanding of how it influences the nucleosome assembly, structure, and dynamics remains obscure. Here, we investigate the effects of cytosine methylation at CpG sites on nucleosome dynamics and stability. By applying long molecular dynamics simulations on several microsecond time scale, we generate extensive atomistic conformational ensembles of full nucleosomes. Our results reveal that methylation induces pronounced changes in geometry for both linker and nucleosomal DNA, leading to a more curved, under-twisted DNA, narrowing the adjacent minor grooves, and shifting the population equilibrium of sugar-phosphate backbone geometry. These DNA conformational changes are associated with a considerable enhancement of interactions between methylated DNA and the histone octamer, doubling the number of contacts at some key arginines. H2A and H3 tails play important roles in these interactions, especially for DNA methylated nucleosomes. This, in turn, prevents a spontaneous DNA unwrapping of 3-4 helical turns for the methylated nucleosome with truncated histone tails, otherwise observed in the unmethylated system on several microseconds time scale.
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Affiliation(s)
- Shuxiang Li
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada
| | - Yunhui Peng
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - David Landsman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada
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147
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Esmaeeli R, Andal B, Perez A. Searching for Low Probability Opening Events in a DNA Sliding Clamp. Life (Basel) 2022; 12:life12020261. [PMID: 35207548 PMCID: PMC8876151 DOI: 10.3390/life12020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/27/2022] Open
Abstract
The β subunit of E. coli DNA polymererase III is a DNA sliding clamp associated with increasing the processivity of DNA synthesis. In its free form, it is a circular homodimer structure that can accomodate double-stranded DNA in a nonspecific manner. An open state of the clamp must be accessible before loading the DNA. The opening mechanism is still a matter of debate, as is the effect of bound DNA on opening/closing kinetics. We use a combination of atomistic, coarse-grained, and enhanced sampling strategies in both explicit and implicit solvents to identify opening events in the sliding clamp. Such simulations of large nucleic acid and their complexes are becoming available and are being driven by improvements in force fields and the creation of faster computers. Different models support alternative opening mechanisms, either through an in-plane or out-of-plane opening event. We further note some of the current limitations, despite advances, in modeling these highly charged systems with implicit solvent.
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148
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Jana SK, Harikrishna S, Sudhakar S, El-Khoury R, Pradeepkumar PI, Damha MJ. Nucleoside Analogues with a Seven-Membered Sugar Ring: Synthesis and Structural Compatibility in DNA-RNA Hybrids. J Org Chem 2022; 87:2367-2379. [PMID: 35133166 DOI: 10.1021/acs.joc.1c02254] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we describe results on the pairing properties of synthetic DNA and RNA oligonucleotides that contain nucleotide analogues with a 7-membered sugar ring (oxepane nucleotides). Specifically, we describe the stereoselective synthesis of a set of three oxepane thymine nucleosides (OxT), their conversion to phosphoramidite derivatives, and their use in solid-phase synthesis to yield chimeric OxT-DNA and OxT-RNA strands. The different regioisomeric OxT phosphoramidites allowed for positional variations of the phosphate bridge and assessment of duplex stability when the oxepane nucleotides were incorporated in dsDNA, dsRNA, and DNA-RNA hybrids. Little to no destabilization was observed when two of the three regioisomeric OxT units were incorporated in the DNA strand of DNA-RNA hybrids, a remarkable result considering the dramatically different structure of oxepanes in comparison to 2'-deoxynucleosides. Extensive molecular modeling and dynamics studies further revealed the various structural features responsible for the tolerance of both OxT modifications in DNA-RNA duplexes, such as base-base stacking and sugar-phosphate H-bond interactions. These studies suggest that oxepane nucleotide analogues may find applications in synthetic biology, where synthetic oligonucleotides can be used to create new tools for biotechnology and medicine.
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Affiliation(s)
- Sunit Kumar Jana
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - S Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Roberto El-Khoury
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
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149
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Galindo-Murillo R, Winkler L, Ma J, Hanelli F, Fleming AM, Burrows CJ, Cheatham TE. Riboflavin Stabilizes Abasic, Oxidized G-Quadruplex Structures. Biochemistry 2022; 61:265-275. [PMID: 35104101 PMCID: PMC8851688 DOI: 10.1021/acs.biochem.1c00598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
The G-quadruplex
is a noncanonical fold of DNA commonly found at
telomeres and within gene promoter regions of the genome. These guanine-rich
sequences are highly susceptible to damages such as base oxidation
and depurination, leading to abasic sites. In the present work, we
address whether a vacancy, such as an abasic site, in a G-quadruplex
serves as a specific ligand recognition site. When the G-tetrad is
all guanines, the vacant (abasic) site is recognized and bound by
free guanine nucleobase. However, we aim to understand whether the
preference for a specific ligand recognition changes with the presence
of a guanine oxidation product 8-oxo-7,8-dihydroguanine (OG) adjacent
to the vacancy in the tetrad. Using molecular dynamics simulation,
circular dichroism, and nuclear magnetic resonance, we examined the
ability for riboflavin to stabilize abasic site-containing G-quadruplex
structures. Through structural and free energy binding analysis, we
observe riboflavin’s ability to stabilize an abasic site-containing
G-quadruplex only in the presence of an adjacent OG-modified base.
Further, when compared to simulation with the vacancy filled by free
guanine, we observe that the free guanine nucleobase is pushed outside
of the tetrad by OG to interact with other parts of the structure,
including loop residues. These results support the preference of riboflavin
over free guanine to fill an OG-adjacent G-quadruplex abasic vacancy.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
| | - Lauren Winkler
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
| | - Jingwei Ma
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Fatjon Hanelli
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
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150
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Rajasekaran T, Freestone GC, Galindo-Murillo R, Lugato B, Rico L, Salinas JC, Gaus H, Migawa MT, Swayze EE, Cheatham TE, Hanessian S, Seth PP. Backbone Hydrocarbon-Constrained Nucleic Acids Modulate Hybridization Kinetics for RNA. J Am Chem Soc 2022; 144:1941-1950. [PMID: 35041415 DOI: 10.1021/jacs.1c12323] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The binding affinity of therapeutic oligonucleotides (ONs) for their cognate RNA is determined by the rates of association (ka) and dissociation (kd). Single-stranded ONs are highly flexible and can adopt multiple conformations in solution, some of which may not be conducive for hybridization. We investigated if restricting rotation around the sugar-phosphate backbone, by tethering two adjacent backbone phosphonate esters using hydrocarbon bridges, can modulate hybridization kinetics of the modified ONs for complementary RNA. Given the large number of possible analogues with different tether lengths and configurations at the phosphorus atoms, we employed molecular dynamic simulations to optimize the size of the hydrocarbon bridge to guide the synthetic efforts. The backbone-constrained nucleotide trimers with stereodefined configurations at the contiguous backbone phosphorus atoms were assembled using a ring-closing metathesis reaction, then incorporated into oligonucleotides by an in situ synthesis of the phosphoramidites followed by coupling to solid supports. Evaluation of the modified oligonucleotides revealed that 15-membered macrocyclic-constrained analogues displayed similar or slightly improved on-rates but significantly increased off-rates compared to unmodified DNA ONs, resulting in reduced duplex stability. In contrast, LNA ONs with conformationally preorganized furanose rings showed similar on-rates to DNA ONs but very slow off-rates, resulting in net improvement in duplex stability. Furthermore, the experimental data generally supported the molecular dynamics simulation results, suggesting that this strategy can be used as a predictive tool for designing the next generation of constrained backbone ON analogues with improved hybridization properties.
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Affiliation(s)
| | - Graeme C Freestone
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 201, Salt Lake City, Utah 84112, United States
| | - Barbara Lugato
- Department of Chemistry, Université de Montréal, Quebec H3C 3J7, Canada
| | - Lorena Rico
- Department of Chemistry, Université de Montréal, Quebec H3C 3J7, Canada
| | - Juan C Salinas
- Department of Chemistry, Université de Montréal, Quebec H3C 3J7, Canada
| | - Hans Gaus
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael T Migawa
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Eric E Swayze
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 201, Salt Lake City, Utah 84112, United States
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, Quebec H3C 3J7, Canada
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
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